Divalent nucleobase compounds and uses therefor

Patent metadata

Field	Value
Publication number	US-11603369-B2
Application number	US-201716336210-A
Country	US
Kind code	B2
Filing date	Sep 26, 2017
Priority date	Sep 26, 2016
Publication date	Mar 14, 2023
Grant date	Mar 14, 2023

Abstract

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.

First claim

We claim:

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:

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:

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:

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:

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

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 , pro

Assignees

• Univ Carnegie Mellon

Inventors

• Ly Danith H
• Thadke Shivaji A
• Nakhi Ali
• Perera J Dinithi Rashmini

Classifications

• C07D251/46

  with oxygen or sulfur atoms attached to the two other ring carbon atoms · CPC title

• C07H1/06

  Separation; Purification · CPC title

• G01N33/5308

  for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites · CPC title

• C12Q1/6837

  using probe arrays or probe chips (C12Q1/6874 takes precedence) · CPC title

• C07H21/04

  with deoxyribosyl as saccharide radical · CPC title