Combinatorial strategies for polymer synthesis

Claim 1

A method of forming oligonucleotides or peptides having diverse sequences on a single substrate, said substrate comprising a surface with a plurality of selected regions, said method comprising the steps of: a) forming a plurality of flow channels adjacent said surface, each of said flow channels at least partially comprising a first wall thereof defined by a first portion of said selected regions and second and third walls which form substantially fluid-tight seals with said surface, and a flow inlet and a flow outlet; and said first portion of said selected regions comprising oligonucleotides or peptides with a first known sequence of nucleic acids or amino acids different from oligonucleotides or peptides with a second known sequence of nucleic acids or amino acids bound to at least one other of said selected regions; b) flowing selected nucleic acids or amino acids through said flow channels and binding covalently said selected nucleic acids or amino acids to said oligonucleotides or peptides at said first portion of said selected regions; and c) repeating steps a) and b) wherein additional flow channels are formed along subsequent portions of said selected regions by altering the relative positions of the substrate surface and the second and third walls until said oligonucleotides or peptides having diverse sequences are formed.

Claim 2

A method of forming oligonucleotides or peptides having diverse sequences on a single substrate, said substrate comprising a surface with a plurality of selected regions, said method comprising the steps of: a) forming a plurality of flow channels adjacent said surface, each of said flow channels at least partially comprising a first wall thereof defined by a first portion of said selected regions and second and third walls which form substantially fluid-tight seals with said surface, and a flow inlet and a flow outlet; and said first portion of said selected regions comprising oligonucleotides or peptides with a first known sequence of nucleic acids or amino acids different from oligonucleotides or peptides with a second known sequence of nucleic acids or amino acids bound to at least one other of said selected regions; b) flowing selected nucleic acids or amino acids through said flow channels and binding covalently said selected nucleic acids or amino acids to said oligonucleotides or peptides at said first portion of said selected regions; and c) repeating steps a) and b) wherein additional flow channels are formed along subsequent portions of said selected regions by altering the relative positions of the substrate surface and the second and third walls until said oligonucleotides or peptides having diverse sequences are formed.

Claim 16

A method of forming oligonucleotides or peptides having diverse sequences on a single substrate, said substrate comprising a surface with a plurality of selected regions, said method comprising the steps of: a) forming a plurality of valves and flow channels adjacent said surface whereby fluid may be directed to said selected regions on said surface, each of said flow channels at least partially comprising a first wall thereof defined by a first portion of said selected regions and second and third walls which form substantially fluid-tight seals with said surface, and a flow inlet and a flow outlet; and said first portion of said selected regions comprising oligonucleotides or peptides with a known sequence of nucleic acids or amino acids different from oligonucleotides or peptides with a second known sequence of nucleic acids or amino acids bound to at least one other of said selected regions; b) selectively operating said valves and flowing said selected nucleic acids or amino acids through said flow channels and binding covalently said selected nucleic acids or amino acids to said oligonucleotides or peptides at said first portion of said selected regions; and c) repeating steps a) and b) wherein additional flow channels are formed along subsequent portions of said selected regions by altering the relative positions of the substrate surface and the second and third walls until said oligonucleotides or peptides having diverse sequences are formed.

Claim 17

A method of forming oligonucleotides or peptides having diverse sequences on a single substrate, said substrate comprising a surface with a plurality of selected regions, said method comprising the steps of: a) forming a plurality of valves and flow channels adjacent said surface whereby fluid may be directed to said selected regions on said surface, each of said flow channels at least partially comprising a first wall thereof defined by a first portion of said selected regions and second and third walls which form substantially fluid-tight seals with said surface, and a flow inlet and a flow outlet; and said first portion of said selected regions comprising oligonucleotides or peptides with a known sequence of nucleic acids or amino acids different from oligonucleotides or peptides with a second known sequence of nucleic acids or amino acids bound to at least one other of said selected regions; b) selectively operating said valves and flowing said selected nucleic acids or amino acids through said flow channels and binding covalently said selected nucleic acids or amino acids to said oligonucleotides or peptides at said first portion of said selected regions; and c) repeating steps a) and b) wherein additional flow channels are formed along subsequent portions of said selected regions by altering the relative positions of the substrate surface and the second and third walls until said oligonucleotides or peptides having diverse sequences are formed.

