期刊
BIOPOLYMERS
卷 110, 期 3, 页码 -出版社
WILEY
DOI: 10.1002/bip.23247
关键词
2,4-dithiouracil; 2-thiouracil; 4-thiouracil; DNA:RNA; microhelix; uridine; 2-thiouridine
The effect of the sulphur atom on the uracil ring was analyzed in different DNA:RNA microhelixes with three nucleotide base-pairs, including uridine, 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, cytidine, adenosine and guanosine. Distinct backbone and helical parameters were optimized at different density functional (DFT) levels. The Watson-Crick pair with 2-thiouridine appears weaker than with uridine, but its interaction with water molecules appears easier. Two types of microhelixes were found, depending on the H-bond of H2 ' hydroxyl atom: A-type appears with the ribose ring in E-3-envelope C-3 '-endo, and B-type in E-2-envelope C-2 '-endo. B-type is less common but it is more stable and with higher dipole-moment. The sulphur atoms significantly increase the dipole-moment of the microhelix, as well as the rise and propeller twist parameters. Simulations with four Na atoms H-bonded to the phosphate groups, and further hydration with explicit water molecules were carried out. A re-definition of the numerical value calculation of several base-pair and base-stacking parameters is suggested.
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