Structural properties and stability of PNA with (2′R,4′R)- and (2′R,4′S)-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbone binding to DNA: A molecular dynamics simulation study

The structural properties and stability of two different stereoisomers of (1S,2S)-2-aminocyclopentanecarboxylic acid (acpcPNA) binding to DNA and self hybrid DNA duplex were investigated using a molecular dynamics simulation. The thermodynamics stability was estimated and revealed that the stability of the simulated duplexes is of the order of (2′R,4′R)-acpcPNA·DNA > (2′R,4′S)-acpcPNA·DNA > DNA·DNA, which is in good agreement with experimental thermal stability. The lowest stability of DNA duplex is caused by a repulsion of two negatively charged backbones. The repulsion is decreased significantly by replacing a non-charged acpcPNA backbone, leading to a strong binding ability of acpcPNA with its complementary DNA.