Deb Indrajit, Sarzynska Joanna, Nilsson Lennart, Lahiri Ansuman
Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, West Bengal, India.
Biopolymers. 2014 Oct;101(10):985-91. doi: 10.1002/bip.22495.
The structural effects of the commonly occurring modified nucleoside dihydrouridine (D) observed experimentally in model oligonucleotides include a strong destabilization of the C3'-endo sugar conformation of D, the disruption of stacking interactions of neighboring residues with D and a possible destabilization of the C3'-endo sugar pucker of the 5'-neighboring nucleoside. Our simulations with a combination of a set of parameters for modified RNA residues with the recently developed AMBER FF99χ force field having reoptimized glycosidic torsion angle parameters for standard nucleosides was found to reproduce the destabilizing effect of dihydrouridine better than with the AMBER FF99 force field for nucleic acids for which the parameters for the modified residues were originally developed.
在模型寡核苷酸中通过实验观察到的常见修饰核苷二氢尿苷（D）的结构效应包括：D的C3'-内型糖构象强烈失稳、与D相邻残基的堆积相互作用被破坏以及5'-相邻核苷的C3'-内型糖环构象可能失稳。我们结合一组修饰RNA残基的参数与最近开发的AMBER FF99χ力场进行模拟，该力场对标准核苷重新优化了糖苷扭转角参数，结果发现，与最初为修饰残基开发参数的核酸AMBER FF99力场相比，此模拟能更好地重现二氢尿苷的失稳效应。
