Divalent nucleobase compounds and uses therefor

11603,369

16/336210

September 26, 2017

Described herein are divalent nucleobases that each binds two nucleic acid strands, matched or mismatched when incorporated into a nucleic acid or nucleic acid analog backbone, such as in a γ-peptide nucleic acid (γPNA). Also provided are genetic recognition reagents comprising one or more of the divalent nucleobases and a nucleic acid or nucleic acid analog backbone, such as a γPNA backbone. Uses for the divalent nucleobases and monomers and genetic recognition reagents containing the divalent nucleobases also are provided.

Carnegie Mellon University (Pittsburgh, PA, US)

Carnegie Mellon University (Pittsburgh, PA, US)

1. A genetic recognition reagent comprising a plurality of nucleobase moieties attached to a nucleic acid backbone or a nucleic acid analog backbone, in which at least one of the plurality of nucleobase moieties is a ring system chosen from: [chemical expression included] [chemical expression included] [chemical expression included] [chemical expression included] [chemical expression included] wherein R 1 is H or a protecting group, and R is a residue of the nucleic acid backbone or a residue of the nucleic acid analog backbone in the genetic recognition reagent.

2. The genetic recognition reagent of claim 1 , in which R 1 is the protecting group, wherein the protecting group is independently: methyl, formyl, ethyl, acetyl, anisyl, benzyl, benzoyl, carbamate, trifluoroacetyl, diphenylmethyl, triphenylmethyl, benzyloxymethyl, benzyloxycarbonyl, 2-nitrobenzoyl, t-Boc (tert-butyloxycarbonyl), 4-methylbenzyl, 4-nitrophenyl, 2-chlorobenzyloxycarbonyl, 2-bromobenzyloxycarbonyl, 2,4,5-trichlorophenyl, thioanizyl, thiocresyl, cbz (carbobenzyloxy), p-methoxybenzyl carbonyl, 9-fluorenylmethyloxycarbonyl, pentafluorophenyl, p-methoxybenzyl, 3,4-dimethozybenzyl, p-methoxyphenyl, 4-toluenesulfonyl, p-nitrobenzenesulfonyl, 9-fluorenylmethyloxycarbonyl, 2-nitrophenylsulfenyl, 2,2,5,7,8-pentamethyl-chroman-6-sulfonyl, or p-bromobenzenesulfonyl.

3. The genetic recognition reagent of claim 1 , in which the nucleic acid backbone or the nucleic acid analog backbone is a DNA backbone, RNA backbone, peptide nucleic acid (PNA) backbone, phosphorothioate backbone, locked nucleic acid backbone, unlocked nucleic acid backbone, 2′—O-methyl—substituted RNA backbone, morpholino nucleic acid backbone, threose nucleic acid backbone, or glycol nucleic acid backbone, or any combination thereof.

4. The genetic recognition reagent of claim 1 , in which the nucleic acid analog backbone is a peptide nucleic acid (PNA) backbone.

5. The genetic recognition reagent of claim 1 , having a structure: [chemical expression included] where each instance of M is the residue of the nucleic acid backbone or the residue of the nucleic acid analog backbone, and each instance of B is independently one of the plurality of nucleobase moieties, where at least one instance of B is the ring system, each instance of E is independently an end group, and “n” is zero or a positive integer ranging from 1 to 48.

6. The genetic recognition reagent of claim 1 , in which all instances of R 1 are H.

7. A compound comprising a nucleobase moiety and R, wherein the compound is: [chemical expression included] [chemical expression included] [chemical expression included] [chemical expression included] [chemical expression included] wherein R 1 is H or a protecting group, and R is: carboxyl, hydroxyl, amine, cyanate, thiol, epoxide, vinyl, N-hydroxysuccinimide (NHS) ester, azide, alkynyl, maleimide, hydrazide, tetrazine, phosphoramidite, cycloalkyne, nitrile, (CH 2)nCO 2 H or (CH 2)nCO 2 Y where n=1-5 and Y=succinimidyl; a solid substrate; a nucleic acid backbone monomer; a nucleic acid analog backbone monomer; a residue of a nucleic acid polymer; or a residue of a nucleic acid analog polymer.

