Improved data analysis method of single-molecule experiments based on probability optimization

doi:10.1088/1674-1056/27/1/018703

Abstract To extract the dynamic parameters from single molecule manipulation experiments, usually lots of data at different forces need to be recorded. But the measuring time of a single molecule is limited due to breakage of the tether or degradation of the molecule. Here we propose a data analysis method based on probability maximization of the recorded time trace to extract the dynamic parameters from a single measurement. The feasibility of this method was verified by dealing with the simulation data of a two-state system. We also applied this method to estimate the parameters of DNA hairpin folding and unfolding dynamics measured by a magnetic tweezers experiment.

Keywords: probability optimization Bell's model DNA hairpin single molecule manipulation

Received: 09 October 2017
Revised: 20 October 2017
Accepted manuscript online:

PACS:	87.80.Nj	(Single-molecule techniques)
	82.37.Rs	(Single molecule manipulation of proteins and other biological molecules)
	87.15.A-	(Theory, modeling, and computer simulation)
	02.50.-r	(Probability theory, stochastic processes, and statistics)

Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 11474237 and 11574310) and the 111 Project, China (Grant No. B16029).

Corresponding Authors: Hu Chen
E-mail: chenhu@xmu.edu.cn

Cite this article:

Weili Zhai(翟伟利), Guohua Yuan(袁国华), Chao Liu(刘超), Hu Chen(陈虎) Improved data analysis method of single-molecule experiments based on probability optimization 2018 Chin. Phys. B 27 018703

[1]	Woodside M T, Behnke-Parks W M, Larizadeh K, Travers K, Herschlag D and Block S M 2006 Proc. Natl. Acad. Sci. USA 103 6190
[2]	Chen H, Yuan G, Winardhi R S, Yao M, Popa I, Fernandez J M and Yan J 2015 J. Am. Chem. Soc. 137 3540
[3]	Neuman K C and Nagy A 2008 Nat. Methods 5 491
[4]	Yuan G, Le S, Yao M, Qian H, Zhou X, Yan J and Chen H 2017 Angew. Chem. Int. Ed. Engl. 56 5490
[5]	Chen H, Zhu X, Cong P, Sheetz M P, Nakamura F and Yan J 2011 Biophys. J. 101 1231
[6]	Cecconi C, Shank E A, Bustamante C and Marqusee S 2005 Science 309 2057
[7]	Liu C, Zhai W, Gong H, Liu Y and Chen H 2017 Chem. Phys. Lett. 678 35
[8]	Carrion-Vazquez M, Oberhauser A F, Fowler S B, Marszalek P E, Broedel S E, Clarke J and Fernandez J M 1999 Proc. Natl. Acad. Sci. USA 96 3694
[9]	Cao Y, Lam C, Wang M and Li H 2006 Angew. Chem. Int. Ed. Engl. 45 642
[10]	Bell G I 1978 Science 200 618
[11]	Xu Y, Chen H, Qu Y J, Efremov A K, Li M, Ou-Yang Z C, Liu D S and Yan J 2014 Chin. Phys. B 23 68702
[12]	Ran S Y, Sun B and Li M 2007 Chin. Phys. Lett. 36 228
[13]	Chen H, Fu H, Zhu X, Cong P, Nakamura F and Yan J 2011 Biophys. J. 100 517
[14]	Zheng H Z, Nong D G and Li M 2013 Chin. Phys. Lett. 30 118702
[15]	Smith S B, Cui Y and Bustamante C 1996 Science 271 795
[16]	Zhang X, Chen H, Fu H, Doyle P S and Yan J 2012 Proc. Natl. Acad. Sci. USA 109 8103
[17]	Strick T R, Allemand J F, Bensimon D, Bensimon A and Croquette V 1996 Science 271 1835
[18]	Dudko O K, Hummer G and Szabo A 2008 Proc. Natl. Acad. Sci. USA 105 15755

[1]	Single-molecular methodologies for the physical biology of protein machines Shuang Wang(王爽), Ying Lu(陆颖), and Ming Li(李明). Chin. Phys. B, 2022, 31(12): 128702.
[2]	New insight into the mechanism of DNA polymerase I revealed by single-molecule FRET studies of Klenow fragment Rokshana Parvin, Qi Jia(贾棋), Jianbing Ma(马建兵), Chunhua Xu(徐春华), Ying Lu(陆颖), Fangfu Ye(叶方富), and Ming Li(李明). Chin. Phys. B, 2022, 31(8): 088701.
[3]	Probing conformational change of T7 RNA polymerase and DNA complex by solid-state nanopores Xin Tong(童鑫), Rui Hu(胡蕊), Xiaoqing Li(李晓晴), Qing Zhao(赵清). Chin. Phys. B, 2018, 27(11): 118705.
[4]	Interaction between human telomeric G-quadruplexes characterized by single molecule magnetic tweezers Yi-Zhou Wang(王一舟), Xi-Miao Hou(侯锡苗), Hai-Peng Ju(车海鹏), Xue Xiao(肖雪), Xu-Guang Xi(奚绪光), Shuo-Xing Dou(窦硕星), Peng-Ye Wang(王鹏业), Wei Li(李伟). Chin. Phys. B, 2018, 27(6): 068701.
[5]	Protein-membrane interactions investigated with surface-induced fluorescence attenuation Li Ma(马丽), Ying Li(李颖), Ming Li(李明), Shuxin Hu(胡书新). Chin. Phys. B, 2017, 26(12): 128708.
[6]	Mechano-chemical selections of two competitive unfolding pathways of a single DNA i-motif 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). Chin. Phys. B, 2014, 23(6): 068702.

No Suggested Reading articles found!

Viewed

Full text

Abstract

Cited

Metrics
Related Articles

Improved data analysis method of single-molecule experiments based on probability optimization

Cite this article:

Online attention