Theoretical study of peptide nucleic acid with(2’R,4’R)-prolyl-(1S,2S)-2-aminocyclobutanecarboxylic acid acid backbone binding to DNA and self-pairing

Amphawan Maitarad

Materials Chemistry Research Center, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand

Nattawee Poomsuk

Materials Chemistry Research Center, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand

Chittima Laohpongspaisan

Materials Chemistry Research Center, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand

Khatcharin Siriwong

Materials Chemistry Research Center, Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand

DOI: https://doi.org/10.14456/kkurj.2018.10

Keywords: Peptide nucleic acid Molecular dynamics simulation Quantum calculation

Abstract

The binding ability of pyrrolidinyl peptide nucleic acid (PNA) binding to its complementary DNA and self-paring has been studied experimentally. However, a detailed understanding of the binding property is still unclear due to the lack of their crystallographic data. In this work, structural and energetic properties of PNA-DNA and PNA-PNA duplexes were studied using molecular dynamics (MD) simulations and quantum calculations. The studied pyrrolidinyl PNA backbone was (2¢R,4¢R)-prolyl-(1S,2S)-2-aminocyclobutanecarboxylic acid. MD simulations of three different forms (A–, B– and P–form) were performed in order to investigate the probable duplex conformation. As the results, PNA-PNA duplex exhibited the structural feature between A- and P-type conformations, while PNA-DNA double helix clearly showed the characteristic of B-form. In addition, quantum calculations revealed that the interaction of PNA-DNA duplex was larger than that of PNA-PNA duplex, indicating higher intrinsic stability of PNA-DNA compared to PNA-PNA double strand. This research may lead to a design of PNA for further applications.

How to Cite

Maitarad, A., Poomsuk, N., Laohpongspaisan, C., & Siriwong, K. (2018). Theoretical study of peptide nucleic acid with(2’R,4’R)-prolyl-(1S,2S)-2-aminocyclobutanecarboxylic acid acid backbone binding to DNA and self-pairing. Asia-Pacific Journal of Science and Technology, 23(2), APST–23. https://doi.org/10.14456/kkurj.2018.10

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