Classifications

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• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B82—NANOTECHNOLOGY
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  • B82Y30/00—Nanotechnology for materials or surface science, e.g. nanocomposites
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  • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
  • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
  • C07K1/045—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers using devices to improve synthesis, e.g. reactors, special vessels
• • C—CHEMISTRY; METALLURGY
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  • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
  • C07K1/04—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length on carriers
  • C07K1/047—Simultaneous synthesis of different peptide species; Peptide libraries
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  • B01J2219/00637—Introduction of reactive groups to the surface by coating it with another layer
• • B—PERFORMING OPERATIONS; TRANSPORTING
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• • C—CHEMISTRY; METALLURGY
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  • C07B—GENERAL METHODS OF ORGANIC CHEMISTRY; APPARATUS THEREFOR
  • C07B2200/00—Indexing scheme relating to specific properties of organic compounds
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• • C—CHEMISTRY; METALLURGY
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  • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
  • C40B50/14—Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
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• • G—PHYSICS
  • G03—PHOTOGRAPHY; CINEMATOGRAPHY; ANALOGOUS TECHNIQUES USING WAVES OTHER THAN OPTICAL WAVES; ELECTROGRAPHY; HOLOGRAPHY
  • G03F—PHOTOMECHANICAL PRODUCTION OF TEXTURED OR PATTERNED SURFACES, e.g. FOR PRINTING, FOR PROCESSING OF SEMICONDUCTOR DEVICES; MATERIALS THEREFOR; ORIGINALS THEREFOR; APPARATUS SPECIALLY ADAPTED THEREFOR
  • G03F7/00—Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printing surfaces; Materials therefor, e.g. comprising photoresists; Apparatus specially adapted therefor

Definitions

• the present invention relates to the field of chemical and biochemical reactions. More specifically, the present invention relates to parallel synthesis and assay of a plurality of organic and bio-organic molecules on a substrate surface in accordance with a predetermined spatial distribution pattern. Methods and apparatus of the present invention are useful for preparing and assaying very-large-scale arrays of DNA and RNA oligonucleotides, peptides, oligosacchrides, phospholipids and other biopolymers and biological samples on a substrate surface.
• MM A molecular microarray
• Prior art biochip-fabrication includes direct on-chip synthesis (making several sequences at a time) using inkjets, direct on-chip parallel synthesis (making the whole array of sequences simultaneously) using photolithography, and immobilization of a library of pre- synthesized molecules using robotic spotting (Ramsay, Nature Biotech. 16, 40-44 (1998)).
• Light-directed on-chip parallel synthesis has been used in the fabrication of very-large-scale oligonucleotide arrays with up to one million sequences on a single chip.
• the photolabile- protecting groups are cleaved from growing oligonucleotide molecules in illuminated surface areas while in non-illuminated surface areas the protecting groups on oligonucleotide molecules are not affected.
• the substrate surface is subsequently contacted with a solution containing monomers having a unprotected first reactive center and a second reactive center protected by a photolabile-protecting group.
• monomers couple via the unprotected first reactive center with the deprotected oligonucleotide molecules.
• oligonucleotides remain protected with the photolabile-protecting groups and, therefore, no coupling reaction takes place.
• oligonucleotide molecules after the coupling are protected by photolabile protecting groups on the second reactive center of the monomer. Therefore, one can continue the above photo-activated chain propagation reaction until all desired oligonucleotides are synthesized.
• a planer substrate surface is linked with oligonucleotide molecules (through appropriate linkers) and is coated with a thin (a few micrometers) polymer or photoresist layer on top of the oligonucleotide molecules.
• the free end of each oligonucleotide molecule is protected with an acid labile group.
• the polymer/photoresist layer contains a photo-acid precursor and an ester (an enhancer), which, in the presence of H + , dissociates and forms an acid.
• acids are produced in illuminated surface areas within the polymer/photoresist layer and acid-labile protecting groups on the ends of the oligonucleotide molecules are cleaved.
• the polymer/photoresist layer is then stripped using a solvent or a stripping solution to expose the oligonucleotide molecules below.
• the substrate surface is then contacted with a solution containing monomers having a reactive center protected by an acid-labile protecting group. The monomers couple via the unprotected first reactive center only with the deprotected oligonucleotide molecules in the illuminated areas. In the non-illuminated areas, oligonucleotide molecules still have their protection groups on and, therefore, do not participate in coupling reaction.
• the substrate is then coated with a photo-acid-precursor containing polymer/photoresist again.
• the illumination, deprotection, coupling, and polymer/photoresist coating steps are repeated until desired oligonucleotides are obtained.
• the method of using chemical amplification chemistry has its limitations as well: (a) The method requires application of a polymer/photoresist layer and is not suitable for reactions performed in solutions routinely used in chemical and biochemical reactions since there is no measure provided for separating sites of reaction on a solid surface, (b) In certain circumstances, destructive chemical conditions required for pre- and post-heating and stripping the polymer/photoresist layer cause the decomposition of oligonucleotides on solid surfaces, (c) The entire process is labor intensive and difficult to automate due to the requirement for many cycles (up to 80 cycles if 20-mers are synthesized!) of photoresist coating, heating, alignment, light exposure and stripping, (d) The method is not applicable to a broad range of biochemical reactions or biological samples to which a photo-generated reagent is applied since embedding of biological samples in a polymer/photoresist layer may be prohibitive.
• the present invention provides methods and apparatus for performing chemical and biochemical reactions in solution using in situ generated photo-products as reagents or co- reagents. These reactions are controlled by irradiation, such as with UV or visible light. Unless otherwise indicated, all reactions described herein occur in solutions of at least one common solvent or a mixture of more than one solvent.
• the solvent can be any conventional solvent traditionally employed in the chemical reaction, including but not limited to such solvents as CH 2 C1 2 , CH 3 CN, toluene, hexane, CH 3 OH, H 2 O, and/or an aqueous solution containing at least one added solute, such as NaCl, MgCl 2 , phosphate salts, etc.
• the solution is contained within defined areas on a solid surface containing an array of reaction sites.
• PGR photo-generated reagent
• PGR modifies reaction conditions and may undergo further reactions in its confined area as desired. Therefore, in the presence of at least one photo-generated reagent (PGR), at least one step of a multi-step reaction at a specific site on the solid surface may be controlled by radiation, such as light, irradiation.
• the present invention has great potential in the applications of parallel reactions, wherein at each step of the reaction only selected sites in a matrix or array of sites are allowed to react.
• the present invention also provides an apparatus for performing the light controlled reactions described above.
