Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif

doi:10.1088/1674-1056/23/6/068702

中国物理B ›› 2014, Vol. 23 ›› Issue (6): 68702-068702.doi: 10.1088/1674-1056/23/6/068702

Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif

徐悦^{a b c e}, 陈虎^{b d}, 璩玉杰^c, 黎明^b, 欧阳钟灿^e, 刘冬生^a, 严洁^f

a State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Beijing 100190, China;
b Mechanobiology Institute, National University of Singapore, Singapore, 117411;
c Department of Physics, National University of Singapore, Singapore, 117542;
d Department of Physics, Xiamen University, Xiamen 361005, China;
e School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China;
f Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China

收稿日期:2014-03-31 修回日期:2014-04-04 出版日期:2014-06-15 发布日期:2014-06-15
基金资助:
Project supported by Grants from the National Research Foundation through the Mechanobiology Institute Singapore and the Ministry of Education of Singapore (Grant No. MOE2012-T3-1-001) [to Yan J], the National Basic Research Program of China (Grant No. 2013CB932800), the Major Research Plan of the National Natural Science Foundation of China (Grant Nos. 91027046 and 91027045), and the Fundamental Research Funds for the Central Universities (Grant No. 2013121005).

Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif

Xu Yue (徐悦)^{a b c e}, Chen Hu (陈虎)^{b d}, Qu Yu-Jie (璩玉杰)^c, Artem K. Efremov^b, Li Ming (黎明)^e, Ouyang Zhong-Can(欧阳钟灿) ^a, Liu Dong-Sheng(刘冬生)^f, Yan Jie (严洁)^{b c}

a State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Beijing 100190, China;
b Mechanobiology Institute, National University of Singapore, Singapore, 117411;
c Department of Physics, National University of Singapore, Singapore, 117542;
d Department of Physics, Xiamen University, Xiamen 361005, China;
e School of Physics, University of Chinese Academy of Sciences, Beijing 100049, China;
f Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China

Received:2014-03-31 Revised:2014-04-04 Online:2014-06-15 Published:2014-06-15
Contact: Liu Dong-Sheng, Yan Jie E-mail:liudongsheng@tsinghua.edu.cn;phyyj@nus.edu.sg
Supported by:
Project supported by Grants from the National Research Foundation through the Mechanobiology Institute Singapore and the Ministry of Education of Singapore (Grant No. MOE2012-T3-1-001) [to Yan J], the National Basic Research Program of China (Grant No. 2013CB932800), the Major Research Plan of the National Natural Science Foundation of China (Grant Nos. 91027046 and 91027045), and the Fundamental Research Funds for the Central Universities (Grant No. 2013121005).

摘要/Abstract

摘要： The DNA i-motif is a quadruplex structure formed in tandem cytosine-rich sequences in slightly acidic conditions. Besides being considered as a building block of DNA nano-devices, it may also play potential roles in regulating chromosome stability and gene transcriptions. The stability of i-motif is crucial for these functions. In this work, we investigated the mechanical stability of a single i-motif formed in the human telomeric sequence 5'-(CCCTAA)₃CCC, which revealed a novel pH and loading rate-dependent bimodal unfolding force distribution. Although the cause of the bimodal unfolding force species is not clear, we proposed a phenomenological model involving a direct unfolding favored at lower loading rate or higher pH value, which is subject to competition with another unfolding pathway through a mechanically stable intermediate state whose nature is yet to be determined. Overall, the unique mechano-chemical responses of i-motif-provide a new perspective to its stability, which may be useful to guide designing new i-motif-based DNA mechanical nano-devices.

关键词: single-molecule techniques, i-motif, folding/structure of biomolecules, mechanical properties/biomolecules

Abstract: The DNA i-motif is a quadruplex structure formed in tandem cytosine-rich sequences in slightly acidic conditions. Besides being considered as a building block of DNA nano-devices, it may also play potential roles in regulating chromosome stability and gene transcriptions. The stability of i-motif is crucial for these functions. In this work, we investigated the mechanical stability of a single i-motif formed in the human telomeric sequence 5'-(CCCTAA)₃CCC, which revealed a novel pH and loading rate-dependent bimodal unfolding force distribution. Although the cause of the bimodal unfolding force species is not clear, we proposed a phenomenological model involving a direct unfolding favored at lower loading rate or higher pH value, which is subject to competition with another unfolding pathway through a mechanically stable intermediate state whose nature is yet to be determined. Overall, the unique mechano-chemical responses of i-motif-provide a new perspective to its stability, which may be useful to guide designing new i-motif-based DNA mechanical nano-devices.

Key words: single-molecule techniques, i-motif, folding/structure of biomolecules, mechanical properties/biomolecules

中图分类号: (Single-molecule techniques)

87.80.Nj

87.14.gk (DNA) 87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways) 87.15.La (Mechanical properties)

徐悦, 陈虎, 璩玉杰, 黎明, 欧阳钟灿, 刘冬生, 严洁. Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif[J]. 中国物理B, 2014, 23(6): 68702-068702.

Xu Yue (徐悦), Chen Hu (陈虎), Qu Yu-Jie (璩玉杰), Artem K. Efremov, Li Ming (黎明), Ouyang Zhong-Can(欧阳钟灿) , Liu Dong-Sheng(刘冬生), Yan Jie (严洁). Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif[J]. Chin. Phys. B, 2014, 23(6): 68702-068702.

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Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif

Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif

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