Patent ID: 7572908
Filing Date: 2009-08-11
Classification: C07H

Abstract:
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 a structure selected from structures (I), (II), (III), (IV), or (V): wherein: R3, R4, R5, R6, R7, R10, and R11 are each independently selected from H, lower alkyl, modified lower alkyl, thioalkyl, hydroxyl, thio, mercapto, amino, amido, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, boronyl, or -Lnk-Sub, wherein Lnk is a linking group and Sub denotes the site at which the substrate is attached to the cleavable linker, provided that one and only one of R3, R4, R5, R6, R7, R10, or R11 is -Lnk-Sub; and RPN denotes the site at which the polynucleotide is attached to the cleavable linker; wherein: R3, R4, R5, R6, R7, R10, and R11 are each independently selected from H, lower alkyl, modified lower alkyl, thioalkyl, hydroxyl, thio, mercapto, amino, amido, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, boronyl, or -Lnk-Sub, wherein Lnk is a linking group and Sub denotes the site at which the substrate is attached to the cleavable linker, provided that one and only one of R3, R4, R5, R6, R7, R10, or R11 is -Lnk-Sub; and RPN denotes the site at which the polynucleotide is attached to the cleavable linker; wherein: R4, R5, R6, and R7 are each independently selected from H, lower alkyl, modified lower alkyl, thioalkyl, hydroxyl, thio, mercapto, amino, amido, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, boronyl, or -Lnk-Sub, wherein Lnk is a linking group and Sub denotes the site at which the substrate is attached to the cleavable linker, provided that one and only one of R4, R5, R6, or R7 is -Lnk-Sub; R13 is selected from lower alkyl, modified lower alkyl, alkyl, or modified alkyl, or aryl; and RPN denotes the site at which the polynucleotide is attached to the cleavable linker; wherein: R4, R5, R6, R7, R10, and R11 are each independently selected from H, lower alkyl, modified lower alkyl, thioalkyl, hydroxyl, thio, mercapto, amino, amido, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, boronyl, or -Lnk-Sub, wherein Lnk is a linking group and Sub denotes the site at which the substrate is attached to the cleavable linker, provided that one and only one of R4, R5, R6, R7, R10, or R11 is -Lnk-Sub; R13 is selected from lower alkyl, modified lower alkyl, alkyl, or modified alkyl, or aryl; and RPN denotes the site at which the polynucleotide is attached to the cleavable linker; wherein: R4, R5, R6, R7, R10, and R11 are each independently selected from H, lower alkyl, modified lower alkyl, thioalkyl, hydroxyl, thio, mercapto, amino, amido, imino, halo, cyano, nitro, nitroso, azido, carboxy, sulfide, sulfone, sulfoxy, phosphoryl, silyl, silyloxy, boronyl, or -Lnk-Sub, wherein Lnk is a linking group and Sub denotes the site at which the substrate is attached to the cleavable linker, provided that one and only one of R4, R5, R6, R7, R10, or R11 is -Lnk-Sub; R13 is selected from lower alkyl, modified lower alkyl, alkyl, or modified alkyl, or aryl; and RPN denotes the site at which the polynucleotide is attached to the cleavable linker.