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WO2001053799A1 - Systemes et dispositifs de transport par electrophorese et d'hybridation d'oligonucleotides - Google Patents

Systemes et dispositifs de transport par electrophorese et d'hybridation d'oligonucleotides Download PDF

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Publication number
WO2001053799A1
WO2001053799A1 PCT/US2001/000926 US0100926W WO0153799A1 WO 2001053799 A1 WO2001053799 A1 WO 2001053799A1 US 0100926 W US0100926 W US 0100926W WO 0153799 A1 WO0153799 A1 WO 0153799A1
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Prior art keywords
dna
devices
effecting
liquid environment
transport
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PCT/US2001/000926
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English (en)
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Carl Frederick Edman
Michael James Heller
Christian Gurtner
Rachel Formosa
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Nanogen, Inc.
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Priority claimed from US09/489,855 external-priority patent/US6706473B1/en
Application filed by Nanogen, Inc. filed Critical Nanogen, Inc.
Priority to AU2001232779A priority Critical patent/AU2001232779A1/en
Publication of WO2001053799A1 publication Critical patent/WO2001053799A1/fr

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    • G—PHYSICS
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    • G11C13/0002—Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00 using resistive RAM [RRAM] elements
    • G11C13/0009—RRAM elements whose operation depends upon chemical change
    • G11C13/0014—RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material
    • G11C13/0019—RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material comprising bio-molecules
    • B—PERFORMING OPERATIONS; TRANSPORTING
    • B82—NANOTECHNOLOGY
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    • B82Y10/00—Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
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    • B82Y20/00—Nanooptics, e.g. quantum optics or photonic crystals
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    • B82—NANOTECHNOLOGY
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Definitions

  • This invention relates to methodologies and techniques which utilize programmable functionalized self-assembling nucleic acids, nucleic acid modified structures, and other selective affinity or binding moieties as building blocks for: (1) creating molecular electronic and photonic mechanisms; (2) for the organization, assembly, and interconnection of nanostructures, submicron and micron sized components onto silicon or other materials; (3) for the organization, assembly, and interconnection of nanostructures, submicron and micron sized components within perimeters of microelectronic or optoelectronic components and devices; (4) for creating, arraying, and manufacturing photonic and electronic structures, devices, and systems; (5) for the development of a high bit density (large byte) three and four dimensional optical data storage materials and devices; and (6) for development of low density optical memory for applications in authentication, anti-counterfeiting, and encryption of information in document or goods.
  • This invention also relates to associated microelectronic and optoelectronic devices, systems, and manufacturing platforms which provide electric field transport and selective addressing of self- assembling, nanostructures, sub-micron and micron sized components to selected locations on the device itself or onto other substrate materials.
  • Nanoteclmology is defined as a projected technology based on a generalized ability to build objects to complex atomic specifications. Drexler, Proc. Natl. Acad. Sci USA. 78:5275-5278, (1981). Nanoteclmology generally means an atom-by-atom or molecule-by-molecule control for organizing and building complex structures all the way to the macroscopic level. Nanoteclmology is a bottom-up approach, in contrast to a top-down strategy like present lithographic techniques used in the semiconductor and integrated circuit industries.
  • nanoteclmology may be based on the development of programmable self-assembling molecular units and molecular level machine tools, so- called assemblers, which will enable the construction of a wide range of molecular structures and devices. Drexler, "Engines of Creation,” Doubleday Publishing Co., New York, NY (1986).
  • nucleic acids deoxyribonucleic acid or DNA
  • Watson, et al. in "Molecular Biology of the Gene," Vol. 1, Benjamin Publishing Co., Menlo Park, CA (1987), which is the carrier of genetic information in all living organisms (See Fig. 1).
  • DNA information is encoded in the linear sequence of nucleotides by their base units adenine, guanine, cytosine, and thymidine (A, G, C, and T).
  • Single strands of DNA (or polynucleotide) have the unique property of recognizing and binding, by hybridization, to their complementary sequence to form a double stranded nucleic acid duplex structure. This is possible because of the inherent base-pairing properties of the nucleic acids: A recognizes T, and G recognizes C. This property leads to a very high degree of specificity since any given polynucleotide sequence will hybridize only to its exact complementary sequence.
  • nucleic Acids Research 16:3671-3691 (1988).
  • F ⁇ rster nonradiative energy transfer is a process by which a fluorescent donor group excited at one wavelength transfers its absorbed energy by a resonant dipole coupling process to a suitable fluorescent acceptor group.
  • the efficiency of energy transfer between a suitable donor and acceptor group has a l/r ⁇ distance dependency (see Lakowicz et al., "Principles of Fluorescent Spectroscopy,” Plenum Press, New York, NY, Chap. 10, pp. 305-337 (1983)).
  • photonic devices they can generally be fabricated in dense arrays using well developed micro-fabrication techniques. However, they can only be integrated over small areas limited by the relatively high defect densities of the substrates employed.
  • the prior art has no integration technique that is capable of creating a sparse array of devices distributed over a large area, when the devices are originally fabricated densely over small areas. This makes large area components made up from integration of micron size devices economically unfeasible.
  • the electronics industry employs a hierarchy of packaging techniques. However, this problem remains unsolved when a regular array of devices is needed on large areas with a relatively small pitch. This problem is probably most noticeable through the high cost associated with the implementation of matrix addressed displays, where the silicon active matrix consists of small transistors that need to be distributed over a large area.
  • prior art microfabrication techniques limit devices to small area components where a dense array of devices are integrated.
  • the solutions include using various types of memory which have different attributes. For example, it is common to use a relatively small amount of fast, and typically expensive, memory directly associated with the processor units, typically called cache memory. Additionally, larger capacity, but generally slower, memory such as DRAM or SRAM is associated with the CPU. This intermediate memory is often large enough for a small number of current applications, but not large enough to hold all system programs and data. Mass storage memory, which is ordinary very large, but relatively inexpensive, is relatively slow. While advances have been continually made in improving the size and speed of all types of memory, and generally reducing the cost per bit of memory, there remains a substantial need especially to serve yet faster processors. For the last 20 years most mass storage devices have utilized a rotating memory medium.
  • Magnetic media have been used for both “floppy” (flexible) disks or “hard” disk drives. Information is stored by the presence or absence of magnetization at defined physical locations on the disk. Ordinarily, magnetic media are “read-write” memories in that the memory may be both written to and read from by the system. Data is written to or read from the disk by heads placed close to the surface of the disk. A more recent development in rotating mass storage media are the optical media. Compact disks are read only memory in which the presence or absence of physical deformations in the disk indicates the data. The information is read by use of a focused laser beam, in which the change in reflectance properties from the disk indicate the data states. Also in the optical realm are various optical memories which utilize magnetooptic properties in the writing and reading of data. These disks are both read only, write once read many (“WORM”) drives and multiple read-write memories. Generally, optical media have proved to have a larger storage capacity, but higher costs per bit and limited write ability, as compared with magnetic media.
  • WORM write once read many
  • the information is stored on a bit-by-bit basis, such that only a single bit of data is obtained by accessing a giving physical location in memory.
  • word-wide memory access systems do exist, generally they store but a single bit of information at a given location, thereby requiring substantially the same amount of physical memory space whether accessed in a bit manner or word- wide manner.
  • systems have generally increased in speed and storage density, and decreased in cost per bit, there remains a clear gap at present between processor speed and system requirements. See generally, “New Memory Architectures to Boost Performance", Tom R. Halfhill, Byte, July, 1993, pp 86 and 87.
  • Inorganic and organic semiconductors are the materials of choice for the generation of photocurrents or photoelectrochemical currents. Although there are a rich variety of semiconductors suitable for solid state devices (solar cells, photodiodes, photoconductors etc), only a limited number of these are adequate for photoelectrochemical current formation. In addition, there is no single low band-gap semiconductor or compound semiconductor material known that can withstand the corrosive environment present during photooxidation of water. Photooxidation of water, however, is the dominant process at the positive electrode (anode) during electrophoresis of negatively charged DNA in aqueous electrolytes.
  • a platform for photoelectrophoretic transport and electronic hybridization of fluorescence labeled DNA oligonucleotides in a low conductivity electrolyte is described.
  • a chemically stabilized semiconductor photodiode or photoconductor surface is coated with a streptavidin-agarose permeation layer. Micro-illumination of the surface generates photo-electrochemical currents that are used to electrophoretically transport and attach capture strands, preferably biotinylated DNA, to arbitrarily selected locations. The same process is then used to transport and electronically hybridize fluorescence labeled DNA target strands to the previously attached capture strands. Signal detection is accomplished either by a fluorescence scanner or a CCD camera.
  • This invention relates to methodologies and manufacturing techniques which utilize programmable functionalized self-assembling nucleic acids, nucleic acid modified structures, and other selective affinity or binding moieties as building blocks for: (1) creating molecular electronic and photonic mechanisms; (2) for the organization, assembly, and interconnection of nanostructures, submicron and micron sized components onto silicon or other materials; (3) for the organization, assembly, and interconnection of nanostructures, submicron and micron sized components within perimeters of microelectronic or optoelectronic components and devices; (4) for creating, arraying, and manufacturing photonic and electronic structures, devices, and systems; (5) for the development of a high bit density (large byte) three and four dimensional optical data storage materials and devices; and (6) for development of low density optical memory for applications in authentication, anti-counterfeiting, and encryption of information in documents or goods.
  • This invention also relates to associated microelectronic and optoelectronic devices, systems, and manufacturing platfonns which provide electric field transport and selective addressing of self- assembling, nanostructures, sub-micron and micron size components to selected locations on the device itself or onto other substrate materials.
  • Functionalized nucleic acids based polymers constitute a vehicle to assemble large numbers of photonic and electronic devices and systems, utilizing the base-pair coding property of the DNA which allows specific complementary double stranded DNA structures to be formed.
  • This unique property of DNA provides a programmable recognition code (via the DNA sequence) which can be used for specific placement and alignment of nanostructures.
  • the process by which photonic devices would be aligned involves first coating them with a specific DNA sequence.
  • the area of the host substrate where attachment of the devices is desired are coated with the specific complementary DNA sequence.
  • the substrate and DNA-covered devices are released into a solution and hybridization between complementary DNA strands occurs. Hybridization effectively grafts the devices to their proper receptor locations on the substrate.
  • the invention in this respect relates to a method for the fabrication of micro scale and nanoscale devices comprising the steps of: fabricating first component devices on a first support, releasing at least one first component device from the first support, transporting the first component device to a second support, and attaching the first component device to the second support.
