| CPC C07H 21/04 (2013.01) [C12Q 1/6806 (2013.01); C12Q 1/6876 (2013.01)] | 9 Claims |
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1. A method for detection of one or more target nucleic acids in a sample, the method comprising:
contacting the sample with a charge-modified oligonucleotide probe, wherein the charge-modified oligonucleotide probe comprises an oligonucleotide sequence that is complimentary, or partially complimentary, to the one or more target nucleic acids, and wherein the charge-modified oligonucleotide probe has the structure (I)
 wherein
each B is independently selected from a nucleobase moiety;
each Q is independently selected from a nucleoside sugar;
each Y is independently selected from a sulfur or oxygen atom;
n is a number from 1 to 250;
each L is, independently for each occurrence, a
 group, a linker selected from —O— or —S—; alkylenes, which may be unsubstituted or substituted with 1 to 3 substituents selected from halo, hydroxy, lower alkoxy, amino, lower alkyl amino, nitro, cyano, perfluoro alkyl, and perfluoro alkoxy; linearly connected carbon and hetero atoms, wherein the heteroatom is selected from O, S and NH, divalent ring systems; or L is not present, in which case L is a covalent bond;
each R1 is, independently for each occurrence, a reporter group, or a group with high specific affinity, or a hydrogen atom;
each Z is independently selected from the group consisting of OH, SH, or a group with Structure (II):
 wherein:
at least one occurrence of Z is selected to be a group according to Structure II;
W is a linker selected from —O— or —S—; C1-10 alkylenes, which may be unsubstituted or substituted with 1 to 3 substituents selected from halo, hydroxy, lower alkoxy, amino, lower alkyl amino, nitro, cyano, perfluoro alkyl, and perfluoro alkoxy; linearly connected carbon and hetero atoms, wherein the heteroatom is selected from O, S and NH, divalent ring systems; or W is not present, in which case W is a covalent bond;
each X is independently selected to be an oxygen or a sulfur atom;
each R2 is independently selected from a group consisting of H, methyl, ethyl, propyl, isopropyl, methoxy, ethoxy, isopropyloxy, straight, branched, or substituted C1-6 alkyl, C2-6 alkene, substituted C2-6 alkene, straight or branched C1-6 alkoxy, or two R2 together with the nitrogen atom to which they are both attached form an 5- to 7-membered single nitrogen heterocyclic ring, or 5- to 7-member heterocyclic ring having up to two additional ring heteroatoms selected from the group consisting of O, S, and N, and wherein the 5- to 7-membered heterocyclic ring may be unsubstituted or substituted with up to three substituents selected from the group consisting of halo, C1-4 alkyl, and C1-4 alkoxy, or is not present, in which case R2 is an electron pair;
R3 is selected from a group consisting of H, methyl, ethyl, propyl, isopropyl, 1,1-dimethyethyl, methoxy, ethoxy, isopropyloxy, tret-butyloxy, C1-6 straight or branched alkyl, substituted C1-6 straight or branched alkyl, C2-6 alkene, and substituted C2-6 alkene;
each R4 is independently selected from a group consisting of H, methyl, ethyl, propyl, isopropyl, methoxy, ethoxy, isopropyloxy, straight, branched, or substituted C1-6 alkyl, C2-6 alkene, substituted C2-6 alkene, straight or branched C1-6 alkoxy, or two R4 together with the carbon atom to which they are both attached form an 3- to 7-membered alicyclic ring, or 5- to 7-member heterocyclic ring having up to two ring heteroatoms selected from the group consisting of O, S, and N, and wherein the alicyclic or heterocyclic ring may be unsubstituted or substituted with up to three substituents selected from the group consisting of halo, C1-4 alkyl, and C1-4 alkoxy;
each k is, independently for each occurrence, selected from 2, 3, 4 or 5;
each m is, independently or each occurrence, selected from 0, 1, 2, 3, 4 or 5.
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