• One of the applications of the instrument is to control reactions on a solid surface containing a plurality of isolated reaction sites, such as wells (the reactor).
• Light patterns for effecting the reactions are generated using a computer and a digital optical projector (the optical module). Patterned light is projected onto specific sites on the reactor, where light controlled reactions occur.
• One of the applications of the present invention provides in situ generation of chemical/biochemical reagents that are used in the subsequent chemical and biochemical reactions in certain selected sites among the many possible sites present.
• One aspect of the invention is to change solution pH by photo-generation of acids or bases in a controlled fashion.
• the pH conditions of selected samples can be controlled by the amount of photo- generated acids or bases present.
• the changes in pH conditions effect chemical or biochemical reactions, such as by activating enzymes and inducing couplings and cross- linking through covalent or non-covalent bond formation between ligand molecules and their corresponding receptors.
• photo-generated reagents themselves act as binding molecules that can interact with other molecules in solution.
• concentration of the binding molecules is determined by the dose of light irradiation and, thus, the ligand binding affinity and specificity in more than one system can be examined in parallel. Therefore, the method and apparatus of the present invention permits investigating and/or monitoring multiple processes simultaneously and high-throughput screening of chemical, biochemical, and biological samples.
• MMA-chips molecular microarray chips
• MMA-chips are used in a wide range of fields, such as functional genomics, diagnosis, therapeutics and genetic agriculture and for detecting and analyzing gene sequences and their interactions with other molecules, such as antibiotics, antitumor agents, oligosacchrides, and proteins.
• the method of the present invention represents fundamental improvements compared to the method of prior arts for parallel synthesis of DNA oligonucleotide arrays (Pirrung et al., U.S. Pat. No. 5,143,854 (1992); Fodor et al., U.S. Pat. No. 5,424,186 (1995); Beecher et al., PCT Publication No. WO 98/20967 (1997)).
• the present invention advantageously employs existing chemistry, replacing at least one of the reagents in a reaction with a photo-reagent precursor. Therefore, unlike methods of the prior art, which require monomers containing photolabile protecting groups or a polymeric coating layer as the reaction medium, the present method uses monomers of conventional chemistry and requires minimal variation of the conventional synthetic chemistry and protocols.
• the method of the present invention is easily expandable to the synthesis of other types of molecular microarrays, such as oligonucleotides containing modified residues, 3 '- oligonucleotides (as opposed to 5 '-oligonucleotides obtained in a normal synthesis), peptides, oligosacchrides, combinatory organic molecules, and the like.
• oligonucleotides containing modified residues 3 '- oligonucleotides (as opposed to 5 '-oligonucleotides obtained in a normal synthesis)
• peptides oligosacchrides
• combinatory organic molecules and the like.
• modified residues and various monomers that are commercially available can be employed, (f)
• the present invention can be applied to all types of reactions and is not limited to polymeric reaction media as is the prior art method using chemical amplification reactions, (g) Additionally, the reaction time for each step of synthesis using the conventional oligonucleotide chemistry (5 min. per step) is much shorter than methods using photolabile blocked monomers (> 15 min. per step).
• Optical patterning in prior art biochip fabrication uses standard photomask-based lithography tools, Karl et al., US Patent No. 5,593,839 (1997).
• a new set of masks have to be prepared. More critical is the high precision
• the present invention replaces the photomasks with a computer-controlled spatial optical modulator so that light patterns for photolithography can be generated by a computer in the same way as it displays black-and-white images on a computer screen.
• This modification provides maximum flexibility for synthesizing any desirable sequence array and simplifies the fabrication process by eliminating the need for performing mask alignment as in the conventional photolithography, which is time consuming and prone to alignment errors.
• both the optical system and the reactor system of the present invention are compact and can be integrated into one desktop enclosure.
• Such an instrument can be fully controlled by a personal computer so that any bench chemists can make biochips of their own sequence design in a way that is similar to bio-oligomer synthesis using a synthesizer.
• the instrument can be operated in any standard chemical lab without the need for a cleanroom.
• the present invention can also be easily adopted to streamline production of large quantities of standard biochips or a fixed number of specialized biochips by automated production lines. Obviously, the cost of making biochips can be significantly reduced by the method and apparatus of the present invention and, therefore, the accessibility of the biochip technology to research and biomedical communities can be significantly increased.
• the method of the present invention using photo-generated reagents in combination with a computer-controlled spatial optical modulator makes MMA-chip fabrication a routine process, overcoming limitations of the prior art methods.
• Figure 1 is a drawing of oligonucleotide synthesis using photo-generated acids.
• Figure 2 is a drawing of the deprotection process using photo-generated acids in oligonucleotide synthesis.
• FIG 3 is a drawing of oligonucleotide synthesis using photo-generated reagents. The process is the same as shown in Figure 1 except that a photo-generated activator, such as dimethoxybenzomyltetrazole, is used, while the deprotection step is accomplished using a conventional acid.
• a photo-generated activator such as dimethoxybenzomyltetrazole
• Figure 4 is a drawing of amino acid deprotection using photo-generated acids or photo- generated bases.
• Boc butyloxylcarbonyl;
• Fmoc fluoroenylmethyloxycarbonyl.
• Figure 5 is a drawing of peptide synthesis using photo-generated acids.
• Figure 6 is a drawing of peptide synthesis using photo-generated bases.
• L - linker group P b - base-labile protecting group
• Figure 7 is a drawing of carbohydrate synthesis using both photo-generated acids and photo-generated bases at various of reaction steps.
• Figure 8 A is a schematic illustration of the synthesis apparatus using a micromirror array modulator.
• Figure 8B is a schematic illustration of the synthesis apparatus using a reflective LCD array modulator.
• Figure 8C is a schematic illustration of the synthesis apparatus using a transmissive LCD array modulator.
• Figure 9A illustrates an isolation mechanism using microwell structures on a back cover.
• Figure 9B illustrates an isolation mechanism using microwell structures on a substrate.
• Figure 9C illustrates an isolation mechanism using a patterned non-wetting film on a substrate.
• Figure 10 is an exploded schematic of a reactor cartridge and an enlarged view of reaction- wells.
• Figure 11A is a schematic illustration of the deprotection reaction in a partially masked reaction-well.
• Figure 11B is a schematic illustration of the deprotection reaction with a reaction-well being partially exposed.
• Figure 12 illustrates a stepping mechanism for parallel synthesis of a plurality of arrays.
• Figure 13 is a plot of H 3 0 + chemical shift (ppm) versus light irradiation time (min) measured from a sample containing a photo-acid precursor.
