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

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

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.

Keywords: single-molecule techniques i-motif folding/structure of biomolecules mechanical properties/biomolecules

Received: 31 March 2014
Revised: 04 April 2014
Accepted manuscript online:

PACS:	87.80.Nj	(Single-molecule techniques)
	87.14.gk	(DNA)
	87.15.Cc	(Folding: thermodynamics, statistical mechanics, models, and pathways)
	87.15.La	(Mechanical properties)

Fund: 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).

Corresponding Authors: Liu Dong-Sheng, Yan Jie
E-mail: liudongsheng@tsinghua.edu.cn;phyyj@nus.edu.sg

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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 2014 Chin. Phys. B 23 068702

[1]	Bacolla A and Wells R D 2004 Biol. Chem. 279 47411
[2]	Wells R D 2007 Trends Biochem. Sci. 32 271
[3]	Fu H X, Chen H, Zhang X H, Qu Y Y, Marko J F and Yan J 2011 Nucleic Acids Res. 39 3473
[4]	Zhang X H, Chen H, Fu H X, Doyle P S and Yan J 2012 Proc. Natl. Acad. Sci. 109 8103
[5]	Keniry M A 2001 Biopolymers 56 123
[6]	Burge S, Parkinson G N, Hazel P, Todd A K and Neidle S 2006 Nucleic Acids Res. 34 5402
[7]	Gehring K, Leroy J L and Gueron M 1993 Nature 363 561
[8]	Leroy J L, Gueron M, Mergny J L and Helene C 1994 Nucleic Acids Res. 22 1600
[9]	Phan A T, Gueron M and Leroy J L 2000 J. Mol. Biol. 299 123
[10]	Blackburn E H 1991 Nature 350 569
[11]	Xu Y and Sugiyama H 2006 Nucleic Acids Res. 34 949
[12]	Guo K X, Gokhale V, Hurley L H and Sun D 2008 Nucleic Acids Res. 36 4598
[13]	Siddiqui-Jain A, Grand C L, Bearss D J and Hurley L H 2002 Proc. Natl. Acad. Sci. 99 11593
[14]	Huppert J L and Balasubramanian S 2007 Nucleic Acids Res. 35 406
[15]	Kendrick S, Akiyama Y, Hecht S M and Hurley L H 2009 J. Am. Chem. Soc. 131 17667
[16]	Dai J X, Hatzakis E, Hurley L H and Yang D Z 2010 PLoS One 5 e11647
[17]	Wang M D, Schnitzer M J, Yin H, Landick R, Gelles J and Block S M 1998 Science 282 902
[18]	Wang H Y, Elston T, Mogilner A and Oster G 1998 Biophys. J. 74 1186
[19]	Liu D S and Balasubramanian S 2003 Angew. Chem. Int. Ed. 42 5734
[20]	Shu W M, Liu D S, Watari M, Riener C K, Strunz T, Welland M E, Balasubramanian S and McKendry R A 2005 J. Am. Chem. Soc. 127 17054
[21]	Liu D S, Cheng E J and Yang Z Q 2011 NPG Asia Mater. 3 109
[22]	Liu D S, Bruckbauer A, Abell C, Balasubramanian S, Kang D J, Klenerman D and Zhou D J 2006 J. Am. Chem. Soc. 128 2067
[23]	Liu H J, Zhou Y C, Yang Y, Wang W X, Qu L, Chen C, Liu D S, Zhang D Q and Zhu D B 2008 J. Phys. Chem. B 112 6893
[24]	Sun Y W, Liu H J, Xu L J, Wang L Y, Fan Q H and Liu D S 2010 Langmuir 26 12496
[25]	Seeman N C 2003 Nature 421 427
[26]	Dhakal S, Schonhoft J D, Koirala D, Yu Z B, Basu S and Mao H B 2010 J. Am. Chem. Soc. 132 8991
[27]	Dhakal S, Lafontaine J L, Yu Z B, Koirala D and Mao H B 2012 PLoS One 7 e39271
[28]	Choi J K and Majima T 2013 Photochem. Photobiol. 89 513
[29]	Choi J K, Kim S Y, Tachikawa T, Fujitsuka M and Majima T 2011 J. Am. Chem. Soc. 133 16146
[30]	Zhang X H, Li M, Wang Y T and Ouyang Z C 2014 Chin. Phys. B 23 020702
[31]	Chen H, Fu H X, Zhu X Y, Cong P W, Nakamura F and Yan J 2011 Biophys. J. 100 517
[32]	Chen H, Zhu X Y, Cong P W, Sheetz M P, Nakamura F and Yan J 2011 Biophys. J. 101 1231
[33]	Smith S B, Cui Y J and Bustamante C 1996 Science 271 795
[34]	Cluzel P, Lebrun A, Heller C, Lavery R, Viovy J L, Chatenay D and Caron F 1996 Science 271 792
[35]	Fu H X, Chen H, Marko J F and Yan J 2010 Nucleic Acids Res. 38 5594
[36]	Cooper C L, Goulding A, Kayitmazer A B, Ulrich S, Stoll S, Turksen S, Yusa S, Kumar A and Dubin P L 2006 Biomacromolecules 7 1025
[37]	Cocco S, Yan J, Leger J F, Chatenay D and Marko J F 2004 Phys. Rev. E 70 011910
[38]	Anderson K L, Radford S E and Brockwell D J 2008 The Dynamical Response of Proteins under Force, in Handbook of Molecular Force Spectroscopy (New York: Springer) pp. 205-249
[39]	Lagarias J C, Reeds J A, Wright M H and Wright P E 1998 SIAM J. Optimiz 9 112
[40]	Chen C, Li M, Xing Y Z, Li Y M, Joedecke C C, Jin J, Yang Z Q and Liu D S 2012 Langmuir 28 17743
[41]	Modi S, Swetha M G, Goswami D, Gupta G D, Mayor S and Krishnan Y 2009 Nat. Nanotechnol. 4 325
[42]	Sharma J, Chhabra R, Yan H and Liu Y 2007 Chem. Commun. 5 477
[43]	Cloutier T E and Widom J 2004 Mol. Cell 14 355
[44]	Yan J and Marko J F 2004 Phys. Rev. Lett. 93 108108
[45]	Du Q, Smith C, Shiffeldrim N, Vologodskaia M and Vologodskii A 2005 Proc. Natl. Acad. Sci. 102 5397

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

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

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