Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

doi:10.1088/1674-1056/23/2/020702

中国物理B ›› 2014, Vol. 23 ›› Issue (2): 20702-020702.doi: 10.1088/1674-1056/23/2/020702

Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

张小虎^a, 黎明^b, 王延颋^a, 欧阳钟灿^a

a State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China;
b Department of Physical Science, University of Chinese Academy of Sciences, Beijing 100190, China

收稿日期:2013-09-22 修回日期:2013-10-17 出版日期:2013-12-12 发布日期:2013-12-12

Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

Zhang Xiao-Hu (张小虎)^a, Li Ming (黎明)^b, Wang Yan-Ting (王延颋)^a, Ouyang Zhong-Can (欧阳钟灿)^a

a State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China;
b Department of Physical Science, University of Chinese Academy of Sciences, Beijing 100190, China

Received:2013-09-22 Revised:2013-10-17 Online:2013-12-12 Published:2013-12-12
Contact: Wang Yan-Ting E-mail:wangyt@itp.ac.cn
About author:07.05.Tp; 87.15.A-; 87.15.-v

摘要/Abstract

摘要： Formation and dissociation mechanisms of C–C⁺ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C–C⁺ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C–C⁺ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.

关键词: ab initio quantum chemical calculation, i-motif, protonated cytosine–, cytosine base pair

Abstract: Formation and dissociation mechanisms of C–C⁺ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C–C⁺ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C–C⁺ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.

Key words: ab initio quantum chemical calculation, i-motif, protonated cytosine–cytosine base pair

中图分类号: (Computer modeling and simulation)

07.05.Tp

87.15.A- (Theory, modeling, and computer simulation) 87.15.-v (Biomolecules: structure and physical properties)

张小虎, 黎明, 王延颋, 欧阳钟灿. Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations[J]. 中国物理B, 2014, 23(2): 20702-020702.

Zhang Xiao-Hu (张小虎), Li Ming (黎明), Wang Yan-Ting (王延颋), Ouyang Zhong-Can (欧阳钟灿). Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations[J]. Chin. Phys. B, 2014, 23(2): 20702-020702.

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Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

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