• Figure 14 shows the HPLC profiles of DNA (Fig. 14A) and RNA (Fig. 14B) nucleosides deprotected using a photo-generated acid.
• Figure 15 shows the HPLC profiles of DNA oligomers synthesized using a photo- generated acid.
• Figure 16 shows the HPLC profiles of an amino acid deprotected using a photo-generated acid.
• Figure 17A illustrates a fabrication process for making microwells on a flat substrate.
• Figure 17B is an enlarged photograph of microwells on a glass substrate.
• Figure 18A illustrates a fabrication process for making a non-wetting-film pattern on a flat substrate.
• Figure 18B is an enlarged photograph of methanol-droplets formed on a glass surface containing non-wetting film patterns.
• Figure 19 is a fluorescence image of fluorescein tagged thymine grown on a non-wetting film patterned glass plate.
• the present invention provides a method for solution based photochemical reactions involving reagents generated in situ by irradiation.
• a conventional chemical/biochemical reaction occurs between at least one reactant (generically denoted as “A”) and at least one reagent (generically denoted as “R”) to give at least one product as depicted below:
• the present invention is to provide reaction conditions that are controlled by irradiation with light.
• the R in the reaction above is photo-generated.
• the photo-generated reagent (PGR) functions the same as a reagent conventionally used and, thus, the reaction proceeds in an otherwise conventional way.
• the overall photo-controlled reaction is depicted below.
• substitutions halogen atoms, NO 2 , CN, OH, CF 3 , C(O)H, C(O)CH 3 , C(O)R 2 , SO 2 CH 3 ,
• Photo-generated acids are also complexes, such as M m X n (Lewis acids, m and n are number of atoms) formed upon irradiation.
• PGR precursors (Table 1) are photo-generated base precursors that yield a base, such as an amine, an oxide or the like, upon irradiation.
• Y O, S. Table 1B. Examples of Radiation Sensitizers for PGR Reactions 3
• Photosensitizers include but not limited to the following: benzophenone, acetophenone, benzoinyl C,-C 12 -alkyl ethers, benzoyl triphenylphosphine oxide, anthracene, thioxanthone, chlorothioxanthones, pyrene, Ru 2+ complexes, their various substituted derivatives, and the like.
• R-H stabilizers include but not limited to the following: propylene carbonate, propylene glycol ethers, t-butane, t- butanol, thiois, cyclohexene, their substituted derivatives and the like.
• substituent groups include but not limited to halogen, N0 2 , CN, OH, SH, CF 3 , C(0)H, C(0)CH 3 , C r C 3 -acyl, S0 2 CH 3 , C,-C 3 -S0 2 R 2 , OCH 3 , SCH 3
• PGR precursors are used in combination with co-reagents, such as radiation sensitizers.
• co-reagents such as radiation sensitizers.
• photosensitizers which are compounds of lower excitation energies than the PGR used. Irradiation excites photosensitizers, which in turn initiate conversion of PGR precursors to give PGR.
• the effect of the photosensitizer is to shift the excitation wavelength used in photochemical reactions and to enhance the efficiency of the formation of photo-generated reagents.
• the present invention makes use of, but is not limited to, photosensitizers as co-reagents in PGR reactions.
• Many radiation sensitizers are known to those skilled in the art and include those previously mentioned. It is to be
• the substrate surface is solid and substantially flat.
• the substrate can be a type of silicate, such as glass, Pyrex or quartz, a type of polymeric material, such as polypropylene or polyethylene, and the like.
• the substrate surfaces are fabricated and derivatized for applications of the present invention.
• linker molecules are attached to a substrate surface on which oligonucleotide sequence arrays are to be synthesized (the linker is an "initiation moiety", a term also broadly including monomers or oligomers on which another monomer can be added).
• the methods for synthesis of oligonucleotides are known, McBride et al., Tetrahedron Letter 24, 245-248 (1983).
• Each linker molecule contains a reactive functional group, such as 5'-OH, protected by an acid- labile protecting group 100.
• a photo-acid precursor or a photo-acid precursor and its photosensitizer (Table 1) are applied to the substrate.
• a predetermined light pattern is then projected onto the substrate surface 110. Acids are produced at the illuminated sites, causing cleavage of the acid-labile protecting group (such as DMT) from the 5'-OH, and the terminal OH groups are free to react with incoming monomers ( Figure 2, "monomers” as used hereafter are broadly defined as chemical entities, which, as defined by chemical structures, may be monomers or oligomers or their derivatives). No acid is produced at the dark (i.e. non-illuminated sites) and, therefore, the acid labile protecting groups of the linker molecules remain intact (a method of preventing H + diffusion between adjacent sites will be described later).
• the acid-labile protecting group such as DMT
• the substrate surface is then washed and subsequently contacted with the first monomer (e.g., a nucleophosphoramidite, a nucleophosphonate or an analog compound which is capable of chain growing), which adds only to the deprotected linker molecules under conventional coupling reaction conditions 120.
• the first monomer e.g., a nucleophosphoramidite, a nucleophosphonate or an analog compound which is capable of chain growing
• a chemical bond is thus formed between the OH groups of the linker molecules and an unprotected reactive site (e.g., phosphorus) of the monomers, for example, a phosphite linkage.
• the attached nucleotide monomer also contains a reactive functional terminal group protected by an acid-labile group.
• the substrate containing the array of growing sequences is then supplied with a second batch of a photo-acid precursor and exposed to a second predetermined light pattern 130.
• the selected sequences are deprotected and the substrate is washed and subsequently supplied with the second monomer.
• the second monomer propagates the nascent oligomer only at the surface sites that have been exposed to light.
• the second residue added to the growing sequences also contains a reactive functional terminal group protected by an acid-labile group 140. This chain propagation process is repeated until polymers of desired lengths and desired chemical sequences are formed at all selected surface sites 150.
• the maximum number of reaction steps is 4 x n, where n is the chain length and 4 is a constant for natural nucleotides. Arrays containing modified sequences may require more
• a photo-activator precursor such as a compound containing tetrazole linked to a photolabile group, is used.
• Linker molecules are attached to a substrate surface, on which oligonucleotide sequence arrays are to be synthesized 300. Acid labile protection groups on linkers are deprotected
• a photo-activator precursor or a photo-activator precursor and its photosensitizer (Table 1) are applied to the substrate.
• a predetermined light pattern is then projected onto the substrate surface 320.
• activator molecules are produced and monomers are coupled to the linker.
• no activator molecules are produced and, therefore, no reaction occurs (a method of preventing activator diffusion between adjacent sites will be described later).
• the attached nucleotide monomer also contains a protected functional terminal group.
