Theoretical study of overstretching DNA-RNA hybrid duplex

doi:10.1088/1674-1056/28/6/068701

中国物理B ›› 2019, Vol. 28 ›› Issue (6): 68701-068701.doi: 10.1088/1674-1056/28/6/068701

• INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY • 上一篇下一篇

Theoretical study of overstretching DNA-RNA hybrid duplex

Dong-Ni Yang(杨东尼), Zhen-Sheng Zhong(钟振声), Wen-Zhao Liu(刘文钊), Thitima Rujiralai, Jie Ma(马杰)

1 School of Physics, Sun Yat-sen University, Guangzhou 510275, China;
2 State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510006, China;
3 Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand

收稿日期:2019-03-11 修回日期:2019-04-08 出版日期:2019-06-05 发布日期:2019-06-05
通讯作者: Jie Ma E-mail:majie6@mail.sysu.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant No. 11674403), the Young Scientists Fund of the National Natural Science Foundation of China (Grant No. 31700809), the Fundamental Research Funds for the Central Universities (Grant No. 18lgzd16), and the Open Fund of the State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University.

Theoretical study of overstretching DNA-RNA hybrid duplex

Dong-Ni Yang(杨东尼)^1,2, Zhen-Sheng Zhong(钟振声)^1,2, Wen-Zhao Liu(刘文钊)^1,2, Thitima Rujiralai³, Jie Ma(马杰)^1,2

1 School of Physics, Sun Yat-sen University, Guangzhou 510275, China;
2 State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510006, China;
3 Department of Chemistry, Center of Excellence for Innovation in Chemistry, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand

Received:2019-03-11 Revised:2019-04-08 Online:2019-06-05 Published:2019-06-05
Contact: Jie Ma E-mail:majie6@mail.sysu.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant No. 11674403), the Young Scientists Fund of the National Natural Science Foundation of China (Grant No. 31700809), the Fundamental Research Funds for the Central Universities (Grant No. 18lgzd16), and the Open Fund of the State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University.

摘要/Abstract

摘要：

DNA-RNA hybrid (DRH) plays important roles in many biological processes. Here, we use a thermodynamic theory to analyze the free energy and unpeeling properties of the overstretching transition for the DRH molecule and compare the results with double-helix DNA. We report that the RNA strand of DRH is easier to get unpeeled than the DNA strand while the difficulty in unpeeling the double helix DNA lies in between. We also investigate the sequence effect, such as GC content and purine content, on the properties of unpeeling the DRH. Further, to study the temperature effect, the force-temperature phase diagram of DRH and DNA are calculated and compared. Finally, using a kinetic model, we calculate the force-extension curves in the DRH stretching and relaxation process under different pulling rates and temperatures. Our results show that both pulling rate and temperature have important influences on the stretching and relaxation kinetics of unpeeling the DRH. Putting all these results together, our work provides a comprehensive view of both the thermodynamics and kinetics in DRH overstretching.

关键词: DNA-RNA hybrid, mechanical properties, overstretching, thermodynamic and kinetic model

Abstract:

Key words: DNA-RNA hybrid, mechanical properties, overstretching, thermodynamic and kinetic model

中图分类号: (Nucleic acids)

87.14.G-

87.15.La (Mechanical properties) 87.15.A- (Theory, modeling, and computer simulation) 87.10.Pq (Elasticity theory)

杨东尼, 钟振声, 刘文钊, Thitima Rujiralai, 马杰. Theoretical study of overstretching DNA-RNA hybrid duplex[J]. 中国物理B, 2019, 28(6): 68701-068701.

Dong-Ni Yang(杨东尼), Zhen-Sheng Zhong(钟振声), Wen-Zhao Liu(刘文钊), Thitima Rujiralai, Jie Ma(马杰). Theoretical study of overstretching DNA-RNA hybrid duplex[J]. Chin. Phys. B, 2019, 28(6): 68701-068701.

