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

Patent metadata

Field	Value
Publication number	US-10260089-B2
Application number	US-201314066006-A
Country	US
Kind code	B2
Filing date	Oct 29, 2013
Priority date	Oct 29, 2012
Publication date	Apr 16, 2019
Grant date	Apr 16, 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

The invention claimed is:

1. A method of forming a pH 7.4-stable peptide nucleic acid-double stranded ribonucleic acid triple helix, comprising:
providing a peptide nucleic acid sequence having at least one basic amino acid covalently linked to a nucleic acid sequence portion configured to selectively bind to a complementary nucleic acid sequence portion, wherein the nucleic acid sequence portion comprises at least one 2-aminopyridine nucleobase; and
contacting a peptide nucleic acid having the peptide nucleic acid sequence with double stranded ribonucleic acid having the complementary nucleic acid sequence portion, to form a peptide nucleic acid double-stranded ribonucleic acid triple helix, in a nucleic acid sequence portion selective manner.

2. The method according to claim 1 , wherein the peptide nucleic acid sequence portion has a higher affinity for the double stranded ribonucleic acid having the complementary nucleic acid sequence portion than for a double stranded deoxyribonucleic acid having a corresponding complementary nucleic acid sequence portion.

3. The method according to claim 1 , wherein the peptide nucleic acid comprises at least six nucleobases including at least three 2-aminopyridine nucleobases.

4. The method according to claim 1 , wherein the at least one amino acid comprises lysine.

5. A method of forming a peptide nucleic acid-double stranded nucleic acid triple helix, comprising:
providing a peptide nucleic acid, comprising a nucleic acid sequence-selective binding portion, the nucleic acid sequence-selective binding portion comprising a plurality of nucleobases and at least one 2-aminopyridine nucleobase, conjugated to at least one basic amino acid; and
interacting the peptide nucleic acid with a double stranded nucleic acid having a nucleic acid sequence corresponding to the nucleic acid sequence-selective binding portion, to form the peptide nucleic acid-double stranded nucleic acid triple helix selectively in dependence on the nucleic acid sequence-selective binding portion.

6. The method according to claim 5 , wherein the nucleic acid sequence-selective binding portion comprises at least six nucleobases.

7. The method according to claim 5 , wherein the nucleic acid sequence-selective binding portion comprises at least three 2-aminopyridine nucleobases.

8. The method according to claim 5 , wherein the nucleic acid sequence-selective binding portion comprises at least six nucleobases including at least three 2-aminopyridine nucleobases.

9. The method according to claim 5 , wherein the nucleic acid sequence-selective binding portion comprises a copolymer comprising 2-aminopyridine and thymidine.

10. The method according to claim 5 , wherein the peptide nucleic acid-double stranded nucleic acid triple helix is stable at pH 7.4 at temperatures less than about 35° C. in a phosphate buffer solution containing 2 mM magnesium chloride, 90 mM potassium chloride, 10 mM sodium chloride, and 50 mM potassium phosphate.

11. The method according to claim 5 , wherein the peptide nucleic acid has a higher affinity for a double stranded ribonucleic acid containing the nucleic acid sequence corresponding to the nucleic acid sequence-selective binding portion than for a double stranded deoxyribonucleic acid containing a deoxyribonucleic acid sequence corresponding to the nucleic acid sequence-selective binding portion.

12. The method according to claim 5 , wherein the at least one 2-aminopyridine selectively binds to guanosine nucleobases of the nucleic acid sequence.

13. The method according to claim 5 , wherein the at least one basic amino acid comprises lysine.

Assignees

• Univ New York State Res Found
• The Research Foundation Of The State Univ Of New York

Inventors

• Rozners Eriks
• Zengeya Thomas

Classifications

• C07K14/003

  Peptide-nucleic acids (PNAs) · CPC title

• C12Q1/6839 Primary

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

• C07K9/00

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