Divalent nucleobase compounds and uses therefor

Patent metadata

Field	Value
Publication number	US-11713340-B2
Application number	US-202117563570-A
Country	US
Kind code	B2
Filing date	Dec 28, 2021
Priority date	Apr 11, 2013
Publication date	Aug 1, 2023
Grant date	Aug 1, 2023

Abstract

Described herein are novel divalent nucleobases that each bind two nucleic acid strands, matched or mismatched when incorporated into a nucleic acid or nucleic acid analog backbone (a genetic recognition reagent, or genetic recognition reagent). In one embodiment, the genetic recognition reagent is a peptide nucleic acid (PNA) or gamma PNA (γPNA) oligomer. Uses of the divalent nucleobases and monomers and genetic recognition reagents containing the divalent nucleobases also are provided.

First claim

We claim:

1. A compound comprising a nucleobase moiety of the formula:

attached to a gamma-peptide nucleic acid (γPNA) backbone.

2. The compound of claim 1 , wherein the γPNA comprises a residue of the formula:

3. The compound of claim 1 , wherein a monomer residue of the γPNA backbone and the nucleobase moiety form:

wherein R is the nucleobase moiety, and R 1 , R 2 and R 3 each are, independently:
an amino acid side chain, methyl, ethyl, 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, —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 , —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 ; or hydrogen,
wherein:
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, and
r and s are each independently integers from 1 to 50, inclusive; and

wherein R 1 and R 2 are different and one of R 1 and R 2 is hydrogen.

4. The compound of claim 3 , wherein one of R 1 and R 2 is

or —CH 2 OH.

5. The compound of claim 1 , wherein the γPNA backbone and the nucleobase moiety form:

wherein R is the nucleobase moiety; R 1 , R 2 and R 4 each are, independently:
an amino acid side chain, methyl, ethyl, 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, —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 , —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 ; or hydrogen,
wherein:
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, and
r and s are each independently integers from 1 to 50, inclusive;

wherein R 1 and R 2 are different and one of R 1 and R 2 is hydrogen; and
R 3 is hydrogen or a protecting group.

6. The compound of claim 5 , wherein one of R 1 and R 2 is

or —CH 2 OH.

7. The compound of claim 5 , wherein the protecting group is selected from: methyl, formyl, ethyl, acetyl, anisyl, benzyl, benzoyl, carbamate, trifluoroacetyl, diphenylmethyl, triphenylmethyl, N-hydroxysuccinimidyl, benzyloxymethyl, benzyloxycarbonyl, 2-nitrobenzoyl, tert-butyloxycarbonyl, 4-methylbenzyl, 4-nitrophenyl, 2-chlorobenzyloxycarbonyl, 2-bromobenzyloxycarbonyl, 2,4,5-trichlorophenyl, thioanizyl, thiocresyl, carbobenzyloxy, p-methoxybenzyl carbonyl, 9-fluorenylmethyloxycarbonyl, pentafluorophenyl, p-methoxybenzyl, 3,4-dimethozybenzyl, p-methoxyphenyl, 4-toluenesulfonyl, p-nitrobenzenesulfonates, 9-fluorenylmethyloxycarbonyl, 2-nitrophenylsulfenyl, 2,2,5,7,8-pentamethyl-chroman-6-sulfonyl, and p-bromobenzene sulfonyl.

8. A method comprising contacting a compound with a nucleic acid, wherein the compound comprises a nucleobase moiety of the formula:

attached to a γPNA backbone.

9. The method of claim 8 , wherein the γPNA comprises a residue of the formula:

10. The method of claim 8 , wherein a monomer residue of the γPNA backbone and the nucleobase moiety form:

wherein R is the nucleobase moiety, and R 1 , R 2 and R 3 each are, independently:
an amino acid side chain, methyl, ethyl, 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, —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 , —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 ) q —NHC(NH)NH 2 , or —CH 2 —(OCH 2 —CH 2 ) r —S—S[CH 2 CH 2 ] s NHC(NH)NH 2 ; or hydrogen,
wherein:
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, and
r and s are each independently integers from 1 to 50, inclusive; and

wherein R 1 and R 2 are different and one of R 1 and R 2 is hydrogen.

11. The method of claim 10 , wherein one of R 1 and R 2 is

or —CH 2 OH.

12. The method of claim 8 , wherein the compound is a fluorochrome.

13. The method of claim 8 , wherein the compound is bound to a solid substrate in an array.

14. The method of claim 8 , wherein the nucleic acid is a marker of genetic disease.

15. The method of claim 8 , wherein the nucleic acid is derived from a bacterial, viral, or fungal infection.

16. The method of claim 8 , wherein the contacting occurs inside a human.

17. The method of claim 8 , wherein the nucleic acid comprises an unstable repeat.

Assignees

• Univ Carnegie Mellon

Inventors

• Ly Danith H
• Gopalsamy Suresh Kumar
• Manna Arunava

Classifications

• C07K14/003 Primary

  Peptide-nucleic acids (PNAs) · CPC title

• C07D239/47

  One nitrogen atom and one oxygen or sulfur atom, e.g. cytosine · CPC title

• C07D239/54

  as doubly bound oxygen atoms or as unsubstituted hydroxy radicals · CPC title

• C07D251/16

  to only one ring carbon atom · CPC title

• C07D471/04

  Ortho-condensed systems · CPC title