  • inventions relate to nanostructures, submicron and micron-sized structures incorporating synthetic DNA polymers.
  • This includes DNA modified with small chromophore molecules, to large structures (e.g., micron-sized) which are modified with DNA sequences.
  • Synthetic DNA polymers can be designed with highly specific binding affinities.
  • DNA polymers can provide a self-assembly fabrication mechanism. This mechanism can be used for both the selective grafting of the devices to specific pre-programmed locations on a desired surface, and for the clustering of devices into pre-programmed 2-D or 3-D lattices.
  • DNA polymers with complementary sequences are first synthesized.
  • the photonic component devices and desired areas of the host substrate (receptor areas) are coated with the complementary DNA sequences.
  • the host substrates are then introduced into a solution.
  • a method for fabrication of nanoscale and microscale structures comprising the steps of: providing a structure with multiple affinity surface identities, orienting the structure in an electric field, and reacting the oriented structure with an affinity site.
  • a method for forming a multiple identity substrate material comprising the steps of: providing a first affinity sequence at multiple locations on a support, providing a functionalized second affinity sequence, which reacts with the first affinity sequence, and has an unhybridized overhang sequence, and selectively cross-linking first affinity sequences and second affinity sequences.
  • a method for the assembly of chromophoric structures comprising the steps of: selectively irradiating a photoactivatable region, whereby an electric field is generated corresponding to the region, providing charged reactants in solution which includes the electric field, and repeating the selective irradiation to sequentially assemble the chromophoric structures.
  • Figs. 1 A and IB shows DNA structure and its related physical dimensions.
  • Fig. 2 is a flow diagram of self-assembly processes.
  • Fig. 3A.a is a perspective drawing of the apparatus and method for redistribution of photonic devices fabricated as dense arrays onto the host substrate without mother substrate layout constraints.
  • Fig. 3B is a perspective view of a clustering of nanospheres by DNA assisted self-assembly to form synthetic photonic crystals.
  • Fig. 4 shows a cross-section of an attachment mechanism for attaching DNA to silicon.
  • Fig. 5 shows steps for preparation of photonic devices for self assembly.
  • Fig. 6 shows a plan view of a structure for selective attachment of fluorescent DNA sequences to aluminum pads on silicon VLSI chips.
  • Fig. 7 is a plan view of a UN write/imaging into monolayers of D ⁇ A on silicon/silicon dioxide/aluminum.
  • Fig. 8 A is a plan view of a UN image mask write followed by hybridization into D ⁇ A optical storage material.
  • Fig. 8B is a plan view of a UN image mask write into D ⁇ A optical storage material (10 micron resolution) .
  • Fig. 9 is a cross-sectional view of an apparatus and method for preparing multiple write materials.
  • Fig. 10 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 11 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 12 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 13 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 14 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 15 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 16 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 17 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 18 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 19 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 20 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 21 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 22 is a cross-sectional view of a step in the process for preparing DNA write materials.
  • Fig. 23 A is a planned image of the background fluorescence for APS-reacted silicon substrate surface before DNA attachment.
  • Fig. 23B is a planned image of the background fluorescence level after capture DNA is bound to the APS-reacted substrate.
  • Fig. 24A is a planned image of a chip treated with APS and capture DNA and then hybridized with a Bodipy Texas Red labeled complementary probe sequence across the entire chip surface.
  • Fig. 24B is a planned image of the chip surface after hybridization of a fluorescent Bodipy Texas Red labeled complementary probe to the non-psoralen cross- linked identity on the right side of the chip surface.
  • Fig. 25 A is a plan image of the chip surface after hybridization of a fluorescent Bodipy Orange (b) complimentary probe to the (b) sequence identity on the left side of the chip surface.
  • Fig. 25B is a plan image of the chip after both cross-linked (B) and non-cross- linked (A) sides are hybridized with their respective fluorescently labeled complimentary DNA (A) and (B) probes.
  • Fig. 26A is a plan image of 160 nanometer beads (white spherical features) electrostatically bound to a DNA polymer layer covalently bound to a silicon dioxide derivitized surface with partial specificity, having 10 micron square dark features where the DNA field has been UN inactivated, the nanospheres not binding in these areas.
  • Fig. 26B is a plan image of a pattern image constructed with 160 nanometer beads (white spherical features) wherein the nanospheres are electrostatically bound to a D ⁇ A polymer layer covalently bound to silicon dioxide derivitized surface with partial specificity, the dark areas showing areas where the D ⁇ A field has been UN inactivated, the nanospheres not binding in these areas.
  • Figs. 27A-C are cross-sectional views of apparatus and method steps for forming fluorescently labeled sequences.
  • Fig. 28A-C are cross-sectional views of apparatus and method steps for providing multicolor images.
  • Fig. 29 is a perspective view of a flip-chip bonding arrangement which conserves the geometrical dimensions leading to the coupling of small dense arrays of specialty devices onto local regions of mother boards.
  • Fig. 30 shows a perspective view of global distribution of small dense structures from small dense chips on to less dense mother boards.
  • Fig. 31 shows a cross-sectional view of a structure for the self-assembly of micro or nanostructures utilizing a selective glue in which speciality devices of the given type are provided with a specific DNA polymer glue, the areas where these devices must attach being covered with the complimentary DNA glue.
  • Fig. 32 shows a cross-sectional view of selective electric field deposition of DNA onto the specially derivitized microelectrode surfaces.
  • Fig. 33 shows a cross-sectional view of a micro or nanoscale structure coupled to its host mother board substrate by selective DNA hybridization between complimentary DNA strands.
  • Fig. 34 shows a cross-sectional view of nanostructures held in place via a DNA bond (left-hand side) and nanostructure held by a metallurgical contact after a high temperature cycle (right-hand side).
  • Fig. 35 shows a cross-sectional view of an apparatus for the orientation of speciality devices prior to hybridization by physical masking and charge guiding.
  • Fig. 36 shows structures for the formation of nanodevices, providing an octahedron using 3-D DNA nanoconstruction techniques (top) and nanospheres arranged into lattice structure and bound to surface to create a 3-D device (lower).
  • Fig. 37 shows the steps in a process for electric field orientation of devices.
  • Fig. 38 shows further steps in the electric field orientation process.
  • Fig. 39 shows a perspective view of nanostructure transport and assembly on a microelectronic array device.
  • Figs. 40A-H show the larger environment of Fig. 39.
  • Fig. 41 shows images of an 8x8 array.
  • Fig. 42 shows an apparatus for attachment and orientation of larger sized devices onto a substrate or motherboard.
  • Fig. 43 shows an apparatus for fabrication of nanostructures.
  • Fig. 44 shows an apparatus for nano fabrication of a nanoscale device.
  • Fig. 45 shows a perspective view of a DNA optical storage system.
  • Figs. 46A-F show steps in a spacial light addressing process.
  • Fig. 47 Schematic cross-section of the electrochemical setup for photoelectrophoresis experiments.
  • Figs. 48A and B Tapping mode AFM images of a Mn 2 O 3 film deposited onto single crystal n-type silicon.
  • the film thickness of this sample is approximately 270 nm with a medium roughness of 50 mn.
  • Figs. 49A and B Current-voltage characteristics of Mn 2 O 3 coated n-type silicon electrodes measured in 50 mM L-histidine solutions. The ten consecutive cyclic voltammograms acquired in the dark (*) and under illumination were measured a) before and b) after deposition of the streptavidin-agarose permeation layer. The scan rate was 100 mN/sec. (Electrochemical potentials were not compensated for ohmic potential drops across the low conductivity electrolyte.).
  • Figs. 50A and B a) Image of an array of fluorescent spots that was produced by photoelectrophoretic transport and biotin-streptavidin mediated immobilization of fluorescence labeled DNA oligonucleotides on a streptavidin-agarose and Mn 2 O 3 coated amorphous silicon electrode. Individual spots were illuminated for 5 sec at a light intensity of 4 W (630 nm) and an applied electrochemical potential of 1.5 V. b) Photo- current transient recorded during formation of the array. Figs. 51 A and B.
  • Fig 52 Microphotograph of photoelectrophoretic bead accumulation on a Mn 2 O 3 coated n-type single crystal silicon electrode. The accumulated 1 m beads appear as a dark spot next to the tip of the single mode optical fiber in the right half of the picture. Accumulation was performed by illuminating with 80 W for 1 min and scanning the applied potential between 0 N and 0.6 N (200 mN/sec).
  • D ⁇ A Structure possesses a number of important properties which make it a useful material for the applications of these inventions. The most important are the molecular recognition (via base pairing) and self-assembly (via hybridization) properties which are inherent in all D ⁇ A molecules. Other important advantages include the ability to easily synthesize D ⁇ A, and to readily modify its structure with a variety of functional groups. We have extensively investigated the photonic and electronic energy transfer mechanisms in self-assembled arrangements of synthetic D ⁇ A functionalized with a wide variety of donor and acceptor chromophore groups. We have paid particular attention to the basic problems involved in communicating or getting information in and out of these molecular structures.
  • the D ⁇ A molecule is considered important to this invention and the proposed applications because it is inherently programmable and can self-assemble. Designing, synthesizing, and organizing these systems requires nanometer range control which few other synthetic polymer systems can match. Additionally, D ⁇ A molecules are relatively stable and have a number of other attributes which make them a preferred material for nanofabrication.
  • DNA polymers have three important advantages over any of the present polymeric materials used for electronic and photonic applications.
  • DNA polymers provide a way to encode highly specific binding-site identities o semiconductor or photonic surfaces. These sites, produced at defined locations, could be of microscopic (micron), sub-micron, or even molecular (nanometer) dimension.
  • DNA polymers provide a way to specifically connect any of these locations. The pre-programmed DNA polymers self-organize automatically.
  • DNA polymers provide the building blocks for nanotechnology; they are self-organizing materials for creating true molecular-level electronic and photonic devices.
  • DNA polymers to be used to form programmable self-assembling structures.
  • a photonic device has one specific DNA polymer sequence attached to it, it will only bind (hybridize) to a device or surface coated with the complementary DNA polymer sequence. Since a large variety of DNA sequences can be used, multiple devices, each attached to a different DNA sequence can in principle be self-assembled simultaneously. The following lists the important advantages of using DNA polymers for self-assembling nanofabrication applications:
  • DNA polymers can by synthesized both rapidly and efficiently with automated instruments. Conventional polymer chemistries can be significantly more complex and costly to develop.