Claim 18

A method of forming a plurality of oligonucleotide sequences on a surface of a single substrate comprising the steps of: a) contacting said substrate with a channel block in a first orientation, said channel block comprising a substantially planar member with a plurality of recessed regions and raised walls on a surface thereof, said recessed regions forming channels, said raised walls effective to produce substantially fluid-tight seals between said raised walls and said substrate upon said contacting to define thereby a first plurality of flow channels between said channel block and said substrate, said first plurality of flow channels dividing said substrate surface into at least a first portion and a second portion; b) flowing at least a first nucleic acid through at least one of said first plurality of flow channels, and covalently coupling said first nucleic acid to said first portion of said substrate surface, said first nucleic acid comprising a reactive group protected by a protecting group; c) flowing at least a second nucleic acid through at least one of said first plurality of flow channels, and covalently coupling said second nucleic acid to said second portion of said substrate surface, said second nucleic acid comprising a reactive group protected by a protecting group; d) translating said channel block relative to said substrate and contacting said substrate with said channel block in a second orientation to produce substantially fluid-tight seals between said raised walls and said substrate upon said contacting to define thereby a second plurality of flow channels between said channel block and said substrate, said second flow channels dividing said substrate surface into at least a third portion and a fourth portion, said third and fourth portions each having at least one intersection with each of said first and second portions of said substrate surface; e) removing said protective group from at least a portion of said first or second nucleic acids to form a first set of deprotected first or second nucleic acids and flowing a third nucleic acid through at least one of said second plurality of flow channels, covalently coupling said third nucleic acid to said third portion of said substrate surface and covalently coupling said third nucleic acid to at least a portion of said first set of deprotected first or second nucleic acids through a oligonucleotide bond therewith where said first and second portions of said substrate surface intersect with said third portion of said substrate surface to form first and second oligonucleotide sequences; and f) removing said protective group from at least a portion of said first and second nucleic acids to form a second set of deprotected first or second nucleic acids and flowing a fourth nucleic acid through at least one of said second plurality of flow channels, covalently coupling said fourth nucleic acid to said fourth portion of said substrate surface and covalently coupling said fourth nucleic acid to at least a portion of said second set of deprotected first or second nucleic acids through a oligonucleotide bond therewith where said fourth portion of said substrate surface intersects with said first and second portions of said substrate surface to form third and fourth oligonucleotide sequences.

Claim 19

A method of forming a plurality of oligonucleotide sequences on a surface of a single substrate comprising the steps of: a) contacting said substrate with a channel block in a first orientation, said channel block comprising a substantially planar member with a plurality of recessed regions and raised walls on a surface thereof, said recessed regions forming channels, said raised walls effective to produce substantially fluid-tight seals between said raised walls and said substrate upon said contacting to define thereby a first plurality of flow channels between said channel block and said substrate, said first plurality of flow channels dividing said substrate surface into at least a first portion and a second portion; b) flowing at least a first nucleic acid through at least one of said first plurality of flow channels, and covalently coupling said first nucleic acid to said first portion of said substrate surface, said first nucleic acid comprising a reactive group protected by a protecting group; c) flowing at least a second nucleic acid through at least one of said first plurality of flow channels, and covalently coupling said second nucleic acid to said second portion of said substrate surface, said second nucleic acid comprising a reactive group protected by a protecting group; d) translating said channel block relative to said substrate and contacting said substrate with said channel block in a second orientation to produce substantially fluid-tight seals between said raised walls and said substrate upon said contacting to define thereby a second plurality of flow channels between said channel block and said substrate, said second flow channels dividing said substrate surface into at least a third portion and a fourth portion, said third and fourth portions each having at least one intersection with each of said first and second portions of said substrate surface; e) removing said protective group from at least a portion of said first or second nucleic acids to form a first set of deprotected first or second nucleic acids and flowing a third nucleic acid through at least one of said second plurality of flow channels, covalently coupling said third nucleic acid to said third portion of said substrate surface and covalently coupling said third nucleic acid to at least a portion of said first set of deprotected first or second nucleic acids through a oligonucleotide bond therewith where said first and second portions of said substrate surface intersect with said third portion of said substrate surface to form first and second oligonucleotide sequences; and f) removing said protective group from at least a portion of said first and second nucleic acids to form a second set of deprotected first or second nucleic acids and flowing a fourth nucleic acid through at least one of said second plurality of flow channels, covalently coupling said fourth nucleic acid to said fourth portion of said substrate surface and covalently coupling said fourth nucleic acid to at least a portion of said second set of deprotected first or second nucleic acids through a oligonucleotide bond therewith where said fourth portion of said substrate surface intersects with said first and second portions of said substrate surface to form third and fourth oligonucleotide sequences.