• the substrate containing the array of growing sequences is then contacted with a second batch of acid 330. Sequences are deprotected and the substrate is washed and subsequently contacted with the second monomer. Again, the second monomer propagates only at the surface sites that have been exposed to light 340. This chain propagation process is repeated until polymers of desired lengths and chemical sequences are formed at all selected surface sites 350.
• the appropriate monomers used in the coupling steps 120, 140, 150, 320, 340 and 350 are nucleotide analogs.
• the reaction of these monomers proceeds as described in Figures 1 and 3 to give oligonucleotides containing
• the appropriate monomers used in the coupling steps 120, 140, 150, 320, 340 and 350 are those containing an acid labile protecting group, such as DMT, at the 3'-OH position.
• the reaction of these monomers proceeds as described in Figures 1 and 3 but with sequence grown in an opposite orientation compared to that using 5'-OH protected monomers.
• Such syntheses produce oligonucleotides containing a terminal 3'-OH, which are of particular use as primers for in situ polymerase chain reactions (PCR).
• PCR in situ polymerase chain reactions
• PGR PGR
• irradiation is from a light source emitting UV and visible light. Heat, IR and X-ray irradiation are also sources of irradiation.
• a PGR is produced by irradiation of a PGR precursor or a photosensitizer (which in turn transfers its energy to a PGR precursor). Chemical transformation occurs to yield at least one product (PGR), which is an intermediate or a stable compound.
• PGR is from part of the PGR precursor molecule dissociated from the parent structure or a rearranged structure of the PGR precursor.
• PGR may be an acid, a base, a nucleophile, an electrophile, or other reagents of specific reactivities (Table 1).
• improved reaction yields and/or suppression of side reactions are achieved by pre-irradiation activation of at least one PGR before mixing with other reactants.
• Pre-irradiation activation allows time for active reaction intermediates, such as free radical species generated during irradiation, to diminish and for products, such as H + , to reach a stable concentration.
• Improved reaction yields and/or suppression of side reactions are also achieved if at least one suitable stabilizer is used.
• One example is to provide at least one reagent to reduce the lifetime of active reaction intermediates such as a free radical species generated during irradiation, and to provide a low energy source of hydrogen. This is illustrated by the following reactions of generating H + from sulfonium salts (Ar 3 S + X ).
• Photo-acid precursors within the scope of the present invention include any compound that produces PGA upon irradiation.
• Examples of such compounds include diazoketones, triarylsulfonium, iodonium salts, o-nitrobenzyloxycarbonate compounds, triazine derivatives and the like. Representative examples of these compounds are illustrated in Table 1A. The table is compiled based on data found in following references: S ⁇ s et al, Liebigs Ann. Chem. 556, 65-84 (1944); Hisashi Sugiyama et al, US Patent 5,158,885 (1997); Cameron et al., J. Am. Chem. Soc. 113, 4303-4313 (1991); Frechet, Pure & Appl. Chem. 64, 1239-1248 (1992); Patchornik et al., J. Am. Chem. Soc. 92, 6333-6335 (1970).
• photo-acid precursor is triarylsulfonium hexafluoroantimonate derivatives (Dektar et al.,1 Org. Chem. 53, 1835-1837 (1988); Welsh et al, J. Org. Chem. 57, 4179-4184 (1992); DeVoe et al.Advances in Photochemistry 17, 313-355 (1992)).
• This compound belongs to a family of onium salts, which undergo photodecompositions, either directly or sensitized, to form free radical species and finally produce diarylsulfides and H + (see above).
• photo-acid precursor is diazonaphthoquionesulfonate triester ester
• the acid is due to a Wolff rearrangement through a carbene species to form a ketene intermediate and the subsequent hydration of ketene (S ⁇ s et al, Liebigs Ann. Chem. 556, 65-
• Photo-acid precursor compounds have been widely used for many years in printing and microelectronics industries as a component in photoresist formulations (Willson, in "Introduction to microlithography”, Thompson et al. Eds., Am. Chem. Soc: Washington D. C, (1994)).
• the electronegative sulfonate group in the indenecarboxylic acid formed helps to stabilize the negative charge on the carboxylic group attached to the same ring moiety to give an acid that effectively deprotects the 5'-O-DMT group ( Figure 2) in a way comparable to that of using the conventional trichloroacetic acid (TCA).
• OR aryl, alkyl, and their substituted derivatives
• Photo-base precursors within the scope of the present invention include any compound that produces PGB upon irradiation.
• examples of such compounds include o- benzocarbamates, benzoinylcarbamates, nitrobenzyloxyamine derivatives listed in Table 1, and the like.
• compounds containing amino groups protected by photolabile groups can release amines in quantitative yields.
• the photoproducts of these reactions, i.e., in situ generated amine compounds, are, in this invention, the basic reagents useful for further reactions.
• Photo-reagent precursors within the scope of the present inversion include any compound that produces a reagent required by a chemical/biochemical reaction upon irradiation.
• Photosensitizers within the scope of the present invention include any compound that are sensitive to irradiation and able to improve excitation profile of PGR by shifting its excitation wavelength and enhancing efficiency of irradiation.
• examples of such compounds include benzophenone, anthracene, thioxanthone, their derivatives (Table IB), and the like.
• photo-generated reagents (Table 1) are applied to on-chip parallel synthesis of peptide arrays using amino acid monomers containing reactive functional groups protected by t-Boc (acid labile) or Fmoc (base labile) groups ( Figure 4).
• the methods of peptide synthesis are known, Sterwart and Young, "Solid phase peptide synthesis", Pierce Chemical Co.; Rockford, IL (1984); Merrifield, Science 232, 341- 347 (1986); Pirrung et al, U.S. Pat. No. 5,143,854 (1992).
• linker molecules are attached to a substrate surface on which peptide sequence arrays are to be synthesized.
• Each linker molecule contains a reactive functional group, such as an -NH 2 group, protected by the acid labile t-Boc group 500.
• a photo- acid precursor or a photo-acid precursor and its photosensitizer are applied to the substrate.
• a predetermined light pattern is then projected onto the substrate surface 505.
• the acid labile protecting groups such as t-Boc, are cleaved from the N-terminal NH 2 thereby enabling it to react with incoming monomers ( Figure 4).
• the dark sites no acid is produced and, therefore, the acid labile protecting groups of the linker molecules remain intact.
• the substrate surface is then washed and subsequently supplied with the first monomer (a protected amino acid, its analogs, or oligomers), which adds only to the deprotected linker molecules under conventional coupling reaction conditions 510.
• the first monomer a protected amino acid, its analogs, or oligomers
• a chemical bond is thus formed between the NH 2 group of the linker molecules and the carbonyl carbon of monomers to afford an amide linkage.
• the attached amino acid monomer also contains a reactive functional group protected by the acid labile t-Boc group.
• the substrate containing the arrays of the growing sequences is then supplied with a second batch of a photo-acid precursor and exposed to a second predetermined light pattern 515.
• the selected sequences are deprotected and the substrate is washed, and supplied, subsequently, with the second monomer. Again, the second monomer propagates only at the surface sites that have been exposed to light.
• the second residue added to the growing chain also contains a reactive functional group protected by an acid-labile group 520. This chain propagation process is repeated until polymers of desired lengths and chemical sequences are formed at all selected surface sites 525.
• the maximum number of reaction steps is 20 x n, where n is the chain length and 20 is a constant, the number of naturally occurring amino acids.
• amino acids may require more than 20 x n steps.
• a photo-base precursor such as an amine protected by a photo-labile group
• a photo-base precursor is applied to solid surface loaded with linkers 600.
• Each linker molecule contains a reactive functional group, such as NH 2 , protected by a base-labile group.
• a photo-base precursor such as (((2- nitrobenzyl)oxy)carbonyl)-piperidine (Cameron and Frechet, J. Am. Chem. Soc. 113, 4303- 4313 (1991)) 8 , is applied to the substrate.
• a predetermined light pattern is then projected onto the substrate surface 605.
• the substrate surface is then washed and subsequently supplied with the first monomer containing a carboxylic acid group, which adds only to the deprotected linker molecules under conventional coupling reaction conditions to afford an amide linkage 610. After proper washing, the addition of the first residue is completed.
• the attached amino acid monomer also contains a reactive functional terminal group protected by a base-labile group.
• the substrate containing the arrays of the growing sequences is then supplied with a second batch of a photo-base precursor and exposed to a second predetermined light pattern 615.
• the selected sequences are deprotected and the substrate is washed, and subsequently supplied with the second monomer. Again, the second monomer propagates only at the surface sites that have been exposed to light.
• the second residue added to the growing sequences also contains a reactive functional terminal group protected by a base-labile group 620. This chain propagation process is repeated until polymers of desired lengths and desired chemical sequences are formed at all selected surface sites 625.
• the present invention is not limited to the parallel synthesis of arrays of oligonucleotides and peptides.
• the method is of general use in solid phase synthesis of molecular arrays where complex synthesis patterns are required at each step of chain extension synthesis.
• One specific example is synthesis of oligosacchride arrays containing sequences of diverse carbohydrate units and branched chains ( Figure 7).
• a photo-acid precursor is applied to a solid surface containing protected carbohydrates.
• Each carbohydrate molecule contains several reactive OH groups, each of which is protected by protecting groups. Each of these protecting groups requires different deprotection conditions.
• a predetermined light pattern is then projected onto the substrate surface.
• acid is produced and the protection groups labile under a particular set of conditions are cleaved.
• Deprotected OH groups are free to react with an incoming molecule.
• no acid is produced and, therefore, the acid labile protecting groups of the carbohydrate molecules remain intact.
• the substrate surface is then washed and subsequently supplied with a monomer (a carbohydrate or oligosacchride), which adds only to the deprotected OH under conventional reaction conditions to afford a glycosidic linkage. Wong et al., J. Am. Chem. Soc. 120, 7137-7138 (1998).
• oligosacchrides containing various glycosidic linkages at the first deprotected OH position are repeated.
• a photo- base precursor is applied to the substrate.
• a second predetermined light pattern is then projected for the second time onto the substrate surface.
• base is produced and the protection groups labile under this condition are cleaved.
• Deprotected OH groups of the second batch are free to react with an incoming molecule.
• no base is produced and, therefore, the base labile protecting groups of the carbohydrate molecules remain intact.
• the substrate surface is then washed and subsequently supplied with a second monomer, which adds only to the second deprotected OH of the second time under conventional reaction conditions to afford a glycosidic linkage. These steps are repeated to give oligosacchrides containing various glycosidic linkages at the second deprotected OH position. Branched oligosacchrides are formed. In continued synthesis, various PGR are used to achieve selective deprotection of the OH protecting groups until desired oligosacchride arrays are synthesized.
• the present invention enables use of photo-generated reagents in more cases than just deprotection reactions to achieve selective reaction in accordance with a predetermined pattern without changing the course of well-developed conventional chemistry.
• Figures 8A thought 8C illustrate three embodiments of the programmable, light-directed synthesis apparatus of this invention.
• the apparatus is comprised of four sections: a reagent manifold 812, an optical system, a reactor assembly, and a computer 814.
• the reagent manifold 812 of Figure 8 A performs standard reagent metering, delivery, circulation, and disposal. It consists of reagent containers, solenoid or pneumatic valves, metering valves, tubing, and process controllers (not shown in Figure 8A).
• the reagent manifold 812 also includes an inert gas handling system for solvent/solution transport and line purge. The design and construction of such a manifold are well known to those who are skilled in the art of fluid and/or gas handling. In many cases, commercial DNA/RNA, peptide, and other types of synthesizers can be used as the reagent manifold 812 of this invention.
• the function of the optical system shown in Figure 8A is to produce patterned light beams or light patterns 807c for initiating photochemical reactions at predetermined locations on a substrate surface 810a.
• the optical system shown in Figure 8 A is comprised of a light source 802, one or more filters 803, one or more condenser lenses 804, a reflector 805, a Digital Micromirror Device (DMD) 801, and a projection lens 806.
• a light beam 807a is generated by the light source 802, passes through the f ⁇ lter(s) 803, and becomes a light beam 807b of desired wavelength.
• a condenser lens 804 and a reflector 805 are used to direct the light beam 807b on to the DMD 801.
• DMD projects a light pattern 807c on the substrate surface 810a of a reactor 810. Details about the DMD 801 are described below.
• a light source 802 may be selected from a wide range of light-emitting devices, such as a mercury lamp, a xenon lamp, a halogen lamp, a laser, a light emitting diode, or any other appropriate light emitter.
• the wavelengths of the light source 802 should cover or fall within the excitation wavelengths of the concerned photochemical reaction.
• the preferred wavelengths for most of the concerned photochemical reactions are between 280 ran and 500 nm.
• the power of the light source 802 should be sufficient to generate a light pattern 807c intense enough to complete the concerned photochemical reactions in a reactor 810 within a reasonable time period.
• the preferred light intensity at the substrate surface 810a position is between 0.1 to 100 mW/cm 2 .
