Citation: WU Shao-Gui, FENG Dan. Free Energy Calculation for Base Pair Dissociation in a DNA Duplex[J]. Acta Physico-Chimica Sinica, ;2016, 32(5): 1282-1288. doi: 10.3866/PKU.WHXB201602185 shu

Free Energy Calculation for Base Pair Dissociation in a DNA Duplex

WU Shao-Gui ^1,2,, ,
FENG Dan ¹

1.
1 College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, P. R. China;
2.
2 State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, P. R. China

Corresponding author: WU Shao-Gui,
Received Date: 16 December 2015
Available Online: 16 February 2016
Fund Project: 国家自然科学基金(11405113) (11405113)四川省科技厅项目(2010JY0122) (2010JY0122)四川师范大学科学研究基金(10MSL02)资助 (10MSL02)

DNA is the main genetic material for living organisms including many viruses. DNA duplex, coded with A＝T and G≡C base pairs, is well suited for biological information storage. The interactions between two bases in a base pair contribute to the stability of DNA duplex, and are further related to gene replication and transcription. In this study, we use all-atom Molecular dynamics (MD) simulations combined with Umbrella sampling (US) method to determine the free energy profiles and explore the molecular details for base pair dissociations. Four groups of DNA duplexes with different sequences have been constructed and a total of 4.3 μs MD simulations have been carried out. In the potential of mean force (PMF) profile for G≡C base pair dissociation (denoted as PMF-PGC), we observed three peaks, which correspond to the three moments G≡C base pair loses its three hydrogen bonds respectively. Differently, A＝T base pair loses its two hydrogen bonds within a very short time. As a result, only one hydrogen bond rupture peak was observed in its PMF curve (denoted as PMF-PAT). Compared with PMF-PAT, the overall free energy barrier in PMF-PGC is higher, which is due to the better stability of G≡C than A＝T. In the latter sections of both PMFs, free energies are still increasing, which is mainly resulted from the rigidity of DNA duplex backbone. We have also investigated the impact of neighboring base pairs on the stability of middle one. It is found that neighboring G≡C base pairs increase the stability of A＝T base pair while neighboring C≡G base pairs reduce the stability of A＝T base pair. Additionally, neighboring T＝A base pairs have little influence on the stability of A＝T base pair.
- Potential of mean force,
- Hydrogen bond,
- Molecular dynamics simulation,
- Umbrella sampling
1. [1]
  (1) Cressey, D. Nature 2015, 526 (7573), 307. doi: 10.1038/nature.2015.18515
2. [2]
  (2) Peyrard, M.; Bishop, A. R. Phys. Rev. Lett. 1989, 62 (23), 2755. doi: 10.1103/PhysRevLett.62.2755
3. [3]
  (3) Santalucia, J. Proc. Natl. Acad. Sci. U. S. A. 1998, 95 (4), 1460. doi: 10.1073/pnas.95.4.1460
4. [4]
  (4) Wu, S. G.; Gao, X. T.; Li, Q.; Liao, J.; Xu, C. G. Acta Phys. -Chim. Sin. 2015, 31 (9), 1803. [伍绍贵, 高晓彤, 李权, 廖杰, 徐成刚. 物理化学学报, 2015, 31 (9), 1803]. doi: 10.3866/PKU.WHXB201508062
5. [5]
  (5) Meng, X. M.; Zhang, S. L.; Zhang, Q. G. Acta Phys. -Chim. Sin. 2016, 32 (2), 436. [孟现美, 张少龙, 张庆刚. 物理化学学报, 2016, 32 (2), 436]. doi: 10.3866/PKU.WHXB201511302
6. [6]
  (6) Silva, D. A.; Weiss, D. R.; Avila, F. P.; Da, L. T.; Levitt, M.; Wang, D.; Huang, X. Proc. Natl. Acad. Sci. U. S. A. 2014, 111 (21), 7665. doi: 10.1073/pnas.1315751111
7. [7]
  (7) Mackerell, A. D.; Banavali, N. K. J. Comput. Chem. 2000, 21 (2), 105. doi: 10.1002/(SICI)1096-987X(20000130)21:2<105::AID-JCC3>3.0.CO;2-P
8. [8]
  (8) Ge, Z.; Li, Q.; Wang, Y. J. Chem. Theory Comput. 2014, 10 (7), 2751. doi: 10.1021/ct500194s
9. [9]
  (9) Delemotte, L.; Tarek, M. J. Membr. Biol. 2012, 245 (9), 531. doi: 10.1007/s00232-012-9434-6
10. [10]
  (10) Da, L.; Avila, F. P.; Wang, D.; Huang, X. PLoS Comput. Biol. 2013, 9 (4), e1003020. doi: 10.1371/journal.pcbi.1003020
11. [11]
  (11) Yang, L. J.; Gao, Y. Q. Acta Phys. -Chim. Sin. 2016, 32 (1), 313. [杨立江, 高毅勤. 物理化学学报, 2016, 32 (1), 313.] doi: 10.3866/PKU.WHXB201512161
12. [12]
  (12) Kutzner, C.; Van Der Spoel, D.; Fechner, M.; Lindahl, E.; Schmitt, U.W.; De Groot, B. L.; Grubmüller, H. J. Comput. Chem. 2007, 28 (12), 2075. doi: 10.1002/jcc.20703
13. [13]
  (13) Pronk, S.; Páll, S.; Schulz, R.; Larsson, P.; Bjelkmar, P.; Apostolov, R.; Shirts, M. R.; Smith, J. C.; Kasson, P. M.; van der Spoel, D. Bioinformatics 2013, 29 (7), 845. doi: 10.1093/bioinformatics/btt055
14. [14]
  (14) Hess, B.; Kutzner, C.; Van Der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4 (3), 435. doi: 10.1021/ct700301q
15. [15]
  (15) Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Biophys. J. 2007, 92 (11), 3817. doi: 10.1529/biophysj.106.097782
16. [16]
  (16) Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13 (8), 952. doi: 10.1002/jcc.540130805
17. [17]
  (17) Ito, H. O.; Soutome, S. M. J. Microbiol. Methods 2003, 55 (1), 29. doi: 10.1016/S0167-7012(03)00111-8
18. [18]
  (18) Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103 (19), 8577. doi: 10.1063/1.470117
19. [19]
  (19) Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98 (12), 10089. doi: 10.1063/1.464397
20. [20]
  (20) Berendsen, H. J.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. J. Chem. Phys. 1984, 81 (8), 3684. doi: 10.1063/1.448118
21. [21]
  (21) Bussi, G.; Donadio, D.; Parrinello, M. J. Chem. Phys. 2007, 126 (1), 014101. doi: 10.1063/1.2408420
22. [22]
  (22) Zimmermann, K. J. Comput. Chem. 1991, 12 (3), 310. doi: 10.1002/jcc.540120305
23. [23]
  (23) Isralewitz, B.; Gao, M.; Schulten, K. Curr. Opin. Struc. Biol. 2001, 11, 224. doi: 10.1016/S0959-440X(00)00194-9
24. [24]
  (24) Hub, J. S.; De Groot, B. L.; Van Der Spoel, D. J. Chem. Theory Comput. 2010, 6 (12), 3713. doi: 10.1021/ct100494z
25. [25]
  (25) Huang, X.; Wang, D.; Weiss, D. R.; Bushnell, D. A.; Kornberg, R. D.; Levitt, M. Proc. Natl. Acad. Sci. U. S. A. 2010, 107 (36), 15745. doi: 10.1073/pnas.1009898107
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