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Chin. Phys. B, 2014, Vol. 23(2): 020702    DOI: 10.1088/1674-1056/23/2/020702
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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
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.
Keywords:  ab initio quantum chemical calculation      i-motif      protonated cytosine–cytosine base pair  
Received:  22 September 2013      Revised:  17 October 2013      Accepted manuscript online: 
PACS:  07.05.Tp (Computer modeling and simulation)  
  87.15.A- (Theory, modeling, and computer simulation)  
  87.15.-v (Biomolecules: structure and physical properties)  
Corresponding Authors:  Wang Yan-Ting     E-mail:  wangyt@itp.ac.cn
About author:  07.05.Tp; 87.15.A-; 87.15.-v

Cite this article: 

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 2014 Chin. Phys. B 23 020702

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