参考文献 32

[1]	Aguilera A and García-Muse T 2012 Mol. Cell 46 115 doi: 10.1016/j.molcel.2012.04.009
[2]	Wright Addison V, Nuñez James K and Doudna Jennifer A 2016 Cell 164 29 doi: 10.1016/j.cell.2015.12.035
[3]	Ogawa T and Okazaki T 1980 Ann. Rev. Biochem. 49 421 doi: 10.1146/annurev.bi.49.070180.002225
[4]	Santos-Pereira J M and Aguilera A 2015 Nat. Rev. Genet. 16 583 doi: 10.1038/nrg3961
[5]	Fazzio T G 2016 Transcription 7 121 doi: 10.1080/21541264.2016.1198298
[6]	Lu W T, Hawley B R, Skalka G L, Baldock R A, Smith E M, Bader A S, Malewicz M, Watts F Z, Wilczynska A and Bushell M 2018 Nature Commun. 9 532 13
[7]	Grunseich C, Wang I X, Watts J A, Burdick J T, Guber R D, Zhu Z, Bruzel A, Lanman T, Chen K, Schindler A B, Edwards N, Ray-Chaudhury A, Yao J, Lehky T, Piszczek G, Crain B, Fischbeck K H and Cheung V G 2018 Mol. Cell 69 426 doi: 10.1016/j.molcel.2017.12.030
[8]	Toubiana S and Selig S 2018 FEBS J. 285 2552 doi: 10.1111/febs.14464
[9]	Biroccio A, Leonetti C and Zupi G 2003 Oncogene 22 6579 doi: 10.1038/sj.onc.1206812
[10]	Groh M and Gromak N 2014 Plos Genetics 10 e1004630
[11]	Zhang C, Fu H, Yang Y, Zhou E, Tan Z, You H and Zhang X 2019 Biophys. J. 116 196 doi: 10.1016/j.bpj.2018.12.005
[12]	Huang Y, Chen C and Russu I M 2009 Biochemistry 48 3988 doi: 10.1021/bi900070f
[13]	Noy A, Perez A, Marquez M, Luque F J and Orozco M 2005 J. Am. Chem. Soc. 127 4910 doi: 10.1021/ja043293v
[14]	Lesnik E A and Freier S M 1995 Biochemistry 34 10807 doi: 10.1021/bi00034a013
[15]	Ratmeyer L, Vinayak R, Zhong Y Y, Zon G and Wilson W D 1994 Biochemistry 33 5298 doi: 10.1021/bi00183a037
[16]	Gyi J I, Gao D Q, Conn G L, Trent J O, Brown T and Lane A N 2003 Nucleic Acids Res. 31 2683 doi: 10.1093/nar/gkg356
[17]	Xiong Y and Sundaralingam M 2000 Nucleic Acids Res. 28 2171 doi: 10.1093/nar/28.10.2171
[18]	Gonzalez C, Stec W, Kobylanska A, Hogrefe R I, Reynolds M and James T L 1994 Biochemistry 33 11062 doi: 10.1021/bi00203a002
[19]	Hall K B and McLaughlin L W 1991 Biochemistry 30 10606 doi: 10.1021/bi00108a002
[20]	Cocco S, Yan J, Leger J F, Chatenay D and Marko J F 2004 Phys. Rev. E 70 011910 doi: 10.1103/PhysRevE.70.011910
[21]	O'Brien E J and MacEwan A W 1970 J. Mol. Biol. 48 243 doi: 10.1016/0022-2836(70)90159-2
[22]	Herrero-Galan E, Fuentes-Perez M E, Carrasco C, Valpuesta J M, Carrascosa J L, Moreno-Herrero F and Arias-Gonzalez J R 2013 J. Am. Chem. Soc. 135 122 doi: 10.1021/ja3054755
[23]	Bizarro C V, Alemany A and Ritort F 2012 Nucleic Acids Res. 40 6922 doi: 10.1093/nar/gks289
[24]	Sugimoto N, Nakano S-i, Katoh M, Matsumura A, Nakamuta H, Ohmichi T, Yoneyama M and Sasaki M 2002 Biochemistry 34 11211
[25]	King G A, Gross P, Bockelmann U, Modesti M, Wuite G J L and Peterman E J G 2013 Proc. Nat. Acad. Sci. USA 110 3859 doi: 10.1073/pnas.1213676110
[26]	Suresh G and Priyakumar U D 2014 Phys. Chem. Chem. Phys. 16 18148 doi: 10.1039/C4CP02478H
[27]	Hantz E, Larue V, Ladam P, Moyec L L, Gouyette C and Dinh T H 2001 Int. J. Biol. Macromol. 28 273 doi: 10.1016/S0141-8130(01)00123-4
[28]	Zhang X, Chen H, Le S, Rouzina I, Doyle P S and Yan J 2013 Proc. Natl. Acad. Sci. USA 110 3865 doi: 10.1073/pnas.1213740110
[29]	Chen H, Fu H X and Koh C G 2008 J. Comput. Theor. Nanosci. 5 1381 doi: 10.1166/jctn.2008.2577
[30]	Bockelmann U, Essevaz-Roulet B and Heslot F 1997 Phys. Rev. Lett. (USA) 79 4489
[31]	Belotserkovskii B P, Tornaletti S, D'Souza A D and Hanawalt P C 2018 DNA Repair 71 69 doi: 10.1016/j.dnarep.2018.08.009
[32]	Drolet M, Broccoli S, Rallu F, Hraiky C, Fortin C, Masse E and Baaklini I 2003 Front. Biosci. 8 D210

Theoretical study of overstretching DNA-RNA hybrid duplex

Theoretical study of overstretching DNA-RNA hybrid duplex

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