Theoretical study of overstretching DNA–RNA hybrid duplex
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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 forcetemperature 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.
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 forcetemperature 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.
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 forcetemperature 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.
引文
[1] Aguilera A and Garcia-Muse T 2012 Mol. Cell 46 115
[2] Wright Addison V, Nunez James K and Doudna Jennifer A 2016 Cell164 29
[3] Ogawa T and Okazaki T 1980 Ann. Rev. Biochem. 49 421
[4] Santos-Pereira J M and Aguilera A 2015 Nat. Rev. Genet. 16 583
[5] Fazzio T G 2016 Transcription 7 121
[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, RayChaudhury A, Yao J, Lehky T, Piszczek G, Crain B, Fischbeck K H and Cheung V G 2018 Mol. Cell 69 426
[8] Toubiana S and Selig S 2018 FEBS J. 285 2552
[9] Biroccio A, Leonetti C and Zupi G 2003 Oncogene 22 6579
[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 2019Biophys. J. 116 196
[12] Huang Y, Chen C and Russu I M 2009 Biochemistry 48 3988
[13] Noy A, Perez A, Marquez M, Luque F J and Orozco M 2005 J. Am.Chem. Soc. 127 4910
[14] Lesnik E A and Freier S M 1995 Biochemistry 34 10807
[15] Ratmeyer L, Vinayak R, Zhong Y Y, Zon G and Wilson W D 1994Biochemistry 33 5298
[16] Gyi J I, Gao D Q, Conn G L, Trent J O, Brown T and Lane A N 2003Nucleic Acids Res. 31 2683
[17] Xiong Y and Sundaralingam M 2000 Nucleic Acids Res. 28 2171
[18] Gonzalez C,Stec W, Kobylanska A,Hogrefe R I,Reynolds M and James T L 1994 Biochemistry 33 11062
[19] Hall K B and McLaughlin L W 1991 Biochemistry 30 10606
[20] Cocco S, Yan J, Leger J F, Chatenay D and Marko J F 2004 Phys. Rev.E70011910
[21] O'Brien E J and MacEwan A W 1970 J. Mol. Biol. 48 243
[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
[23] Bizarro C V, Alemany A and Ritort F 2012 Nucleic Acids Res. 40 6922
[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
[26] Suresh G and Priyakumar U D 2014 Phys. Chem. Chem. Phys. 1618148
[27] Hantz E, Larue V, Ladam P, Moyec L L, Gouyette C and Dinh T H2001 Int. J. Biol. Macromol. 28 273
[28] Zhang X, Chen H, Le S, Rouzina I, Doyle P S and Yan J 2013 Proc.Natl. Acad. Sci. USA 110 3865
[29] Chen H, Fu H X and Koh C G 2008 J. Comput. Theor. Nanosci. 5 1381
[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 2018DNA Repair 71 69
[32] Drolet M, Broccoli S, Rallu F, Hraiky C, Fortin C, Masse E and Baaklini I 2003 Front. Biosci. 8 D210
[2] Wright Addison V, Nunez James K and Doudna Jennifer A 2016 Cell164 29
[3] Ogawa T and Okazaki T 1980 Ann. Rev. Biochem. 49 421
[4] Santos-Pereira J M and Aguilera A 2015 Nat. Rev. Genet. 16 583
[5] Fazzio T G 2016 Transcription 7 121
[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, RayChaudhury A, Yao J, Lehky T, Piszczek G, Crain B, Fischbeck K H and Cheung V G 2018 Mol. Cell 69 426
[8] Toubiana S and Selig S 2018 FEBS J. 285 2552
[9] Biroccio A, Leonetti C and Zupi G 2003 Oncogene 22 6579
[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 2019Biophys. J. 116 196
[12] Huang Y, Chen C and Russu I M 2009 Biochemistry 48 3988
[13] Noy A, Perez A, Marquez M, Luque F J and Orozco M 2005 J. Am.Chem. Soc. 127 4910
[14] Lesnik E A and Freier S M 1995 Biochemistry 34 10807
[15] Ratmeyer L, Vinayak R, Zhong Y Y, Zon G and Wilson W D 1994Biochemistry 33 5298
[16] Gyi J I, Gao D Q, Conn G L, Trent J O, Brown T and Lane A N 2003Nucleic Acids Res. 31 2683
[17] Xiong Y and Sundaralingam M 2000 Nucleic Acids Res. 28 2171
[18] Gonzalez C,Stec W, Kobylanska A,Hogrefe R I,Reynolds M and James T L 1994 Biochemistry 33 11062
[19] Hall K B and McLaughlin L W 1991 Biochemistry 30 10606
[20] Cocco S, Yan J, Leger J F, Chatenay D and Marko J F 2004 Phys. Rev.E70011910
[21] O'Brien E J and MacEwan A W 1970 J. Mol. Biol. 48 243
[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
[23] Bizarro C V, Alemany A and Ritort F 2012 Nucleic Acids Res. 40 6922
[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
[26] Suresh G and Priyakumar U D 2014 Phys. Chem. Chem. Phys. 1618148
[27] Hantz E, Larue V, Ladam P, Moyec L L, Gouyette C and Dinh T H2001 Int. J. Biol. Macromol. 28 273
[28] Zhang X, Chen H, Le S, Rouzina I, Doyle P S and Yan J 2013 Proc.Natl. Acad. Sci. USA 110 3865
[29] Chen H, Fu H X and Koh C G 2008 J. Comput. Theor. Nanosci. 5 1381
[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 2018DNA Repair 71 69
[32] Drolet M, Broccoli S, Rallu F, Hraiky C, Fortin C, Masse E and Baaklini I 2003 Front. Biosci. 8 D210