  • DNA polymers can be synthesized in lengths from 2 to 150 nucleotides, which is the appropriate size range (1 nm to 60 nm) for self-assembling unit cells.
  • DNA polymers can be synthesized with any desired base sequence, therein providing programmable recognition for an almost unlimited number of specific connections. 4. DNA polymers with unique sequences of as few as ten nucleotides are highly specific and will bind only to their complementary sequence. Thus, the material allows specific connections as small as 3.4 nm to be made between molecular units.
  • DNA polymers can be covalently labeled with fluorophores, chromophores, affinity labels, metal chelates, chemically reactive functional groups and enzymes. This allows important photonic and electronic properties to be directly incorporated into the DNA polymers.
  • DNA polymers can be modified at any position in their sequence, and at several places within the individual nucleotide unit. This provides a means to position functional groups for maximum performance.
  • DNA polymers can be both covalently and non-covalently linked to solid surfaces: glass, metals, silicon, organic polymers, and bio-polymers. These attachment chemistries are both existing and easily developed.
  • the backbone structure of the DNA molecule itself can be highly modified to produce different properties. Thus, there is compatibility with existing semiconductor and photonic substrate materials.
  • Modified DNA polymers can be used to form three-dimensional structures, thus leading to ultra high density secondary storage schemes.
  • DNA polymers can be reversibly assembled and disassembled by cooling and heating, or modified to remain in the assembled state. This is a critical property for self-organizing materials as it allows for more options in the manufacture of resulting systems.
  • DNA polymers nucleic acids in general
  • DNA polymers are well understood and can be easily modeled by simple computer programs. Thus, more complex molecular photonic and electronic devices can be designed.
  • This invention relates to methodologies, techniques, and devices which utilize self-assembling DNA polymers, modified DNA polymers, DNA derivitized structures and other affinity binding moieties for nanofabrication and microfabrication of electronic and photonic mechanisms, devices and systems.
  • This invention also relates to processes which allow mutiplex and multi-step fabrication, organization or assembly of modified DNA polymers, DNA derivitized structures, and other types of affinity or charged structures into more complex structures on or within silicon or other surfaces.
  • DNA polymers is broadly defined as polymeric or oligomeric forms (linear or three-dimensional) of nucleic acids including: deoxyribonucleic acid, ribonucleic acids (synthetic or natural); peptide nucleic acids (PNA); methyphosphonates; and other forms of DNA in which the backbone structure has been modified to produce negative, positive or neutral species, or linkages other than the natural phosphate ester.
  • nucleotide or polynucleotide units are interspersed with other units including but not limited to phosphate ester spacer moieties, amino acids, peptides, polysaccharides, synthetic organic polymers, silicon or inorganic polymers, conductive polymers, chromophoric polymers and nanoparticles or nanostructures.
  • Modified or Derivitized DNA polymers are broadly defined as nucleic acids which have been functionalized with chemical or biological moieties (e.g., amines, thiols, aldehydes, carboxyl groups, active esters, biotin and haptens) which allow the DNA to be attached covalently or non-covalently to other molecules, structures, or materials. Also included are forms of DNA which have been modified or Derivitized with chromophores, fluorophores, chelates, metal ions, amino acids, peptides, proteins, enzymes, antibodies, or aliphatic or aromatic moieties which change solubility, and moieties which change the net charge on the DNA molecule.
  • chemical or biological moieties e.g., amines, thiols, aldehydes, carboxyl groups, active esters, biotin and haptens
  • forms of DNA which have been modified or Derivitized with chromophores, fluorophores, chelates, metal
  • DNA Derivitized structures are broadly defined as nanostructures (organic, inorganic, biological); nanoparticles (gold, silica, and other inorganic materials); organic or polymeric nanobeads; submicron devices, components, particles, (silicon based devices produced by photolithography or E-beam lithography); and micron scale devices or particles which have been functionalized with a specific DNA sequence which allows the structure to be specifically attached or interconnected to another structure, device, or to a specific location on a surface.
  • nanostructure refers to sub-micron sized structures
  • terms such as “nano” or “micro” are not intended to be limited in the sense that a micron scale device can be functionalized with DNA polymers which technically have lengths of 10- 180 nanometers.
  • the unique properties of DNA provides a programmable recognition code (via the DNA base sequence) which can be used for specific placement and alignment of sub-micron and nanoscale structures.
  • the basic chemistry and technology required to attach specific DNA sequences to organic, semiconductor, and metallic compounds is known to the art and specific chemistries are described for carrying out such applications.
  • the process by which photonic devices are aligned and fixed to substrate surfaces involves first coating them with a specific DNA polymer sequences.
  • the area of the host substrate where attachment of the specific device is desired, would then be coated with the specific complementary DNA sequence.
  • the substrate would be exposed to a solution containing the DNA covered devices, and hybridization between complementary DNA strands allowed to occur.
  • This hybridization process effectively grafts the devices to their proper receptor locations on the substrate surface.
  • This self-assembly fabrication process can be used for, by way of example, (1) the fabrication of light emitter arrays over large surface areas, and (2) the fabrication of two or three-dimensional photonic band-gap crystal structures.
  • This fabrication technique has major applications in the field of optoelectronics and in the manufacturing of various hybrid-integrated components including flat panel displays, medical diagnostic equipment and data storage systems.
  • Novel devices with very small physical dimensions take advantage of various quantum confinement techniques, hi most cases, these devices are preferably distributed over large areas (e.g. smart pixels and displays).
  • Other devices may be brought together in dense regular crystal lattices (e.g. photonic bandgap crystals).
  • the physics of the devices are now understood, and viable fabrication techniques of these inventions are required.
  • DNA self-assembly technology allows these devices to be constructed.
  • Integrated photonic and electronic systems utilize the inventive fabrication technologies including nanostructure fabrication, integration, interconnection and self- assembly techniques.
  • DNA self-assembly fabrication technology involves the following steps. Synthetic DNA polymers are designed with highly specific binding affinities. When covalently attached to nanoscale organic, metallic or semiconductor component devices, DNA polymers provide a self-assembly fabrication mechanism. This mechanism can be used for both the selective grafting of devices to specific pre-programmed locations on a desired surface, and for the clustering of devices into pre-programmed 2 and 3 dimensional lattices. For grafting an array of photonic component devices onto a host substrates,
  • DNA polymers with complementary sequences are first synthesized as shown in Figure 2.
  • the photonic component devices and desired areas of the host substrate (receptor areas) are coated with the complementary DNA sequences.
  • the host substrate is then introduced into a hybridization solution.
  • the devices coated with the specific DNA polymers are also released from their mother substrate into the solution.
  • the released devices can be actively transported to their receptor areas under the influence of electrically or optically induced local fields (electrophoresis).
  • Hybridization is carried out by carefully controlling the solution temperature, ionic strength, or the electric field strength. Once the devices are grafted via hybridization to their specific receptor areas, the solution is removed and the substrate is dried.
  • Metallurgical (or eutectic) bonding can now be carried out at a higher temperature to fully bond the devices to the host substrate material.
  • the clustering of sub-micron and nanoscale elements into 2-D or 3-D structures e.g., photonic band-gap crystals
  • the host substrate is replaced by other nanoscale elements.
  • the self-assembly fabrication technique based on DNA polymers offers two unique features. First, by removing the requirement for conservation of relative device spacing (as defined by the mother substrate) during the device grafting (hybridization) process, the technique enables the micron, sub-micron or nanoscale devices to be fabricated densely on their mother substrates and then be redistributed in a preprogrammed fashion onto the host substrate (Figure 3A).
  • the second feature is the ability to manipulate and orient with respect to each other a large number of nanoscale devices (e.g. organic or metallic nanospheres).
  • This feature allows the "growth" of synthetic photonic crystals with large lattice constants possessing desired orientation symmetries for exhibiting photonic bandgap properties ( Figure 3B).
  • bonding structures such as gold, tin or solder structures as bonding pads
  • these applications require four steps in the process.
  • the first involves the design and synthesis of the DNA polymer sequences and their selective attachment to the sub-micron and nanoscale devices of interest.
  • Second attachment of specific complementary DNA polymers to pre-selected receptor locations on a host substrate surface.
  • Third the self-assembly of the devices by the DNA hybridization process.
  • the fourth process involves establisliing the electrical contacts.
  • This invention brings together molecular biological (DNA structure and function) and photonic and electronic device principles in a synergistic manner.
  • novel devices with very small physical dimensions take advantage of various quantum confinement techniques. In most cases, these devices must be distributed over large areas (e.g. smart pixels and displays). In other cases, these devices must be brought together densely to form regular crystal lattices (e.g. photonic bandgap crystals).
  • processing techniques self-assembly DNA techniques with its well developed base of DNA synthesis, modification, and hybridization is an enabling technology for these applications.
  • DNA linkage to solid supports and various other materials is possible via a variety of processes for attaching DNA selectively to silicon, gold, aluminum and other inorganic and organic materials.
  • a number of thin film processing techniques are highly complementary with these DNA processes. For example, as will be described later, the lift-off process can be easily adapted to produce micron, and sub-micron devices with attached DNA sequences.
  • DNA sequences are synthesized using automated DNA synthesizer and phosphoramidite chemistry procedures and reagents, using well known procedures.
  • DNA polymers polynucleotide, oligonucleotides, oligomers
  • DNA polymers can have primary amine groups incorporated at chemical bonding sites for subsequent attachment or functionalization reactions. These primary amine groups can be incorporated at precise locations on the DNA structure, according to the need for that particular sequence.
  • Attachment sequences can also contain a terminal ribonucleotide group for subsequent surface coupling reactions.
  • Sequences including the amino modified oligomers, can be purified by preparative gel electrophoresis (PAGE) or high pressure liquid chromatography (HPLC). Attachment sequences with terminal amino groups can be designed for covalent bonding to gold, silver, or aluminum metalized features or to small areas where silicon dioxide is present. These sequences can be further Derivitized with a thiolation reagent called succinimidyl 3-(2- pyridyldithio)propionate (SPDP). This particular reagent produces a sequence with a terminal sulfhydryl group which can be used for subsequent attachment to metal surfaces.
  • SPDP succinimidyl 3-(2- pyridyldithio)propionate
  • attachment sequences containing a terminal ribonucleotide group can be converted to a dialdehyde derivative via Schiff s base reaction. These attachment sequences can then be coupled to ammopropylated silicon dioxide surfaces.
