Compositions and methods for recognition of RNA using triple helix forming peptide nucleic acids

Patent metadata

Field	Value
Publication number	US-10385100-B2
Application number	US-201615221021-A
Country	US
Kind code	B2
Filing date	Jul 27, 2016
Priority date	Oct 29, 2012
Publication date	Aug 20, 2019
Grant date	Aug 20, 2019

Abstract

Peptide nucleic acids containing thymidine and 2-aminopyridine (M) nucleobases formed stable and sequence selective triple helices with double stranded RNA at physiologically relevant conditions. The M-modified PNA displayed unique RNA selectivity by having two orders of magnitude higher affinity for the double stranded RNAs than for the same DNA sequences. Preliminary results suggested that nucleobase-modified PNA could bind and recognize double helical precursors of microRNAs.

First claim

What is claimed is:

1. A peptide nucleic acid, comprising:
a polypeptide comprising a series of N-(2-aminoethyl)-glycines,
each N-(2-aminoethyl)-glycine being ligated to a respective Base,

and
wherein at least one of the respective Bases is 2-aminopyridine:

such that at least one N-(2-aminoethyl)-glycine ligated to a Base is 2-aminopyridine-ligated to a N-(2-aminoethyl)-glycine:

further comprising at least one basic amino acid ligated to the polypeptide.

2. The peptide nucleic acid according to claim 1 , wherein the at least one basic amino acid comprises at least one terminal lysine ligated to the polypeptide.

3. The peptide nucleic acid according to claim 1 , wherein at least four bases are 2-aminopyridine.

4. The peptide nucleic acid according to claim 1 , wherein at least two sequential bases are 2-aminopyridine.

5. The peptide nucleic acid according to claim 1 , wherein the polypeptide comprises at least six sequential base-ligated N-(2-aminoethyl)-glycines.

6. The peptide nucleic acid according to claim 1 , in combination with a double stranded RNA, wherein the peptide nucleic acid forms a base sequence selective triple helix with the double stranded RNA substantially without strand invasion.

7. The peptide nucleic acid according to claim 1 , wherein the peptide nucleic acid is configured to form a triple helix with a double stranded RNA having a corresponding base sequence with the peptide nucleic acid, substantially without strand invasion, which is stable at pH 7.4.

8. The peptide nucleic acid according to claim 7 , wherein the peptide nucleic acid is configured to form the triple helix with the double stranded RNA, in a base sequence-selective manner at pH 7.4 at a temperature of 37° C. in an aqueous buffer comprising 2 mM MgCl 2 , 90-mM KCl, 10 mM NaCl, and 50 mM potassium phosphate.

9. A peptide nucleic acid (PNA), comprising:
a polypeptide comprising a series of at least six N-(2-aminoethyl)-glycines,
each N-(2-aminoethyl)-glycine being ligated to a respective Base,

wherein at least one respective Base comprises 2-aminopyridine,
further comprising at least one basic amino acid ligated to the polypeptide.

10. The peptide nucleic acid according to claim 9 , wherein the at least one basic amino acid ligated to the polypeptide comprises lysine.

11. The peptide nucleic acid according to claim 9 , wherein at least two bases are 2-aminopyridine Bases.

12. The peptide nucleic acid according to claim 9 , wherein the polypeptide comprises at least six sequential base-ligated N-(2-aminoethyl)-glycines.

13. The peptide nucleic acid according to claim 9 , in combination with a double stranded RNA, wherein the peptide nucleic acid forms a base sequence-selective triple helix with the double stranded RNA.

14. A peptide nucleic acid (PNA), comprising a polypeptide comprising a series of N-(2-aminoethyl)-glycines, each N-(2-aminoethyl)-glycine being ligated to a respective base, wherein at least one respective base comprises 2-aminopyridine, configured to form a triple helix in sequence-selective manner with a double stranded ribonucleic acid which is stable at 37° C. in a pH 7.4 aqueous buffer comprising 2 mM MgCl 2 , 90-mM KCl, 10 mM NaCl, and 50 mM potassium phosphate.

15. The peptide nucleic acid according to claim 14 , configured to form, in combination with a double stranded RNA, a base sequence selective triple helix with the double stranded RNA substantially without strand invasion.

16. The peptide nucleic acid according to claim 14 , wherein at least one N-(2-aminoethyl)-glycine ligated to the respective base comprises:

17. The peptide nucleic acid according to claim 14 , further comprising at least one amino acid ligated to the series of N-(2-aminoethyl)-glycines.

18. The peptide nucleic acid according to claim 17 , wherein the at least one amino acid comprises lysine.

19. The peptide nucleic acid according to claim 9 , wherein at least one N-(2-aminoethyl)-glycine ligated to the respective Base comprises:

Assignees

• Univ New York State Res Found
• The Research Foundation For The State Univ O

Inventors

• Rozners Eriks
• Zengeya Thomas

Classifications

• C07K14/003 Primary

  Peptide-nucleic acids (PNAs) · CPC title

• C07K9/00

  Peptides having up to 20 amino acids, containing saccharide radicals and having a fully defined sequence; Derivatives thereof · CPC title

• C12Q1/6839 Primary

  Triple helix formation or other higher order conformations in hybridisation assays · CPC title

• C07K7/08

  having 12 to 20 amino acids (gastrins C07K14/595; somatostatins C07K14/655; melanotropins C07K14/68) · CPC title

• C12Q2525/107

  incorporating a peptide nucleic acid · CPC title