TREA

Thiocarbonate linkers for polynucleotides

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Information

  • Patent Application
  • 20070224602
  • Publication Number
    20070224602
  • Date Filed
    March 23, 2006
    18 years ago
  • Date Published
    September 27, 2007
    16 years ago
Information
Abstract
In various embodiments of the invention, novel compositions having a polynucleotide bound to a substrate via a cleavable linker are provided, and methods of cleaving a polynucleotide from a substrate are provided.
Description

BRIEF DESCRIPTION OF THE DRAWINGS

These and other features of the invention will be understood from the description of representative embodiments of the method herein and the disclosure of illustrative materials for carrying out the method, taken together with the Figures, wherein



FIG. 1 is a chromatogram of a polynucleotide cleaved from a substrate in an embodiment of the present invention.


Claims
  • 1. A method comprising: contacting a polynucleotide bound to a substrate via a cleavable linker with a solution comprising an α-effect nucleophile to result in cleavage of the polynucleotide from the substrate; wherein the cleavable linker has the structure (I):
  • 2. The method of claim 1 wherein the solution is at a pH of about 6 to about 12.
  • 3. The method of claim 1 wherein the α-effect nucleophile is characterized as having a pKa in the range of about 4 to 13.
  • 4. The method of claim 1 wherein the solution comprising the α-effect nucleophile is a solution comprising one or more species selected from hydrogen peroxide, a peracid, a perboric acid, an alkylperoxide, a hydroperoxide, a butylhydroperoxide, a benzylhydroperoxide, a phenylhydroperoxide, a cumene hydroperoxide, performic acid, a peracetic acid, perbenzoic acid, a substituted perbenzoic acid, chloroperbenzoic acid, perbutyric acid, tertiary-butylperoxybenzoic acid, decanediperoxoic acid, corresponding salts of said species, and combinations thereof.
  • 5. The method of claim 1 wherein the solution comprising the α-effect nucleophile is a solution comprising one or more species selected from hydrogen peroxide, salts of hydrogen peroxide, and mixtures of hydrogen peroxide and performic acid.
  • 6. The method of claim 1 wherein the α-effect nucleophile is formed in situ by a reaction of hydrogen peroxide and a carboxylic acid or carboxylic acid salt.
  • 7. The method of claim 1, wherein the linking group Lnk is selected from: (1) a lower alkyl group;(2) a modified lower alkyl group in which one or more linkages selected from ether-, thio-, amino-, oxo-, ester-, and amido- is present;(3) a modified lower alkyl substituted with one or more groups including lower alkyl; aryl, aralkyl, alkoxyl, thioalkyl, hydroxyl, amino, amido, sulfonyl, halo; or(4) a modified lower alkyl substituted with one or more groups including lower alkyl; alkoxyl, thioalkyl, hydroxyl, amino, amido, sulfonyl, halo, and in which one or more linkages selected from ether-, thio-, amino-, oxo-, ester-, and amido- is present.
  • 8. The method of claim 1, wherein the linking group Lnk has the structure —(CH2)m-Lkg-(CH2)n-wherein:m and n are integers independently selected from the range of 1 to about 12, andLkg is a linkage selected from ether-, thio-, amino-, oxo-, ester-, or amido-.
  • 9. The method of claim 1, further comprising recovering the polynucleotide after cleavage of the polynucleotide from the substrate.
  • 10. The method of claim 1, wherein the polynucleotide comprises at least one protecting group selected from a nucleobase protecting group, a 2′-hydroxyl protecting group, and a phosphate protecting group, wherein said at least one protecting group is labile under conditions which include an α-effect nucleophile; and wherein said contacting results in concurrent cleavage of the polynucleotide from the substrate and deprotection of the polynucleotide.
  • 11. The method of claim 1: wherein the polynucleotide bound to the substrate via the cleavable linker is an RNA, said RNA has a 2′-hydroxyl protecting group, said 2′hydroxyl protecting group is characterized as being peroxyanion-labile;wherein the α-effect nucleophile is a peroxyanion; andwherein said contacting results in concurrent cleavage of the RNA from the substrate and cleavage of the 2′-hydroxyl protecting group.
  • 12. The method of claim 1: wherein the polynucleotide comprises a 2′-hydroxyl protecting group and at least one additional protecting group selected from a nucleobase protecting group and a phosphorus protecting group;wherein said 2′-hydroxyl protecting group is stable under conditions which include an α-effect nucleophile;wherein said at least one additional protecting group is labile under conditions which include an α-effect nucleophile; andwherein said contacting results in concurrent cleavage of the polynucleotide from the substrate and cleavage of said at least one additional protecting group.
  • 13. The method of claim 12 further comprising cleaving the 2′hydroxyl protecting group under conditions sufficient to result in cleavage of the 2′hydroxyl protecting group, wherein said conditions do not include α-effect nucleophile.
  • 14. A composition comprising a polynucleotide bound to a substrate via a cleavable linker, wherein the cleavable linker has the structure (I):
  • 15. The composition of claim 14 wherein the cleavable linker is characterized as being a peroxyanion-labile linker.
  • 16. The composition of claim 14, wherein the linking group Lnk is selected from: (1) a lower alkyl group;(2) a modified lower alkyl group in which one or more linkages selected from ether-, thio-, amino-, oxo-, ester-, and amido- is present;(3) a modified lower alkyl substituted with one or more groups including lower alkyl; aryl, aralkyl, alkoxyl, thioalkyl, hydroxyl, amino, amido, sulfonyl, halo; or(4) a modified lower alkyl substituted with one or more groups including lower alkyl; alkoxyl, thioalkyl, hydroxyl, amino, amido, sulfonyl, halo, and in which one or more linkages selected from ether-, thio-, amino-, oxo-, ester-, and amido- is present.
  • 17. The composition of claim 14, wherein the linking group Lnk has the structure —(CH2)m-Lkg-(CH2)n-wherein:m and n are integers independently selected from the range of 1 to about 12, andLkg is a linkage selected from ether-, thio-, amino-, oxo-, ester-, or amido-.
  • 18. The composition of claim 14 wherein the polynucleotide comprises at least one protecting group selected from a nucleobase protecting group, a 2′-hydroxyl protecting group, and a phosphorus protecting group, wherein said at least one protecting group and the cleavable linker are both characterized as labile under conditions which include an α-effect nucleophile.
  • 19. The composition of claim 14: wherein the polynucleotide bound to the substrate via the cleavable linker is an RNA, said RNA has a 2′-hydroxyl protecting group; andwherein said 2′hydroxyl protecting group and the cleavable linker are characterized as being labile under conditions which include an α-effect nucleophile.
  • 20. The composition of claim 14: wherein the polynucleotide comprises a 2′-hydroxyl protecting group and at least one additional protecting group selected from a nucleobase protecting group and a phosphorus protecting group,wherein said 2′-hydroxyl protecting group is characterized as stable under conditions which include an α-effect nucleophile;wherein said at least one additional protecting group is characterized as labile under conditions which include an α-effect nucleophile.
  • 21. The composition of claim 14: wherein the polynucleotide comprises a 2′-hydroxyl protecting group, a phosphorus protecting group, and a nucleobase protecting group,wherein said 2′-hydroxyl protecting group is characterized as stable under conditions which include an α-effect nucleophile;wherein said phosphate protecting group is characterized as stable under conditions which include an α-effect nucleophile; andwherein said nucleobase protecting group is characterized as labile under conditions which include an α-effect nucleophile.