  • Specific sequences designed for electronic or photonic transfer responses can be functionalized with their appropriate chromophore, fluorophore, or charge transfer groups. Many of these groups are available off-the-shelf as activated reagents that readily couple with the chemical bonding sites described above to form stable derivatives.
  • This step involves the covalent coupling of the attachment sequences to solid support materials, h the general area of DNA attachment to solid materials, sequences have been covalently attached to a number of materials which include: (i) Glass (Si ⁇ 2), (ii) Silicon (Si), (iii) Metals (Gold, Silver, Aluminum), and (iv) Langmuir-Blodgett (LB) films.
  • Glass, silicon, and aluminum structures have been prepared in the following manner. Glass and silicon (SiO 2 ) are first treated with dilute sodium hydroxide solution and aluminum with dilute hydrogen fluoride solution. The materials are then Derivitized for covalent coupling with the attachment sequences by treatment with 3- aminopropyltriethoxysilane (APS).
  • the selective attachment can be realized by using the inherent selectivity of DNA sequences, selective attachment chemistries, or by directed electrophoretic transport. Alternatively after attachment, the DNA strands in unwanted regions can be destroyed by UV radiation. This approach is useful only when one group of devices need to be self-assembled. This approach would in normal operation preclude subsequent DNA attachment processes, and would not allow for the self-assembly of several specialty device groups. Attachment chemistry is strongly dependent upon the materials used to which the DNA polymers may be attached.
  • the aluminum regions are activated by dipping the sample for a short period of time into a dilute buffered HF solution.
  • the end result of this process is that only a few DNA strands are attached to the protective glass layer while the exposed aluminum pads are highly reactive to DNA.
  • This material selectivity is a convenient and general way to attach DNA to the desired regions. When material selectivity is combined with UV directed inactivation and electrophoretic transport, this allows for repeatable attachment processes to be carried out sequentially.
  • each pad group needs to be coated with a specific DNA sequence complementary to the DNA sequence attached to the specialty device that it would be bonded to.
  • each DNA sequence is attached sequentially to the proper pads. This can be easily achieved by using the electrophoretic transport process and by applying a negative potential to the pads where DNA attachment is not desired. Simultaneously, a positive voltage can be applied to enhance attachment to the desired locations. Alternatively, an optically induced electric field can be used to migrate the DNA strands to desired locations. For a second set of DNA sequence attachment, the procedure is repeated. It should be pointed out that when only one type of device needs to be self-assembled on the host substrate, the use of the material selectivity of the DNA attacliment chemistry alone is sufficient. UV radiation of the regions where DNA hybridization is not desired, would be carried out.
  • Another key step for the self-assembly process is the preparation of the sub- micron and micron-scale component devices for DNA attachment, their handling during the attachment process, and their final release into solution prior to hybridization.
  • the epitaxial lift-off (ELO) process can substantially improve these aspects of this technique.
  • Epitaxial films in the thickness range of 20 nm to 10 mm have been separated from their growth substrates, handled and manipulated.
  • thin III-V semiconductor films have been direct-bonded to foreign substrates, such as processed silicon wafers.
  • Prior to lift-off various devices can be fabricated on the films while still on their mother substrates.
  • the first step in our self- assembly technique is the preparation of the photonic devices that are to be grafted.
  • Figure 5 describes a preferred process flow for this preparation step.
  • the photonic devices are fabricated in a standard fashion on their mother substrates on a sacrificial layer as required by the ELO process.
  • a suitable coating layer is then deposited on these devices.
  • the behavior of the devices once released into the saline solution can be controlled.
  • the direction of the devices in the solution can be controlled.
  • a thick polyimide film is spun to provide a physical support to the devices after the ELO process.
  • the ELO process is carried out and the thin film devices are separated from their mother substrates.
  • the polyimide holding membrane is recessed in areas with no devices. If needed, a metal layer can be deposited to assure good electrical contacts to the photonic devices.
  • the DNA attacliment process is then carried out and a specific
  • DNA sequence is covalently attached on all metal surfaces.
  • the photonic devices are used as a self-aligned mask enabling exposure of polyimide areas coated with DNA polymer. In these areas, the DNA polymers react to a form that is not suitable for further hybridization.
  • the polyimide may then be removed and the devices released into the saline solution used for the further hybridization processes.
  • all devices may be released simultaneously into the solution.
  • hybridization of the complementary DNA strands takes place as the proper device-receptor pairs come into contact.
  • the probability of hybridization taking place may be related directly to the probability of the proper device-host pad pairs coming into contact. Since the probability distribution is most likely random, this process may take longer to achieve reasonable hybridization yields on large area surfaces unless the solution is saturated with the devices.
  • several controlled heating and cooling cycles may be carried out during the hybridization process. During the heat cycle, weakly hybridized components are dissociated away to increase the chances of forming stronger bonds.
  • the motherboard itself or another electrode array manufacturing device are used to produce localized electric fields which attract and concentrate selected component devices at selected locations.
  • the motherboard or manufacturing device has sites which can be used as an electrodes.
  • a potential is applied across the solution between selected receptor sites and auxiliary electrodes.
  • Receptor sites biased opposite (+) to the net charge (-) on selected devices now affect the electrophoretic transport and concentration of these devices thereby increasing the rate of hybridization and binding.
  • These sites can be selectively switched on or off using electronic or photonic addressing.
  • a pulsing DC or biased AC electric field can be applied at a suitable frequency to eliminate the screening effect of the unwanted device types.
  • the electric field effect can also be used in a protective manner.
  • the receptor pads are now biased the same (-) as the net charge (-) on the devices.
  • the devices are then repelled from these regions and interact or bind only to those locations which have the opposite charge (+) or are neutral.
  • Active electric field transport can be used to carry out multiplex and multi-step addressing of component devices and structures to any location on the motherboard array.
  • Another important consideration during hybridization is the alignment accuracy of the photonic devices on the motherboard or host substrate. It is assumed cylindrical photonic devices that rotation is invariant. In this case, if the device and host pad diameter is d, an alignment accuracy of d/2 may be first achieved with the natural hybridization process prior to the drying process. Devices that are mis-aligned with more than d/2 misalignment will not form a strong bond during the hybridization process and will not be held in place during the heating and cooling cycles of the hybridization process. Better alignment accuracy and orientation are possible when active electric field hybridization is used. Once the substrates are removed from the solution, increased surface tension during the drying process could further improve the alignment accuracy.
  • the specialty devices are held in their proper places through the formation of the double-stranded DNA structure which has a very high bonding strength.
  • the entire assembly is then cleaned by rinsing and then dried.
  • the DNA bond strength remains in the solid state and serves to keep the devices in place.
  • One method to achieve a metallurgical bond exhibiting an ohmic contact between the host substrate and the photonic devices is to use conductive materials on the pads and devices that can be bonded together eutectically at low temperatures.
  • a second method is to use metals with low melting temperatures like solder or indium under a metal layer that is active for DNA attachment.
  • emitter arrays can be advantageously formed.
  • Specific DNA polymer sequences may be covalently attached to semiconductor light emitting diodes (LED) and the complementary DNA sequences may be attached to receptor pads on the host silicon substrate.
  • UV/DNA patterning techniques may be used for selective activation/inactivation of DNA on the coated surfaces. All DNA Derivitized test structures and materials will then be tested for selective hybridizability using complementary fluorescent DNA probes. LED test devices Derivitized with specific DNA sequences may be hybridized to test substrates Derivitized with complementary DNA sequences.
  • Photonic or crystals may be formed using the DNA self-assembly technique.
  • Photonic Bandgap Structures are artificial periodic lattice structures in two- or three- dimensional arrangements and composed of elements of proper dimensions, density and separations. Such structures result in the modification of photonic density of states and a gap in the electromagnetic wave dispersion. Indeed, photonic bandgap structures operating at specific optical wavelengths have been demonstrated. Potential applications of photonic bandgap materials include tailoring of the spontaneous emission of a laser to achieve ultra-low threshold lazing, improved wave guiding structures without radiation loss, novel optical modulators, etc.
  • nano-scale rods or spheres of higher dielectric constant are positioned in a medium of lower dielectric constant.
  • a three-dimensional diamond lattice arrangement of close-packed tetrahedrally-connected dielectric spheres (200 nm in diameter and a refractive index of 3.6) embedded in a lower-dielectric- constant medium such as air exhibits photonic bandgaps.
  • This invention relates to new ways of constructing photonic crystals by self-assembling high dielectric constant elements with desired geometry's in lower dielectric materials.
  • Metal spheres exhibiting magnetic properties may have attached DNA strands. Magnetic properties may be used to control the orientation of the spheres (or rods for 2-D crystals).
  • the metal spheres may be dipped into a DNA solution, aligned using a magnetic field, and exposed under UN radiation. This technique allows 2D and 3D photonic-bandgap structures to be "grown" around active optoelectronic devices with minimum fabrication complexity.
  • this technique may also provide a means of realizing tunable photonic bandgap structures.
  • the process for electronic orientation is discussed in the "Process for Electric Field Orientation Synthesis of Nanospheres and Sub-Micron Devices", below.
  • 20-mer to 50-mer size range may be synthesized on automated DNA synthesizers using phosphoramidite chemistry.
  • Longer DNA sequences are generally required to bind larger objects to surfaces because the binding force must be sufficient to overcome forces (e.g., shearing forces) tending to remove the object.
  • Longer DNA sequences (> 50 mers) may be constructed using the polymerize chain reaction (PCR) technique.
  • the DNA sequences may be further Derivitized with appropriate functional groups (amines, thiols, aldehydes, fluorophores, etc.). All sequences may be purified by either PAGE gel electrophoresis or HPLC. After purification, all sequences may be checked on analytical PAGE gels for purity, and then tested for specificity by hybridization analysis.
  • DNA sequences may be used to develop and test additional chemistries for the covalently attachment to various, organic polymer based nanospheres, semiconductor, and other material substrates (glass, gold, indium tin oxide, etc.). Additional attacliment chemistries provide more options and flexibility for attachment selectivity to different semi-conductor materials.
  • Specific DNA polymer sequences may be covalently attached to semi-conductor test structures and the complementary DNA sequences to test substrate (motherboard) materials. UV/DNA patterning techniques may be used for selective activation/inactivation of DNA on the coated surfaces. All DNA Derivitized test structures and materials will then be tested for selective hybridizability using complementary fluorescent DNA probes. Nanospheres, nanoparticles, and semi-conductor test structures Derivitized with specific DNA sequences will now be hybridized using both conventional (temperature, salt, and chaotropic agents) and electronic (electrophoretic) techniques to the test substrates (motherboards) Derivitized with complementary DNA sequences. The hybridization techniques may be optimized for highest selectivity and least amount of non-specific binding.
