Compositions and methods for recognition of RNA using triple helix forming peptide nucleic acids
View Patent ↗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.
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: