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. (C) 2013 Elsevier B.V. All rights reserved.