Chem. J. Chinese Universities ›› 2009, Vol. 30 ›› Issue (12): 2445.

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Theoretical Study for DNA and RNA on Their Stability Difference

FENG Feng, YU Jian-Guo*, FANG Wei-Hai   

  1. College of Chemistry, Beijing Normal University, Beijing 100875, China
  • Received:2009-03-10 Online:2009-12-10 Published:2009-12-10
  • Contact: YU Jian-Guo. E-mail: jianguo_yu@bnu.edu.cn
  • Supported by:

    国家“九七三”计划项目(批准号: 2004CB719903)和国家自然科学基金(批准号: 20573011, 20733002, 20873008)资助.

Abstract:

The semi-empirical method RM1BH, was employed to explore the reasons and nature of the intrinsic stability of the RNA and DNA duplexes. RM1BH is based on the convenient RM1 and modified to deal with the weak interactions between molecules, especially for the hydrogen bonding between biological systems, and embedded to our software module SimuCal_SE. And the calculations were processed using our software package SimuPac 1.0, with the linear scale algorithm to treat large molecular systems. The calculations in this study include 4 different sets of base pairs appeared in both DNA and RNA. By our calculations, the hydrogen bonding interaction energy of r(A\5U) is little bit larger than that of d(A\5T). When including more base pairs, the hydrogen bonding energies of RNA become much larger than DNA. Arrangements of purine and pyrimidine in RNA and DNA have contributions for the stabilities of both RNA and DNA. The calculation results in this study support and agree with the experimental results and conclutions.

Key words: Semi-empirical calculation; RM1BH method; SimuCal_SE method; Stability difference of DNA and RNA; Hydrogen bonding energy

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