  • Specific DNA polymer sequences may be covalently attached to semi-conductor light emitting diode (LED) component devices and the complementary DNA sequences to motherboard materials.
  • UN/DNA patterning techniques may be used for selective activation inactivation of DNA on the coated surfaces.
  • LED component devices Derivitized with specific DNA sequences are then hybridized to test substrates (motherboards) Derivitized with complementary DNA sequences.
  • Self- Assembly Fabrication of a Photonic Crystal Structure Multiple specific DNA polymer identities may be incorporated into nanoparticles or nanospheres for the self-assembly around emitter test devices located on motherboard materials.
  • UN/DNA patterning techniques may be used for selective activation/inactivation of DNA on the coated surfaces. Nanoparticles Derivitized with specific DNA sequences will now hybridized to the emitter test devices located on the substrates (motherboards) Derivitized with complementary DNA polymers.
  • This invention provides for assembling specialty devices in parallel and over larger areas (up to several meters on a side) using a "self-assembly" technique, hi this approach, each device to be grafted somehow "Icnows" where it is destined to be on the motherboard.
  • This invention relates to a new integration technique based on programmable self-assembly principles encountered in biological systems. This new technique removes the requirement of dimension conservation during the grafting process.
  • Our objective is to demonstrate the self-assembly of micro/nano structures on silicon using DNA (Deoxyribonucleic Acid) polymers as "selective glues", thereby developing techniques for integrating these structures sparsely onto large area motherboards.
  • the second is a method for electrophoretically transporting D ⁇ A-nanostructures (nanostructures to which specific D ⁇ A sequences are attached) to selected locations on substrate materials.
  • the technique for UN lithography with D ⁇ A involves first coating a substrate material with a molecular layer of specific attachment D ⁇ A polymer sequences. An appropriate mask can be used to imprint a pattern into the attachment layer of D ⁇ A by exposure to UN irradiation (300 nm) for several seconds. The D ⁇ A in the area on the substrate exposed to UN light becomes in-active to hybridization with its complementary
  • D ⁇ A sequence i.e., it is not able to form the double-stranded structure.
  • Figure 7 show fluorescent DNA on a silicon structure was patterned with 10 micron lines using an electron microscope grid pattern. After UN patterning the material is hybridized with a complementary fluorescent labeled D ⁇ A probe, and examined epifluorescent microscopy. The fluorescent image analysis shows where the complementary probe has hybridized (fluorescent), and where no hybridization has occurred (no fluorescence).
  • other electric field based process allows derivitized D ⁇ A and charged fluorescent nanospheres to be electrophoretically transported and deposited onto selective microscopic locations on solid supports. The basic method and apparatus for this technology is shown in Figure 32.
  • Negatively charged DNA, sub-micron or micron-scale structures can be suspended in aqueous solutions and transported via an electric field (electrophoresis in solutions) to microscopic locations which are biased positive, relative to other locations which are biased negative. This is a particularly important technique in that it provides a mechanism to direct the transport of specifically labeled devices to specific locations on a substrate material.
  • the first step in our self-assembly technique is the preparation of the specialty devices to grafting.
  • the specialty devices are fabricated in a standard fashion on their mother substrates on a sacrificial layer as required by the ELO process.
  • a suitable coating layer is then deposited on these devices to assure they have a Brownian like motion in the saline solution.
  • the behavior of the devices once released into the saline solution can be controlled. For example, by controlling the coating material properties we could control the direction of the devices in the solution.
  • a thick polyimide film may be spun to provide a physical support to the devices after the ELO process.
  • the ELO process may be carried out and the thin film devices may be separated from their mother substrates.
  • the polyimide film may be recessed to provide sufficient steps to prevent the metal layer from being continuous.
  • the DNA attachment process is then carried out and a specific DNA sequence may be covalently attach on all the metal surfaces.
  • the DNA areas that are exposed and not protected may be destroyed or put in a form that is not suitable for further hybridization.
  • the polyimide will then be removed and the devices may be released into the saline solution used for the further hybridization processes.
  • a selective attachment procedure for the complementary DNA polymer must be carried out.
  • the selective attachment can be realized by using the inherent selectivity of DNA sequences, selective attachment chemistries, or by directed electrophoretic transport. Alternatively after attachment, the DNA strands in unwanted regions can be destroyed by UV radiation. This approach is useful only when one group of devices need to be self-assembled.
  • DNA attachment chemistry is strongly dependent on the materials used to which the DNA polymers may be attached.
  • we first activate the aluminum regions by dipping the sample for a short period of time into a dilute buffered HF solution.
  • the end result of this process is that only a few DNA strands are attached to the protective glass layer while the exposed aluminum pads are highly reactive to DNA.
  • This material selectivity is a convenient and general way to attach DNA to the desired regions. When material selectivity is combined with UV directed inactivation and electrophoretic transport process, this allows for repeatable attachment processes to be carried out sequentially.
  • the pads need then to be grouped according to the device to which they are to be coupled. In this case, each pad group needs to be coated with a specific DNA sequence complementary to the
  • each DNA sequence can be attached sequentially to the proper pads. This can be easily achieved by using the electrophoresis process and by applying a negative potential to the pads where DNA attachment is not desired. Simultaneously, a positive voltage can be applied to enhance attachment to the desired locations. For a second set of DNA sequence attachment, the procedure may be repeated with a different set of programming voltages.
  • the motherboard receiving pads may be programmed by applying a proper set of positive and negative potentials to the pads. When only one type of device needs to be self-assembled on the motherboard, the use of the material selectivity of the DNA attachment chemistry alone is sufficient.
  • the self-assembly process can take place.
  • hybridization stringency temperature
  • by agitating gently the devices in the solution hybridization of complementary DNA strands may be allowed to take place as the proper device-pad pairs come into contact (see Figure 33).
  • Conventional and Electronic Hybridization In this methods all devices may be released simultaneously into the solution, and the probability of a hybridization process talcing place may be related directly to the probability of the proper device-pad pairs to come into contact.
  • the probability of a hybridization P h may be roughly related to the ratio of the total available pad area A-, to the mother board area A--., P h NA p /A ⁇ b where N is the real density of one of the specialty device groups in the solution. Since the probability distribution is expected to be random, this process may take very long times to achieve reasonable hybridization yields. Alternatively it may require the solution to be saturated with the specialty devices. This may increase the cost of the process and limit the number of types of specialty devices that can be self-assembled.
  • a key part of the self-assembly process is the preparation of the micro/nano scale devices for DNA attachment, their handling during the attachment and finally their release into the saline solution prior to hybridization.
  • the most popular ELO approach is to employ the selectivity of dilute HF acid on the Al GaAs series of alloys.
  • the Aluminum rich alloys etch at a rate of approximately 1 mm/hr, while the etch rate of Gallium rich alloys is almost undetectable, less than 0.1 nrn/hr.
  • An intermediate layer of AlAs dissolves, allowing upper epitaxial layers to simply float away from the substrate.
  • Other separation methods have also been used, including mechanical cleavage (CLEFT), and total substrate etching down to an etch stop layer.
  • Epitaxial films in the thickness range between 20 nm and 10 mm have been separated from their growth substrates, handled and manipulated.
  • ELO is a true thin-film technology, allowing thin-film metal wiring which passes back and forth over the edge of a thin III-V film and onto a silicon micro-chip substrate. At the same time, the thin film is grown lattice-matched and essentially homo-epitaxially. Material quality, of the utmost importance for minority carrier devices such as light emitters, is never compromised. Advantages of the ELO technology over hybrid flip-chip technology include low packaging capacitance and high packing density. For high speed micro- circuits, wiring capacitance must be very low. The penalty is not merely the burden of added power dissipation.
  • the ELO may offer more in this aspect than the solder bump technique.
  • ELO films grafting on processed silicon micro-circuits requires consideration of the ultra-fine scale roughness of the deposited oxide surfaces of the micro-chip. Surface roughness interferes with the quality of the Van der Waals or metallurgical bond.
  • a second method is to introduce each device group separately and to confine the specialty devices within regions near the positively biased pads. This confinement can be done under the influence of a DC electric field by applying a suitable positive voltage to the pads. The effect of the electric field can then be viewed as increasing the ratio of the areas, or equivalently increasing the device density, N, in the above equation.
  • each device group must be introduced sequentially, so the unwanted device groups do not screen the right devices from reaching the pad.
  • An alternative method is to introduce all device types concurrently into the solution, to apply an initial DC voltage to create a distribution of the devices around each pad, and then to apply an AC voltage at a suitable frequency to eliminate the screening effect of the unwanted devices types.
  • the effect of the AC field can be seen as a stronger stirring mechanism.
  • Metallurgical bonds After the hybridization process the specialty devices are held in their proper places through the formation of the double-stranded DNA structure which has very high bonding strength. The entire assembly is then cleaned by rinsing and then dried. At this point there is no electrical contact between the motherboard and the specialty devices. The DNA bond strength remains in the solid state and serves to keep the devices in place.
  • One method to achieve a metallurgical bond with ohmic contact is to use conductive materials on the pads and devices that can be bonded together eutectically at low temperatures.
  • a second method is to use metals with low melting temperatures like solder or indium under a metal layer that is active for DNA attachment. In this case the bumps must be made in nanometer dimensions.
  • the devices may be self-aligned to the pads in a similar fashion as with the C4 technology used for flip-chip bonding.
  • Electric field synthesis is preferably used for producing nanostructures or microstructures (e.g., nanospheres, nanoparticles, sub-micron and micro scale devices) with multiple DNA surface identities. These multiple surface identities can be in the form of specific DNA sequences which are located at different co-ordinates on the particle surface. These co-ordinates can be, for example, polar or tetrahedral in nature, and impart potential self-assembly properties which allow the nanostructures to form 2 and 3 dimensional photonic and electronic structures (such as the photonic band gap structures).
  • Figure 36 (upper) shows a generalized diagram of a the nanosphere (20 nm diameter) with multiple DNA sequence identities in polar and equatorial positions. Figure 36 (lower) also shows some simple structures that could be formed by hybridizing the nanospheres together.
  • Fig. 37 shows the initial steps for producing such nanostructures.