8. The compound of claim 7 , wherein R is the nucleic acid backbone monomer or the nucleic acid analog backbone monomer.

9. The compound of claim 7 , wherein R is the solid substrate, wherein the solid substrate is a silicon wafer, a multi-well dish, a polymeric bead, or an array.

10. The compound of claim 7 , wherein each R 1 is the protecting group, wherein the protecting group is independently methyl, formyl, ethyl, acetyl, anisyl, benzyl, benzoyl, carbamate, trifluoroacetyl, diphenylmethyl, triphenylmethyl, benzyloxymethyl, benzyloxycarbonyl, 2-nitrobenzoyl, t-Boc (tert-butyloxycarbonyl), 4-methylbenzyl, 4-nitrophenyl, 2-chlorobenzyloxycarbonyl, 2-bromobenzyloxycarbonyl, 2,4,5-trichlorophenyl, thioanizyl, thiocresyl, cbz (carbobenzyloxy), p-methoxybenzyl carbonyl, 9-fluorenylmethyloxycarbonyl, pentafluorophenyl, p-methoxybenzyl, 3,4-dimethozybenzyl, p-methoxyphenyl, 4-toluenesulfonyl, p-nitrobenzenesulfonyl, 9-fluorenylmethyloxycarbonyl, 2-nitrophenylsulfenyl, 2,2,5,7,8-pentamethyl-chroman-6-sulfonyl, or p-bromobenzenesulfonyl.

11. The compound of claim 7 , wherein R is the nucleic acid analog backbone monomer, wherein the nucleic acid analog backbone monomer is a peptide nucleic acid (PNA) backbone monomer.

12. The compound of claim 7 , wherein R is the nucleic acid analog backbone monomer, and the nucleic acid analog backbone monomer is: a phosphorothioate backbone monomer, a locked nucleic acid backbone monomer, an unlocked nucleic acid backbone monomer, a 2′—O-methyl—substituted RNA backbone monomer, a morpholino nucleic acid backbone monomer, a threose nucleic acid backbone monomer, or a glycol nucleic acid backbone monomer.

13. The compound of claim 7 , wherein R is the nucleic acid backbone monomer, wherein the nucleic acid backbone monomer is a ribose mono-, di-, or tri-phosphate, or a deoxyribose mono-, di-, or tri-phosphate.

14. A compound comprising a nucleobase moiety and R, wherein the compound is: [chemical expression included] [chemical expression included] [chemical expression included] [chemical expression included] wherein R 1 is H or a protecting group, and R is: carboxyl, hydroxyl, amine, cyanate, thiol, epoxide, vinyl, allyl, N-hydroxysuccinimide (NHS) ester, azide, alkynyl, maleimide, hydrazide, tetrazine, phosphoramidite, cycloalkyne, nitrile, (CH 2) n CO 2 H where n=1-5, a solid substrate, a nucleic acid backbone monomer, a nucleic acid analog backbone monomer, a residue of a nucleic acid polymer, or a residue of a nucleic acid analog polymer.

