Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand.
Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok, 10330, Thailand.
J Mol Graph Model. 2018 Sep;84:36-42. doi: 10.1016/j.jmgm.2018.06.008. Epub 2018 Jun 12.
Peptide nucleic acid (PNA) is a powerful biomolecule with a wide variety of important applications. In this work, the molecular structures and binding affinity of PNA with a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) that binds to both DNA and RNA were studied using molecular dynamics simulations. The simulated structures of acpcPNA-DNA and acpcPNA-RNA duplexes more closely resembled the typical structures of B-DNA and A-RNA than the corresponding duplexes of aegPNA. The calculated binding free energies are in good agreement with the experimental results that the acpcPNA-DNA duplex is more stable than the acpcPNA-RNA duplex regardless of the base sequences. The results provide further insights in the relationship between structure and stability of this unique PNA system.
肽核酸（PNA）是一种具有广泛重要应用的强大生物分子。在这项工作中，使用分子动力学模拟研究了具有 D-脯氨酰-2-氨基环戊烷羧酸骨架（acpcPNA）的 PNA 与 DNA 和 RNA 结合的分子结构和结合亲和力。acpcPNA-DNA 和 acpcPNA-RNA 双链体的模拟结构比 aegPNA 的相应双链体更类似于典型的 B-DNA 和 A-RNA 结构。计算的结合自由能与实验结果非常吻合，即无论碱基序列如何，acpcPNA-DNA 双链体都比 acpcPNA-RNA 双链体更稳定。结果为这个独特的 PNA 系统的结构与稳定性之间的关系提供了进一步的深入了解。