  • step (1) a suitably functionalized nanosphere (with amine groups) is reacted with aldehyde modified oligonucleotides with sequence identity (A).
  • Identity (A) refers to a unique sequence of bases in the DNA; for example a 20-mer oligonucleotide with a 5'- GCACCGATTCGAT ACCGTAG-3' sequence.
  • the oligo (A) modified nanospheres are now hybridized to a microlocation surface (with an underlying electrode) which has a complementary A' sequence (5'- CTACGGTATCGAATCGGTGC-3').
  • the (A') sequence contains a crosslinker agent (psoralen) and extends into a secondary sequence with (B) identity (5'- TTCAGGCAATTGATCGTACA-3'), which was in turn hybridized to a (B') DNA sequence (5'-TGTACGATCAATTGC CTGAA-3') covalently linked to the surface.
  • step 3 the hybridized nanospheres are now given a short exposure to UV irradiation which causes the psoralen moiety within the (A/A') hybridized sequence to covalently crosslink.
  • the nanospheres are now de-hybridized (passively or electronically) from the surface.
  • the nanospheres now have a (B) DNA sequence identity imparted to a polar position on the structures.
  • Figure 38 shows the continuation of the processing scheme.
  • the (B) DNA sequence identity modified nanospheres are now "partially hybridized” to a new microlocation which in turn has been hybridized with a (C-A') sequence, to a complementary C sequence which is covalently linked to the surface.
  • the (C) sequence is different form the (A) and the (B) DNA sequences.
  • the (B) DNA sequence nanobeads partially hybridize to the surface via the (A/A') DNA sequences, however they are not oriented in any particular fashion on the surface. Because the (B) DNA nanospheres have a non-uniform negative charge distribution on their surface (due to the extra charge from the (B) DNA, they can be oriented in an electric field.
  • a secondary electrode is positioned above the lower electrode, and an electric field strength is applied which is strong enough to orient the nanospheres, but does not de-hybridize them from the surface.
  • Figure 38 shows the nanospheres in a polar orientation, in terms of the (B) and (C) sequences; the relative positioning of the electrodes can produce electric fields which yield other angles for the relative position of the (B) and (C) DNA sequences.
  • the nanospheres When the nanospheres are in their correct alignment, they can be completely hybridized (A'- C/C), by lowering the temperature, and then exposed to UV irradiation to crosslink the (A/A') sequences.
  • FIG. 39 shows a microelectronic array device with 64 microelectrodes arranged in an 8x8 matrix, and four larger control electrodes just outside the matrix. Electrode structures on the device can range in size from ⁇ 1 micron to several centimeters or more in large scale or macroscopic versions of these devices. Permeation layers and/or template materials may be placed over such devices which would allow the devices to be used to cany out multi-step and multiplex synthesis reactions and fabrication steps on substrate materials.
  • devices can be used for multi-step and multiplex reactions and fabrication on “themselves”; as well as manufacturing devices, which produce the assembled systems on various substrate materials.
  • multi-step processes as these which have more than one synthesis or fabrication step at one or more locations on the device; and “multiplex” as processes involving the synthesis or fabrication of different components on different locations on the device.
  • Fig. 40 shows the process by which multi-step transport and positioning of nanospheres or nanoparticles can be carried out using such devices.
  • negatively charged nanostructures type 1 are transported and concentrated from the bulk solution onto specific microlocations on the left side of the array. This is achieved by biasing the microlocations positive, relative to the control electrodes biased negative.
  • the negatively charged type 1 nanostructures within the electric field are transported and concentrated (electrophoretically) at the specific microlocations.
  • the type 1 nanostructures can be various devices or structures which have specific DNA sequences which allows them to hybridize at other specific locations on the device itself or to other nanostructures which contain complimentary DNA sequences.
  • type 2 nanostructures are transported and concentrated at specific microlocations on the right side of the device.
  • the type 1 nanostructures are transported to specific microlocations at the center of the array which have complimentary DNA attached.
  • the type 1 nanostructures are transported to specific microlocations at the center of the array which have complimentary DNA attached.
  • the type 1 nanostructure hybridize and become specifically attached to these locations.
  • the type 2 nanostructures are now transported to the same center location, as the type 1 nanostructures.
  • the type 2 nanostructures are now transported to the same center location as the type 1 nanostructures.
  • the type 2 nanostructures contain attached DNA sequences which are complimentary to the type 1 nanostructures.
  • the type 2 nanostructures hybridize and become a bound layer over the type 1 nanostructures.
  • microlocations are 50 m x 50 m in size.
  • the negatively charged 200 nm fluorescent nanospheres are rapidly transported and concentrated onto the positively charged microlocations.
  • nanospheres have been moved from one location to other locations on the device; and it is possible to form various patterns or arrangements of nanostructures on these devices. Positioning and Orientation of Large Structures
  • One useful application of this invention involves the attachment and orientation of larger (10-100 micron) sized devices onto substrate or motherboard materials. This process is shown in Figure 42.
  • a device is selectively derivatized with four different DNA sequences, and the motherboard is selectively derivatized with the four complimentary sequences.
  • the devices are then allowed to hybridize and attach to the motherboard substrate by the processes which were described in earlier sections on passive and active electric field methods for hybridization.
  • microelectronic deivces are designed and built by classical procedures, but contain areas which are designed for self-assembly of nanostructures and sub-micron cmponents.
  • Figure 43 shows one such device.
  • a microelectronic device built in silicon using classical photolithographic techniques has a well structure with an underlying micro microelectrode.
  • This microelectrode is now used to carry out the electric field assisted self-assembly of various nanostructures and sub-micron components within the parameter of the microelectronic components.
  • This technique allows interconnection between the microelectronic components and the nanoscale components, as well as the creation of much denser integrated devices including arrangements of multiple layers (3D fabrication) of components.
  • this invention is considered a way to synergize both classical microelectronics (optoelectronic) fabrication techniques, with self-assemblying nanofabrication techniques.
  • Figure 44 shows an example of this methodology.
  • four sub-micron attachment structures are deposited onto a suitable substrate material.
  • Two of the structures are of mataerial which can be selectively activated for subsequent attachment of DNA sequences (i.e., gold for thiol attacliment chemistry).
  • the other two of a material which can be selectively activated for another specific attachment chemistry (i.e., silicon dioxide for silane aldehyde/amine attachment chemistry).
  • DNA optical storage involves the design and synthesis of chromophoric DNA polymers which absorb light energy at a single wavelength and re-emit at predetermined multiple wavelengths.
  • Our work shows that DNA polymers can be attached in a self- organized manner to solid surfaces and made into unit cells that have the designed functionality.
  • DNA polymers attached to solid surfaces could exhibit multiple chromophoric responses, photonic energy transfer, and quenching.
  • Figure 6 and Figure 7 show results related to attachment of fluorescent DNA polymers to silicon dioxide and aluminum surfaces and UV writing (imaging) into monolayers of DNA on the surface of these substrates.
  • DNA substrate materials Four different mechanisms exist by which information can be written into DNA substrate materials: i) spatial UV inactivation of thymidines within DNA sequences; ii) spatial UV inactivation of fluorophores and chromophores; iii) spatial UV inactivation or activation of quencher chromophores; and iv) spatial UV activation or inactivation of subsequent hybridization by crosslinking (e.g., psoralens).
  • crosslinking e.g., psoralens
  • Figure 8 a and b shows UV write/hybridization results using a logo mask and a four color write mask. These represent images that are produced in monolayers of DNA on silicon substrates to which complementary fluorescent DNA sequences are hybridized.
  • FIGS 9 thru 19 schematically show the complete process for preparing a "four identity DNA substrate material". This process imparts multiple DNA identities in substrate materials using psoralen crosslinking agents. DNA intercalated psoralen compounds when exposed to low-energy UV light (365 mn) are able to covalently crosslink the DNA strands together. Linking DNA strands together with psoralen allows creation multiple identities on substrate surfaces.
  • Figure 9 shows DNA sequences with identity (A) covalently attached to the
  • the chip surface is first reacted with aminopropyltriethoxysilane (APS) reagent, which provides amine groups on the substrate surface for attaching the DNA sequences.
  • APS aminopropyltriethoxysilane
  • the capture DNA sequences (A) are functionalized in their tenninal position with a ribonucleoside group which is subsequently oxidized to form an amine reactive dialdehyde group.
  • the DNA (A) sequences can now be covalently coupled to the amine groups on the APS functionalized substrate surface.
  • the figures show four individual DNA strands as a way to depict the four potential write identity quadrants (refereed to as locations in the figures). In the actual material there are from ⁇ 2.5 X 10 4 to 2.5 X 10 5 DNA strands per quadrant (quadrant size is preferably about 250 nm square).
  • Figure 10 shows the write identity process is initiated by hybridizing a (B) identity psoralen modified DNA sequence that is also partially complementary to the (A) identity capture sequence existing in all four quadrants (locations).
  • the psoralen molecules intercalate within the hybridized double-stranded DNA.
  • Figure 11 shows a UV mask is now used to block quadrant 1 , while quadrants 2, 3 and 4 are exposed.
  • the unmasked quadrants (2, 3 & 4) are irradiated with low- energy UV light (365 nm).
  • the UV exposure causes the intercalated psoralen molecules within the hybridized double-stranded DNA to covalently crosslink the strands.
  • Figure 12 shows the entire surface is now subjected to a dehybridization process.
  • the non-crosslinked (B) identity DNA sequence in quadrant 1 is removed, leaving the (A) identity DNA sequence in that position.
  • Quadrants 2, 3 & 4 now have the (B) identity DNA sequence in their positions.
  • Figure 13 shows the process is now repeated with a (C) identity DNA sequence, containing the partial (B) identity DNA complement, being hybridized to the (B) sequence in quadrants 2, 3 and 4.
  • Figures 14 thru 18 depict essentially the repetition of the processes shown in figures 9 thru 13.
  • the final material contains four separate DNA identity sequences (A, B, C, & D) each located in a separate quadrant.
  • Figure 19 shows, at this point, where one can check the specificity of the four DNA sequences (A, B, C, & D) by hybridizing the four fluorescently labeled complementary sequences to the surface. Each quadrant should now produce its specific fluorescent color.
  • the actual information UV write process (to the four DNA identity substrate) is carried out by another masking and UV exposure procedure (see Figures 20, 21, and 22).
  • a higher energy UV irradiation (254 nm) is used to render the DNA in the UV exposed regions non-hybridizable.
  • This procedure can thus be used to inactivate the individual quadrants or "turn them off.
