Suitable conformations for peptide nucleic acid (PNA) self-hybrids with (2'R,4'R)- and (2'R,4'S)-prolyl(1S,2S)-2-aminocyclopentanecarboxylic acid backbones (namely, acpcPNA and epi-acpcPNA, respectively) were investigated based on molecular dynamics simulations. The results revealed that hybridization of the acpcPNA was observed only in the parallel direction, with a conformation close to the P-type structure. In contrast, self-hybrids of the epi-acpcPNA were formed in the antiparallel and parallel directions; the antiparallel duplex adopted the B-form conformation, and the parallel duplex was between Band P-forms. The calculated binding energies and the experimental data indicate that the antiparallel epiacpc-PNA self-hybrid was more stable than the parallel duplex. (C) 2018 Elsevier B.V. All rights reserved.