2-Guanidyl pyridine PNA nucleobase for triple-helical Hoogsteen recognition of cytosine in double-stranded RNA

Abstract

In triplex-forming peptide nucleic acid, a novel 2-guanidyl pyridine nucleobase (V) enables recognition of up to two cytosine interruptions in polypurine tracts of dsRNA by engaging the entire Hoogsteen face of C–G base pair. Ab initio and molecular dynamics simulations provided insights into H-bonding interactions that stabilized V·C–G triplets. Our results provided insights for future design of improved nucleobases, which is an important step towards the ultimate goal of recognition of any sequence of dsRNA.