  • the fluorescently labeled complementary DNA sequences are hybridized to the material, only the quadrants with hybridizable complementary DNA sequences will have the appropriate fluorescent color. This is the mechanism by which data can be selectively written into DNA.
  • Figures 20 & 21 show turning "On” the B and D identities, and turning "Off the A and C identities.
  • the specific A, B, C, & D sequences in all four quadrants 1, 2, 3, & 4 are hybridizable.
  • the write process is initiated by masking quadrants 2 and 4, and exposing the surface to the high-energy (254 nm) UV irradiation. Quadrants 1 and 3 are now effectively inactivated or made unhybridizable by UV exposure, while the DNA sequences in 2 & 4 remain hybridizable.
  • Figure 22 shows how the material can now be hybridized with the fluorescent DNA complements to all four DNA identities, however, only the fluorescent DNA complements to the B and D identities will effectively hybridize and produce the final fluorescent colors.
  • the UV write process being completed, the material now has two distinct fluorescent colors in the B and D quadrants, and no fluorescent colors in the A and C quadrants.
  • FIG. 23 A &B, 24 A&B, and 25 A&B show the actual photographs of the substrate and fluorescent write materials.
  • Figures 27 A, B &C, and 28 A, B&C, provide further schematic descriptions of the process.
  • Step 1 A control chip surface (Silicon Dioxide/ Aluminum Silicon) was treated with Aminopropyltriethoxysilane (APS).
  • Figure 23 -A shows the chip surface appears basically black, because of the relatively low level of background fluorescence.
  • Figure 27-A is a schematic representation of the material at this point of the process. All photographs were taken using the Jenalumar Epi-fluorescent microscope/Hammamatsu Intensified CCD Camera/ Argus Ten Imaging system.
  • Step 2 A second control chip surface (APS reacted) was then reacted with the DNA (A) identity capture sequence that contains the proper base composition for subsequent psoralen crosslinking.
  • the DNA (A) sequence has a ribo group on the 3' end that is oxidized to a dialdehyde, this reacts with the amine groups on the surface to covalently attach the DNA.
  • Figure 23-B shows a photograph of the substrate surface with the DNA (A) present, but without any fluorescent complementary DNA present. The chip surface still appears black, because of the relatively low level of background fluorescence.
  • Figure 27-B is a schematic representation of the material at this point of the process.
  • Step 3 A third control chip surface which has been APS reacted and has the DNA (A) capture sequence attached, is hybridized with a Bodipy Texas Red fluorescently labeled complementary sequence.
  • Figure 24-A now shows the entire chip surface producing intense red fluorescence.
  • Figure 27-C is a schematic representation of the material at this point of the process.
  • Step 4 A fourth chip is treated with APS and (A) identity DNA capture sequence is then bound to the surface as in Step 2.
  • Step 5 The complementary (B) identity sequence, with a psoralen molecule attached, is then hybridized to the (A) identity sequence over the entire surface.
  • Step 6 One half of the chip surface is masked, while the other half is exposed to low-energy (365 nm) UN light. This causes the covalent crosslinking of the (A) identity D ⁇ A sequence with the (B) identity D ⁇ A sequence.
  • Step 7 The surface is then treated with a 0.1 normal Sodium Hydroxide solution to remove (dehybridize) the non-crosslinked D ⁇ A from the masked side of the chip. At this point one half of the chip is covered with covalently linked (B) identity D ⁇ A sequence, and the half contains the original (A) identity D ⁇ A sequence.
  • Step 8 A complementary (A) identity D ⁇ A sequence labeled with Bodipy
  • Texas Red fluorescent dye (excitation maximum 595 nm and emission maximum 626 nm) is now hybridized to the chip.
  • the complementary fluorescent (A) identity D ⁇ A sequence hybridizes only to the half of the chip surface containing the (A) identity capture sequence (figure 24-B).
  • Figure 28-A is a schematic representation of the material at this point of the process. Steps 4 thru 7 are repeated on a fifth chip surface.
  • Step 9 A Bodipy Orange fluorescent dye (excitation maximum 558 nm and emission maximum 568 nm) labeled sequence complementary only to the (B) identity sequence is then hybridized across the whole chip. This D ⁇ A sequence hybridizes only to the half of the chip containing the (B) identity (figure 25-A).
  • Figure 28-B is a schematic representation of the material at this point of the process.
  • Step 10 A sequence complementary only to the (A) identity capture sequence, labeled with Bodipy Texas Red fluorescent dye is hybridized to the fifth chip. Again this fluorescently labeled DNA attaches only to the half of the chip containing the (A) identity. The chip now contains both identities with their corresponding colors (figure 25-B).
  • Figure 28-C is a schematic representation of the material at this point of the process.
  • Figures 26 A and 26B show results on attaching 160 nm DNA Derivitized fluorescent nanospheres to a DNA Derivitized silicon dioxide surface.
  • the nanospheres are bound to the image sections with the active DNA, as opposed to the DNA inactivated sections.
  • the binding is believed to be due to electrostatic as well as to hybridization interactions.
  • DNA polymers may be used for many photonic and electronic applications.
  • One of the main applications using DNA polymers are for high density optical data storage media.
  • chromophoric DNA polymers absorb light energy at a single wavelength and re-emit at predetermined multiple wavelengths. (See Fig.
  • these inventions relate to a method called photo-electronic write process. This process involves using spatial light addressing to a photoactive substrate material which creates microscopic electric fields, which then affect the selective transport and attachment of charged chromophoric (color) DNA's to these selected locations.
  • the basic principle involved in the photo/electronic write process is show in Figs. 46.a and 46.b.
  • the proposed write substrate would be a photoelectronic activated matrix material (e.g., a photoconductive film) onto which DNA polymer sequences would be attached. Each of these DNA sequences would have multiple identities.
  • Figure 46. a shows three photoactivated sites, which contain DNA sequences with three identities (A, B, & C).
  • a solution containing chromophoric DNA with complementary identity (A') would be exposed to the substrate material, and a counter electrode would be positioned over the solution and lower substrate material.
  • the specific microlocations on the substrate material can now be activated by spatial light addressing which would cause a charge to develop in the material at that location (see Figure 46.b).
  • the production of a charge produces an electric field in the solution which causes the attraction of oppositely charged molecules to the location, or will repel molecules of the same charge identity.
  • Natural DNA would contain a net negative charge, and will migrate to a positively charged location.
  • Synthetic DNA's can be made with net negative charge, net positive charge, or in a neutral state.
  • Figure 46.b shows the light activation of the center microlocation 2, with chromophoric DNA (A') migrating to this location and then binding (hybridizing) to the DNA (A) identity sequence position.
  • the electric field strength is high enough, the transport and concentration of the DNA chromophore units is extremely rapid; occurring in 1 to 2 seconds.
  • Figures 46.c through 46.fi Figure 46.c shows a group of six microlocations, each of which contains a DNA polymer with A, B, and C sequence identities (only one capture strand is shown in these figures). Spatial light addressing of positions 1, 3 , and 5 is carried out. Chromophoric DNA A' sequences (red) are transported, concentrated, and hybridized selectively to these locations. Figure 46. d shows the process repeated for the next chromophoric DNA B' sequences (green). Spatial light addressing of positions
  • f shows the final optical material which now has chromophore DNA A'/B'/C (red/green/blue) at microlocations 1 and 3, chromophoric DNA A'/C (red/blue) at microlocation 5, chromophoric DNA B' (green) at microlocation 4, chromophoric DNA C (blue) at microlocation 6, and no chromophoric DNA (no color) at microlocation 2.
  • chromophore DNA A'/B'/C red/green/blue
  • chromophoric DNA A'/C red/blue
  • chromophoric DNA B' green
  • chromophoric DNA C blue
  • no chromophoric DNA no color at microlocation 2.
  • electrode array devices may be switched by spatial light addressing.
  • electrode arrays may be switched by electronics.
  • N-type single crystal silicon wafers of (100) and. (111) orientation and resistivities ranging between 0.1-0.9 Ohm-cm and 1-4 Ohm- cm were received from various commercial sources.
  • the wafers were provided with an ohmic back contact by deposition of either a 300 nm aluminum layer (thermal evaporation) or a 50 nm platinum (sputter deposition) layer followed by thermal annealing. Annealing steps were performed under nitrogen at 300 C for 1 hr for aluminum layers and at 500 C for 45 min for platinum layers.
  • Amorphous silicon surfaces were obtained by sputter deposition of 50 nm silicon onto oxide stripped (buffered HF) n-type single crystal wafers with ohmic back contacts.
  • the sample surfaces were sensitized by exposure (2 min) to an aqueous solution containing 1 wt% SnCl 2 (Aldrich) and 4 vol% HC1. This step was followed by rinsing with 4 vol% HC1 and deionized water. The sensitized surfaces were then decorated with Pd islands by immersion (2 min) in an aqueous solution containing 1 vol% HC1 and 0.05 wt% PdCl 2 (Aldrich). Traces of Sn 4+ were removed by soaking in 5% HC1 for 5 min followed by rinsing with deionized water.
  • the deposition of the Mn(OH) 2 layer was performed by adding a freshly prepared aqueous solution containing 0.25 M NH 4 C1, 0.1 M NH 4 OH and 0.03 M MnCl 2 to the samples in the petri dish. Upon addition of the solution the petri dishes were placed on a shaker table for 10 min to allow vigorous stirring. A light brownish precipitate was observed to fonn within 30-60 sec. After completion of the deposition reaction, the samples were rinsed thoroughly with deionized water and dried in air. At this point, the sample surfaces have a slightly structured, brown-grayish appearance.
  • FIG. 47 shows a cross-sectional view of a device capable of perfonning the photoelectric transport and hybridization of oligonucleotides of the present invention.
  • An electrochemical cell 100 was constructed by first attaching a stripe of conducting material 102, preferably copper tape to a glass slide 100.
  • a semiconductive substrate 104 such as an n-type silicon substrate, is disposed adjacent the conducting material 102.
  • the Mn 2 O 3 106 and agarose coated silicon sample was then mounted onto the Cu tape using conducting silver paint (Ted Pella).
  • the active electrode area was defined by attaching a sheet 110 (e.g., a 2 mm thin piece of teflon sheet) with a circular opening to the sample.
  • the electrode area exposed to the light measured about 0.25 cm 2 .
  • the electrochemical cell was completed by placing a circular Pt auxiliary electrode 112 and a Ag quasi-reference electrode 114 above the sample surface.
  • Sample illumination for photoelectrophoretic transport and hybridization was accomplished by an optical fiber 116, preferably a single-mode optical fiber (Oriel) that was mounted on a motorized micromanipulator stage (Eppendorf 5171) and coupled to a laser 118, such as a 8 mW 630 nm HeNe laser (Research Electro Optics) that was attenuated by a filter wheel (New Focus).
  • Photoelectrochemical stability measurements were performed by illuminating the whole sample area with a halogen light source (Bausch & Lomb).
  • Electrochemical experiments were performed either with a Pine AFRDE5 or an Autolab PGSTAT10 potentiostat system. Fluorescence signals were measured either on a high-resolution fluorescence scanner (Avalanche, Molecular Dynamics) or on a cooled CCD camera (Princeton Instruments). Surface morphologies and film thickness were recorded with a commercial atomic force microscope ( ⁇ anoscope III, Digital Instruments).
  • Kainthla et al. The original procedure for surface protection of n-type single crystal silicon surfaces with Mn 2 O 3 layers published by Kainthla et al. (Kainthla, R.C.; Zelenay, B.; Bockris, J. O. M. j. Electrochem. Soc. 1986, 133, 248-253) involved a stain etch pretreatment (HF:H ⁇ O 3 :HCl) followed by electrochemical deposition of a Pd mono layer and deposition of a Mn(OH) 2 precursor film from solution. The Mn(OH) 2 film was then converted into Mn 2 O 3 by heating in high vacuum. Kainthla et al.
  • the surfaces to be plated are sensitized in a first step by adsorption of Sn 2+ ions.
  • the Sn 2+ ions are used to reduce Pd 2+ to metallic Pd, thereby producing a submonolayer of Pd.
  • This change in deposition of the Pd monolayer allowed us also to omit the recommended but undesirable stain-etch pretreatment that was part of the original procedure by Kainthla et al.
  • a further modification involved the actual Mn(OH) 2 deposition step. It was observed that the use of 1.4 M NH 4 OH leads to immediate precipitation of Mn(OH) 2 and not to a gradual formation of a light brown precipitate as described in the original paper. This rapid precipitation was found to introduce further irreproducible behavior that we were able to avoid by decreasing the NH 4 OH concentration to 0.1 M. The resulting surfaces still displayed a certain degree of visual inhomogeneity but had very reproducible photoelectrochemical characteristics.
  • Figs. 48A and B show two tapping mode atomic force images of a typical Mn 2 O 3 surface at 50 m and 5 m full scale, respectively.
  • the surface has a granular structure with an average grain size of approximately 2 m and a mean roughness of 50 nm (with a small number of larger precipitates).
  • the grains exhibit a preferred orientation probably caused by fluid flow during solution deposition of the Mn(OH) 2 precursor film.
  • Film thickness' obtained from step height measurements ranged from 250 to 350 nm. This is at least a factor of ten more than the thickness reported by Kainthla et al. The difference reflects the increased deposition rate of Mn(OH) 2 that is caused by the lower concentration of NH 4 OH used in our procedure.
  • Typical cyclic voltammograms of Mn 2 O 3 coated silicon electrodes before and after deposition of the agarose penneation layer are shown in Figs. 49A and B, respectively.
  • the two sequences of consecutive scans show that Mn 2 O 3 coatings deposited with our modified procedure stabilize the silicon surface against photocorrosion. That is, after an initial decrease of about 5-20%, photocurrents are stable for hours of continuous operation (> 12 hrs). While we do not wish to be bound by this theory, the initial loss is probably due to rapid passivation of unprotected electrode areas such as pinholes. Dark current levels are typically 10 to 50 times smaller than photocurrents but tend to increase after deposition of the agarose permeation layer.
  • Mn 2 O 3 coated thin film amorphous silicon electrodes displayed very similar cyclic voltammograms compared to single crystal silicon electrodes. However, the amorphous silicon electrodes exhibited better performance in photoelectrophoresis experiments, as will be discussed below.
  • the ability to photoelectrophoretically transport DNA oligonucleotides to specific locations on an agarose coated silicon substrate depends both on the ratio between photocurrent and dark current and on the degree of lateral diffusion of the photocurrent.
  • a large dark current leads to reduced contrast between illuminated and non-illuminated areas and eventually to a reduced signal to background ratio during fluorescence detection.
  • Lateral diffusion of the photocurrent reduces the spatial resolution that is otherwise limited by the spot size of the illumination source.
  • dark current levels can be minimized by careful preparation of the semiconductor surface (avoiding large numbers of surface traps) and by working with a semiconductor with low to moderate conductivity.
  • Photocurrent diffusion depends on the minority carrier diffusion length within the semiconductor depletion zone and, specifically for this platform, on the lateral electrical conductivity within the Pd and Mn 2 O 3 layers. Minority carrier or hole diffusion lengths can be reduced to a few microns by using highly doped silicon substrates, however, this comes at the expense of higher dark currents. Minimal minority carrier diffusion lengths can also be achieved by using amorphous silicon substrates. The conductivity across the Pd layer is minimal as long as its thickness does not exceed a few monolayers. A much more difficult task is to assess how deposition and heating parameters affect the electrical and electrochemical properties of the Mn 2 O 3 layers. The literature value for room temperature resistivity of dry, crystalline Mn 2 O 3 is 10-100 Ohm-cm.
  • Fig. 50A shows an array of fluorescent oligonucleotide spots that was produced by successively illuminating nine individual locations on a streptavidin-agarose and Mn 2 O 3 coated amorphous silicon sample. Although, there was still some non-uniformities in spot size and fluorescence intensity (40% standard deviation), fluorescent spots were reproducibly generated at any location on a given chip with signal to background ratios greater than 100.
  • Fig. 50B shows the current transient recorded during formation of the array of fluorescent oligonucleotide spots.
  • stability and reproducibility of the photocurrents recorded at different locations is excellent.
  • the relatively low light levels and short illumination times sufficient to immobilize fluorescence labeled DNA oligonucleotides on amorphous silicon electrodes make it possible to use other fluorescent dyes with abso ⁇ tion maximums at higher wavelengths (e.g. BTR 588/616 or BTR 630/650).
  • this method allows for the detection of DNA oligonucleotides by electronic hybridization in an extremely short period of time which is a clear advantage over assays relying on passive hybridization.
  • a further advantage is that a large number of different capture probes can be deposited in arbitrary patterns with arbitrary spot sizes in order to accommodate different kinds of sampling and imaging requirements.
  • Fig. 52 shows an example of localized bead aggregation induced by application of a scanned potential under illumination with the optical fiber.
  • the diameter of the bead cluster is only slightly larger than the illuminated spot size of about 20 m (no agarose), indicating minimal photocurrent spreading on this sample.
  • the applied potential was scanned rather than kept constant because it was observed that the beads adhered to the surface unless the potential was periodically lowered to 0 N. By slowly changing the position of the optical fiber, beads can also be transported across the surface. Potentially, this may be useful for micropositioning applications performed in aqueous or non-aqueous environments.
  • Table 1 Sequences of DNA oligonucleotides
  • Mn 2 O 3 stabilized n-type silicon photoelectrodes coated with a streptavidin-agarose permeation layer constitute a simple platform for rapid manipulation of DNA oligonucleotides by electronic hybridization.
  • the same platfonn can be used for accumulation or transport of micron sized objects e.g. polystyrene beads, which could be ultimately employed in rm ⁇ ropositioning or object sorting tasks.

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Abstract

L'invention porte sur une plate-forme de transport par électrophorèse et d'hybridation électronique d'oligonucléotides d'ADN marqués par fluorescence dans un électrolyte à basse conductivité. La surface stabilisée chimiquement d'une photodiode semi-conductrice ou d'un photoconducteur est enduite d'une couche de perméation de streptavidine-agarose. Le micro-éclairage de la surface produit des courants photoélectriques servant au transport par électrophorèse et à la fixation des brins capturés, de préférence biotinylés, sur des sites arbitrairement sélectionnés. On utilise ensuite le même processus pour le transport et l'hybridation électronique de brins cibles d'ADN sur des brins capturés préalablement fixés. La détection des signaux est assurée soit par un balayage de fluorescence soit par une caméra CCD. On a ainsi une plate-forme souple d'essais électroniques sur l'ADN ne devant pas dépendre de réseaux de micro-électronique prédessinés.
PCT/US2001/000926 2000-01-24 2001-01-12 Systemes et dispositifs de transport par electrophorese et d'hybridation d'oligonucleotides WO2001053799A1 (fr)

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EP1362121A2 (fr) * 2000-08-11 2003-11-19 Nanosphere, Inc. Nanoparticules comportant des oligonucleotides fixes dessus et utilisations associees
EP1548103A1 (fr) * 2002-08-20 2005-06-29 Sony Corporation Partie de detection d'hybridation, puce de detection et procede d'hybridation
US7524672B2 (en) 2004-09-22 2009-04-28 Sandia Corporation Microfluidic microarray systems and methods thereof
US7592139B2 (en) 2004-09-24 2009-09-22 Sandia National Laboratories High temperature flow-through device for rapid solubilization and analysis
US7671117B2 (en) 2002-09-09 2010-03-02 Sony Corporation Resin composition

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US5466575A (en) * 1988-11-14 1995-11-14 I-Stat Corporation Process for the manufacture of wholly microfabricated biosensors
US5972692A (en) * 1990-09-28 1999-10-26 Kabushiki Kaisha Toshiba Gene detection method
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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1362121A2 (fr) * 2000-08-11 2003-11-19 Nanosphere, Inc. Nanoparticules comportant des oligonucleotides fixes dessus et utilisations associees
EP1548103A1 (fr) * 2002-08-20 2005-06-29 Sony Corporation Partie de detection d'hybridation, puce de detection et procede d'hybridation
EP1548103A4 (fr) * 2002-08-20 2008-06-25 Sony Corp Partie de detection d'hybridation, puce de detection et procede d'hybridation
US7671117B2 (en) 2002-09-09 2010-03-02 Sony Corporation Resin composition
US7524672B2 (en) 2004-09-22 2009-04-28 Sandia Corporation Microfluidic microarray systems and methods thereof
US7592139B2 (en) 2004-09-24 2009-09-22 Sandia National Laboratories High temperature flow-through device for rapid solubilization and analysis
US8426135B1 (en) 2004-09-24 2013-04-23 Sandia National Laboratories High temperature flow-through device for rapid solubilization and analysis

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