The 2-Aminopyridine Nucleobase Improves Triple-Helical Recognition of RNA and DNA When Used Instead of Pseudoisocytosine in Peptide Nucleic Acids

Biochemistry. 2021 Jun 22;60(24):1919-1925. doi: 10.1021/acs.biochem.1c00275. Epub 2021 Jun 7.

Abstract

Pseudoisocytosine (J), a neutral analogue of protonated cytosine, is currently the gold standard modified nucleobase in peptide nucleic acids (PNAs) for the formation of J·G-C triplets that are stable at physiological pH. This study shows that triple-helical recognition of RNA and DNA is significantly improved by using 2-aminopyridine (M) instead of J. The positively charged M forms 3-fold stronger M+·G-C triplets than J with uncompromised sequence selectivity. Replacement of six Js with Ms in a PNA 9-mer increased its binding affinity by ∼2 orders of magnitude. M-modified PNAs prefer binding double-stranded RNA over DNA and disfavor off-target binding to single-stranded nucleic acids. Taken together, the results show that M is a promising modified nucleobase that significantly improves triplex-forming PNAs and may provide breakthrough developments for therapeutic and biotechnology applications.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aminopyridines / chemistry*
  • Aminopyridines / metabolism
  • Cytosine / analogs & derivatives
  • Cytosine / chemistry
  • DNA / chemistry
  • DNA / metabolism
  • Nucleic Acid Conformation / drug effects*
  • Peptide Nucleic Acids / metabolism*
  • RNA, Double-Stranded

Substances

  • Aminopyridines
  • Peptide Nucleic Acids
  • RNA, Double-Stranded
  • pseudoisocytosine
  • Cytosine
  • DNA
  • alpha-aminopyridine