Claim 33

A method of forming oligonucleotides or peptides having diverse sequences on a single substrate, said substrate comprising a surface with a plurality of selected regions, said method comprising the steps of: a) on said surface providing a photoresist; b) selectively removing said photoresist to expose a portion of said plurality of selected regions; c) removing protecting groups on said surface by exposing said surface to a protecting group removal agent; d) contacting and covalently binding selected nucleic acids or amino acids with said surface at said portion of said plurality of selected regions; and e) repeating steps a), b), c) and d) to form oligonucleotides or peptides having diverse sequences at the selected regions.

Claim 34

A method of forming oligonucleotides or peptides having diverse sequences on a single substrate, said substrate comprising a surface with a plurality of selected regions, said method comprising the steps of: a) on said surface providing a photoresist; b) selectively removing said photoresist to expose a portion of said plurality of selected regions; c) removing protecting groups on said surface by exposing said surface to a protecting group removal agent; d) contacting and covalently binding selected nucleic acids or amino acids with said surface at said portion of said plurality of selected regions; and e) repeating steps a), b), c) and d) to form oligonucleotides or peptides having diverse sequences at the selected regions.

Claim 40

A method of forming oligonucleotides or peptides having diverse sequences on a single substrate, said substrate comprising a surface with a plurality of selected regions with acid-labile protecting groups protecting activated sites capable of covalently binding nucleic acids or amino acids, said method comprising the steps of: a) providing on said surface a photoresist wherein said photoresist is an acid generating polymer; b) selectively irradiating a portion of said plurality of selected regions whereby acid is generated thereby removing said acid-labile protecting groups to provide said activated sites in said selectively irradiated portion; c) removing said photoresist in said selectively irradiated portion of said plurality of selected regions; d) contacting and covalently binding selected nucleic acids or amino acids to said activated sites in said selectively irradiated portion; e) sequentially contacting and covalently bonding one or more selected nucleic acids or amino acids to the substrate of step d) to form said oligonucleotides or peptides having diverse sequences at the selectively irradiated portions.

Claim 41

A method of forming oligonucleotides or peptides having diverse sequences on a single substrate, said substrate comprising a surface with a plurality of selected regions with acid-labile protecting groups protecting activated sites capable of covalently binding nucleic acids or amino acids, said method comprising the steps of: a) providing on said surface a photoresist wherein said photoresist is an acid generating polymer; b) selectively irradiating a portion of said plurality of selected regions whereby acid is generated thereby removing said acid-labile protecting groups to provide said activated sites in said selectively irradiated portion; c) removing said photoresist in said selectively irradiated portion of said plurality of selected regions; d) contacting and covalently binding selected nucleic acids or amino acids to said activated sites in said selectively irradiated portion; e) sequentially contacting and covalently bonding one or more selected nucleic acids or amino acids to the substrate of step d) to form said oligonucleotides or peptides having diverse sequences at the selectively irradiated portions.