The conformational flexibility of nucleic acid bases paired in gas phase: a Car-Parrinello molecular dynamics study.
The flexibilities of pyrimidine and imidazole rings in the paired nucleobases are investigated using Car-Parrinello molecular dynamics simulation in gas phase. The pairing influence on the stiffness of rings is analyzed based on the molecular structure of the nucleobases and constraints caused by pairing. We prove that the flexibilities of pyrimidine rings in isolated state have subtle correlation with the degree of aromaticity of the rings. The pairings in nucleic base pairs cause the rings to be more rigid for G, T, and U but more flexible for A and the same for C.
CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.
Shiyan
S
Xiao
Haojun
H
Liang
D020029:Base Pairing; D005740:Gases / Q000737:chemistry; D007093:Imidazoles / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009696:Nucleic Acids / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*
D005740:Gases; D007093:Imidazoles; D009696:Nucleic Acids; D011743:Pyrimidines; C029899:imidazole; C030986:pyrimidine