15. The genetic recognition reagent of claim 1 , wherein the nucleic acid analog backbone is a peptide nucleic acid (PNA) backbone in which R and one nucleobase moiety of the plurality of nucleobase moieties form [chemical expression included] wherein: each R 2 , R 3 and R 4 is independently methyl, ethyl, amino acid side chains, linear or branched (C 3 -C 8)alkyl, (C 2 -C 8)alkenyl, (C 2 -C 8)alkynyl, (C 1 -C 8)hydroxyalkyl, (C 3 -C 8)aryl, (C 3 -C 8)cycloalkyl, (C 3 -C 8)aryl(C 1 -C 6)alkylene, (C 3 -C 8)cycloalkyl(C 1 -C 6)alkylene, a PEGylated moiety of the preceding comprising from 1 to 50 (—O—CH 2 —CH 2 —) residues, H, —CH 2 —(OCH 2 —CH 2) q OP 1 , —CH 2 —(OCH 2 —CH 2) q —NHP 1 , —CH 2 —(OCH 2 —CH 2) q —SP 1 and —CH 2 —(SCH 2 —CH 2) q —SP 1 , —CH 2 —(OCH 2 —CH 2) r —OH, —CH 2 —(OCH 2 —CH 2) r —NH 2 , —CH 2 —(OCH 2 —CH 2) r —NHC(NH)NH 2 , or —CH 2 —(OCH 2 —CH 2) r —S—S [CH 2 CH 2 ] s NHC(NH)NH 2 , provided that R 2 and R 3 are different and one of R 2 or R 3 is H; or R 3 and R 4 together form a 1,3-propylene linkage and R 2 is H; or R 2 and R 4 together form a 1,3-propylene linkage and R 3 is H; P 1 is selected from the group consisting of H, (C 1 -C 8)alkyl, (C 2 -C 8)alkenyl, (C 2 -C 8)alkynyl, (C 3 -C 8)aryl, (C 3 -C 8)cycloalkyl, (C 3 -C 8)aryl(C 1 -C 6)alkylene and (C 3 -C 8)cycloalkyl(C 1 -C 6)alkylene; q is an integer from 0 to 10, inclusive; r and s are each independently integers from 1 to 50, inclusive; and Base is the one nucleobase moiety of the plurality of nucleobase moieties.

16. The genetic recognition reagent of claim 15 , in which R 3 is H, R 2 is an amino acid side chain that is PEGylated, with one or more PEG moieties of one to twelve (—O—CH 2 —CH 2 —) residues.

17. The compound of claim 11 , wherein the PNA backbone monomer comprises a residue of the formula: [chemical expression included]

18. The compound of claim 11 , wherein the PNA backbone monomer is a gamma peptide nucleic acid (γPNA) backbone monomer.

19. The compound of claim 11 , wherein the PNA backbone monomer and the nucleobase moiety form [chemical expression included] wherein each R 2 , R 3 and R 4 is independently methyl, ethyl, amino acid side chains, linear or branched (C 3 -C 8)alkyl, (C 2 -C 8)alkenyl, (C 2 -C 8)alkynyl, (C 1 -C 8)hydroxyalkyl, (C 3 -C 8)aryl, (C 3 -C 8)cycloalkyl, (C 3 -C 8)aryl(C 1 -C 6)alkylene, (C 3 -C 8)cycloalkyl(C 1 -C 6)alkylene, a PEGylated moiety of the preceding comprising from 1 to 50 (—O—CH 2 —CH 2 —) residues, H, —CH 2 —(OCH 2 —CH 2) q OP 1 , —CH 2 —(OCH 2 —CH 2) q —NHP 1 , —CH 2 —(OCH 2 —CH 2) q —SP 1 and —CH 2 —(SCH 2 —CH 2) q —SP 1 , —CH 2 —(OCH 2 —CH 2) r —OH, —CH 2 —(OCH 2 —CH 2) r —NH 2 , —CH 2 —(OCH 2 —CH 2) r —NHC(NH)NH 2 , or —CH 2 —(OCH 2 —CH 2) r —S—S [CH 2 CH 2 ] s NHC(NH)NH 2 , provided that R 2 and R 3 are different and one of R 2 or R 3 is H; or R 3 and R 4 together form a 1,3-propylene linkage and R 2 is H; or R 2 and R 4 together form a 1,3-propylene linkage and R 3 is H; R 5 is a protecting group or H; P 1 is selected from the group consisting of H, (C 1 -C 8)alkyl, (C 2 -C 8)alkenyl, (C 2 -C 8)alkynyl, (C 3 -C 8)aryl, (C 3 -C 8)cycloalkyl, (C 3 -C 8)aryl(C 1 -C 6)alkylene and (C 3 -C 8)cycloalkyl(C 1 -C 6)alkylene; q is an integer from 0 to 10, inclusive; r and s are each independently integers from 1 to 50, inclusive; and Base is the nucleobase moiety.

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