• a mercury lamp is preferred due to its broad wavelengths and availability of various powers.
• Selection criterions for a f ⁇ lter(s) 803 are based on the excitation wavelength of concerned photochemical reactions and other considerations. For example, it is often desirable to remove undesirably short and long wavelengths from the light beam 807a in order to avoid unwanted photo-degradation reactions and heating in a reactor 810. For example, in the synthesis of oligonucleotides and other bio-related molecules, it is preferred to remove wavelengths shorter than 340 nm. To avoid heating, an infrared cut-off filter is preferably used to remove wavelengths beyond 700 nm. Therefore, more than one filter may be needed.
• a key component in the Optical System shown in Figure 8A is a Digital Micromirror Device 801, which is used to generate light patterns 807b.
• a DMD is an electronically controlled display device and it is capable of producing graphical and text images in the same manner as a computer monitor. The device is commercially available from Texas Instruments Inc., Dallas, Texas USA, for projection display applications (Hornbeck, L. J., "Digital light processing and MEMS, reflecting the digital display needs of the networked society," SPIE Europe Proceedings, 2783, 135-145 (1996)).
• Each DMD 801 contains a plurality of small and individually controllable rocking-mirrors 801a, which steer light beams to produce images or light patterns 807c.
• DMD 801 is a preferred means of producing light patterns in the present invention for several reasons. First, it is capable of handling relatively short wavelengths that are needed for initiating concerned photochemical reactions. Second, the device has high optical efficiency. Third, it can produce light patterns of high contrast ratio. In addition, devices of
• the apparatus of this invention is highly flexible as compared with the prior art method of producing sequence arrays using photomasks.
• FIG. 8B illustrates an exemplary embodiment of the present invention, using a reflective liquid crystal array display (LCD) device 821.
• LCD liquid crystal array display
• Reflective LCD devices are commercially available from a number of companies, such Displaytech, Inc. Longmont,
• Each reflective LCD device 821 contains a plurality of small reflectors (not shown) with a liquid crystal shutter 821a placed in front of each reflector to produce images or light patterns.
• the optical system shown in Figure 8B is like that of the device of Figure 8A except for the optical arrangement for directing light onto display devices.
• a beam splitter
• a transmissive LCD display 841 is used to generate light patterns, as shown in Figure 8C.
• a transmissive LCD display 841 contains a plurality of liquid crystal light valves 841a, shown as short bars in Figure 8C. When a liquid crystal light valve 841a is on, light passes; when a liquid crystal light valve is off, light is blocked. Therefore, a transmissive LCD display can be used in the same way as an ordinary photomask is used in a standard photolithography process (L. F. Thompson et al, "Introduction to Microlithography” , American Chemical Society, Washington, DC (1994)).
• a reflector 845 is used to direct a light beam 847b to the transmissive LCD display 841.
• FIG. 8A through 8C depict apparatus designs for making one array chip at a time.
• the present invention also encompasses devices for producing a plurality of chips.
• Figure 12 schematically illustrates a mechanical/optical stepping mechanism for enhancing the throughput and the efficiency of the synthesis apparatus of this invention.
• a light beam 1204a is projected from a display device, (not shown in the figure,) passes through a projection lens 1202, and is directed by a reflector 1203 towards a reactor 1201a forming an image or a light pattern 1204b.
• the reflector 1203 has a rotating mechanism that can direct the light pattern 1204b towards any one of the several surrounding reactors 1201a through 1201f.
• the light pattern 1204b is directed towards a specific reactor, e.g. 1201a, only during a photochemical deprotection reaction step. Then the light pattern 1204b is directed towards other reactors, while reactor 1201a goes through the rest of synthesis steps, such as flushing, coupling, capping, etc.
• stepping mechanisms may also be used in the present invention.
• a step-and-repeat exposure scheme which is routinely used in photolithography of semiconductors, may be used.
• General descriptions of step-and-repeat photolithography were given by L. F. Thompson et al., in Introduction to Microlithography, American Chemical Society, Washington, DC (1994).
• a large substrate containing multiple reaction-well arrays is used.
• the substrate is mounted on a x-y translation stage.
• an optical exposure covers one or several arrays.
• the substrate is moved to the next position and another optical exposure is performed. The process is repeated until all reaction-well arrays are exposed.
• the present invention is not limited to the use of electronically controlled display devices as the means of generating photolithography patterns.
• Conventional photomasks which are made of glass plates coated with patterned chromium or any other appropriate films, may be used as well.
• the transmissive LCD display device 841 shown in Figure 8C is replaced with a conventional photomask while rest of the apparatus remains the same.
• the use of conventional photomasks is preferred for the production of a large number of the same products.
• a conventional photomask may contain a large number of array patterns so that a large number of molecular arrays can be synthesized in parallel.
• the use of electronically controlled display devices is much preferred due to its flexibility.
• FIGS 9A through 9C schematically illustrate three preferred embodiments of isolation mechanisms of the present invention.
• a transparent substrate 901 and a cap 902 form a reaction cell or a reactor, which is filled with a solution containing one or more photo-reagent precursors.
• Reactionwells, bounded by barriers 903, are embossed on the cap 902.
• the cap 902 is preferably made of a plastic or an elastomer material inert to all chemicals involved in the reaction.
• the cap 902 Before a photolytic reaction takes place, the cap 902 is pushed against the substrate 901 forming contacts between the barriers 903 and the substrate and isolates of individual reaction- wells. Light beams are then projected into a number of selected reaction-wells 904a and 904c, as shown in Step 3 of Figure 9A. Photolytic and other photo-reagent-induced reactions take place in the light- exposed reaction-wells 904a and 904c while there is no photo activate reaction in the unexposed reaction-well 904b. When properly constructed and operated, the isolation mechanism described prevents diffusion of reagents across individual reaction-wells. In addition, the space between adjacent reaction-wells 904b and 904c provides a buffer zone
• the buffer zone 904d shown in Figure 9A, provides space for addition mechanisms of preventing interference among individual reaction-wells.
• Figure 10 illustrates detailed structure of the reaction-wells of the current invention in a three-dimensional perspective view. The figure shows that the buffer zones (labeled as 1006 in Figure 10) are all interconnected. This interconnected structure permits one to flush the buffer zone with appropriate solutions while all the reaction-wells are closed. In are preferred method, buffer zone 904d is flushed after the completion of the photolytic and photo-reagent-induced reactions and before the lifting of the cap 902, with a solution that would either quench the photo-reagent-induced chemical reactions or neutralize the photogenerated reagents inside the exposed reaction-wells 904a and 904c.
• Figure 9B illustrates another embodiment of the isolation mechanism of the present invention.
• reaction-well structures or reaction-well barriers 913, are constructed on a transparent substrate 911 while the cap 912 has a flat inner surface.
• the substrate 911 is preferably made of glass.
• the cap 912 is preferably made of a plastic or an elastomer material inert to all chemicals involved in the reactions.
• the seal mechanism and the preferred operation mode are similar to those described earlier for the embodiment shown in Figure 9A.
• Figure 9C illustrates the third embodiment of the isolation mechanism of the present invention.
• a pattern of non- wetting film 933 is coated on the surface of a transparent substrate 931.
• a reactor is first filled with a solution 934.
• the solution 934 is drained from the reactor and droplets are formed on the substrate 931 surface because the solution wets the substrate 931 surface but not the non- wetting film 933 surface.
• the droplets are isolated from each other.
• Light beams 935 can then be projected onto predetermined droplets 934a and 934c to initiate photolytic and other photo-reagent- induced reactions.
• This embodiment eliminates the need for a sealing mechanism and is suitable for large-scale biochip production using large substrates.
• the use of non-wetting films to confine fluid is well-know in the art and has been described by Thomas M. Brennan in U.S. Patent No. 5,474,596 for the synthesis of DNA oligomers using an inkjet-printing method.
• each cartridge contains a transparent substrate 1001, which can be made of glass or polymer materials of suitable chemical and optical properties.
• a barrier layer 1003 containing pluralities of openings to form arrays of isolated reaction- wells 1004.
• the reaction-wells can be of any reasonable shapes and sizes. Circular and square wells are
• wells are of circular shape of 10 to 1,000 ⁇ m in diameter and 5 to
• reaction-wells 100 ⁇ m in depth.
• circular reaction-wells 140 ⁇ m in
• the barrier layer 1003 is made of opaque materials, such as metals or blackened polymers, to optically isolate individual reaction-wells from each other.
• the third layer is a reactor cap 1002.
• the cap 1002 has three functions: reactor enclosure, reagent connection/distribution, and reaction-well isolation.
• the cap 1002 is preferably made of a polymer material that is flexible and resistant to chemicals/solvents involved in the concerned synthesis processes.
• the material may be selected from a group of polymers including polyethylene, polypropylene, polyethylene-polypropylene copolymer, fluorinated polymers and various other suitable ones.
• the reagent inlet 1012 and outlet 1013 are placed at two opposite ends of the reactor. Branching channels 1011 are made to distribute reagents evenly across the reactor.
• the center region of the cap is a pad 1015 that can be pushed down to tightly seal the reaction- wells 1004 below.
• a mechanical actuator not shown in Figure 10 but shown in Figures 8A through 8C as 811, 831, and 851), which can be, for example, driven either solenoidally or pneumatically.
• the actuator can either push the pad of the reactor cap to seal all reaction-wells or retract to open all the reaction- wells. This operation is to accommodate the sealing mechanism shown in Figures 9 A and 9B.
• the inset in Figure 10 shows an enlarged view of the reaction- well structures, which contain extruded rims 1005 to facilitate sealing. While not shown in Figure 10, the reactor substrate contains alignment marks, which permit the alignment of the reactor in an optical lithography system of the present invention.
• the reactor cartridge shown in Figure 10 is most suitable for use in an ordinary chemical and biochemical laboratory environment.
• the enclosed construction of the cartridge prevents chemical and particulate contamination from the environment.
• the cartridges are preferably manufactured in a controlled environment to ensure the chemical integrity inside the cartridge.
• the cartridges are then filled with an inert gas, such as Ar, and sealed by plugging the inlet and outlet of the reactor. Then the cartridges can be stored and/or shipped to user laboratories.
• the reactors of the present invention can be fabricated using various well-known microfabrication processes, such as photolithography, thin film deposition, electroplating, and molding (M. Madou, Fundamentals of Microfabrication, CRC Press, New York, (1997)). These techniques have been widely used for making various of microfluidics devices, electromechanical devices, chemical sensors, and optical micro- devices.
• the reaction- well structure shown in Figure 10 can be fabricated by using electroplating of suitable metal films on a glass substrate. At the end of this description, an example is given to demonstrate the fabrications processes involved.
• reaction-well structures on a glass substrate may also be made using chemical etching processes, which have been widely used to make various microfluidics devices (Peter C. Simpson et al. Proc. Natl. Acad. Sci., 95: 2256-2261 (1998)).
• Reactor cap 1002 shown in Figure 10, can be fabricated using a precision molding process. Such a process is widely available in plastic fabrication industry.
• the polymer material used is preferably in black color to minimize light reflection and scattering during light exposure. Welding and adhesive bounding methods can be used to assemble the plastic cap 1002 and a substrate 1001 into an integrated cartridge.
• SAM self-assembled molecules
• Teflon low surface energy material
• SAMs on glass substrates include various hydrocarbon alkylsilanes and fluoroalkylsilanes, such as octadecyltrichlorosiliane and 1H, 1H, 2H, 2H - perfluorodecyltrichlorosiliane.
• the patterning process involves the use of photoresists and photolithography.
• Example VII at the end of this description provides a detailed patterning procedure.
• Thin polymer films such as Teflon, can be printed onto glass and plastic surfaces by using a screen printing process.
• the screen printing process is a well-know art in printing industry and in electronic industry. General procedures of screen printing for microfabrication applications are described by M. Madou in Fundamentals of Microfabrication, CRC Press, New York, (1997).
• hydrophobic printed slides are commercially available from vendors, such as Erie Scientific Company, Portsmouth, New Hampshire USA.
• the reactor configuration can be simplified because the reaction-well-sealing mechanisms shown in Figures 8 A through 8C and Figure 10 are no longer needed.
• the synthesis apparatus of the present invention is controlled by a computer 814, which coordinates the actions of the DMD 801, the seal actuator 811 of the reactor 810, and the reagent manifold 812.
• the synthesis apparatus operates as a conventional synthesizer and the computer 814 controls reagent manifold 812 to deliver various reagents to the reactor 810.
• the reagent manifold 812 delivers a photo-acid precursor into the reactor 810.
• the computer 814 activates the seal actuator 811 to isolate reaction- wells and, then, sends data to DMD 801 to project a light pattern 807c onto the reactor 801.
• the light pattern 807c is switched off, a quenching solution is delivered into the reactor 801, the seal actuator 811 is lifted, and the synthesis control system resumes the steps of conventional synthesis.
• Figure 11A illustrates a variation of reaction-well structure.
• a mask layer 1103 is added to the bottom of the reaction well.
• the mask layer 1103 is preferably made of a thin and chemical resistant metal film, such as Cr.
• a SiO 2 film (not shown) is deposited to facilitate immobilization of linker molecules.
• This reaction-well design permits the spatial separation of a photochemical reaction and photogenerated-reagent-induced chemical reactions.
• Figure 11A illustrates a photo-acid induced chemical reaction.
• protons H + are produced from a photo-acid precursor in the open areas.
• the protons diffuse into surrounding areas in the well to cleave acid-labile protecting groups P a on immobilized oligomer molecules 1106. This arrangement helps to minimize the contact between photo-generated radical intermediates and the oligomers and thus, to suppress undesirable side-reactions that might occur due to the presence of radical intermediates.
• Figure 11B illustrates another variation of the reaction- well structure and light exposure strategy. This embodiment is also designed to decrease the possibility of undesirable side- reactions due radical intermediates. Only a fraction of the reaction- well surface is exposed to light 1114. The chance for undesirable side-reactions in other areas is, consequently, decreased.
• the apparatus using DMD 801 shown in Figure 8A may be used as a general-purpose assay apparatus for studying chemical and biochemical reactions.
• the Digital Micromirror Device 801 controls precisely and simultaneously light dosages in all individual reaction-wells of a reactor 810. This feature allows one to precisely control the production of photogenerated reagent in all reaction-wells and, therefore, to perform a large-scale, parallel assay.
• photo-acid precursors such as 2,1,4-diazonaphthoquionesulfonate triester, triaryl sulfonium hexafluroantimonate and hexaflurophosphate (Secant Chemicals, Boston, MA), and perhalogenated triazine (Midori Kagaku), were also used for these deprotection reactions. Complete deprotection of the DMT group was achieved with these phot acid precursors.
• Example II except that the PGA solution (0.4% of 50% triaryl sulfonium hexafluroantimonate in propylene carbonate) was first irradiated at 365 nm for 2 min. before adding the CPG attached DMT-nucleoside.
• Pre-irradiation (UVGL-25, 0.72 mW) at 365 nm for 2 min was perform using a PGA solution (0.4% of 50% triaryl sulfonium hexafluroantimonate in propylene carbonate).
• the HPLC profile of the crude product of DMT-TTTT synthesized using a PGA is shown (1510 of Figure 15A).
• 1500 of Figure 15 shows DMT-TTTT using the conventional TCA deprotection chemistry.
• 1520 and 1530 of Figure 15B show HPLC profiles of the crude octanucleotides which was synthesized using the PGA approach.
• Protocol is adopted from an Expedite 8909 synthesizer used for oligonucleotide synthesis using PGA deprotection.
• Washing step is being optimized at this time to reduce the cycle time.
• t-Boc-Tyr was employed. Deprotection was performed in a CH 2 C1 2 solution containing a PGA (10% of 50% triaryl sulfonium hexafluroantimonate in propylene carbonate) by irradiating the same solution at 365 nm for 15 min. The reaction was incubated for an additional 15 min and the resin was washed with CH 2 C1 2 . The possible presence of residual amino groups was detected using ninhydrin color tests and the result was negative. The resin was then washed and the amino acid cleaved from the resin using NaOH (0.1 M in CH 3 OH). 1610 of Figure 16 shows the HPLC profile of the PGA deprotected Tyr. 1600 of Figure 16 shows the HPLC profile of Tyr obtained using conventional trifluoroacetic acid (TFA) deprotection.
• TFA trifluoroacetic acid
• FIG. 17A schematically illustrates the fabrication procedure used.
• a thin bimetal film 1702 of Cr/Cu 200/1000 A thick was evaporated on a glass substrate 1701 in a sputtering evaporator, he bimetal film 1702 Cr provides good adhesion to the glass surface and Cu provides a good base for subsequent
• the photoresist film 1703 was then patterned using photolithography (exposure to UV light using a photomask aligner and development). Electroplating using a plating solution for
• FIG. 18A schematically illustrates a fabrication procedure for coating a patterned non- wetting film on a glass substrate 1801.
• the substrate 1801 was then spin-coated with a
• a photomask aligner and developed.
• a photomask containing a matrix of circular dots were used and, therefore, the same pattern was formed in the photoresist film 1802.
• the patterned glass substrate was dipped into a 1 mM FDTS (1H, 1H,
• Tests of wetting effects were performed in an enclosed cell to avoid evaporation of volatile solvents. During a test, the cell was filled with a testing solvent or solution and then drained. Tests were made on various organic/inorganic solvents and solutions including CH 2 C1 2 , CH 3 CN, CH 3 OH, CH 3 CH 2 OH, TCA/ CH 2 C1 2 solution, I 2 /tetrahydrofuran-water- pyridine solution, and other solutions involved in oligonucleotide synthesis. Formation of droplet arrays was observed for each testing solvent/solution.
• Figure 18B shows a photograph of methanol droplet array formed on a non-wetting film patterned glass plate.
• Fabricated glass substrates containing isolated reaction wells at specified areas as described in Example VI were employed.
• the glass plates were derivatized with linker molecules (10%> N-(3-triethoxysilylpropyl)-4-hydroxylbutyramide in ethanol) containing free OH groups.
• linker molecules (10%> N-(3-triethoxysilylpropyl)-4-hydroxylbutyramide in ethanol) containing free OH groups.
• Synthesis on the glass substrate was performed using a reactor and a digital light projector as described in this specification and a DNA synthesizer (Perspective). Oligonucleotide synthesis was accomplished according to the protocol shown in Table 2.
• the glass surface was first contacted with DMT-T phosphoramidite to couple the first residue.
• the sequences were treated, in subsequent steps, with capping and oxidation reagents and washed with CH 3 CN before and after each step of the reactions.
• the glass plate was then treated with a PGA (0.4% of 50%o triaryl sulfonium hexaflurophosphate in CH 2 C1 2 ) delivered by the synthesizer and exposed to computer generated patterned light irradiation (30 s) from a collimated light source at 365 nm and 3 mw of light source intensity, (Stanford, CA).
• the surface was then extensively washed with CH 3 CN. In the light exposed areas, free hydroxyl groups were generated. After oxidation and wash steps, the surface was contacted by fluorescein-labeled phosphoramidite monomers in a second coupling step.
• the molecular arrays synthesized were treated with NaOH aqueous solution (0.1 M). The array contains fluorescence labeled dimers were visualized under a fluoromicroscope (Bio-Rad, Richmond, CA). The results of which are shown in Figure 19.

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