References
- E.K. Wilson, Chem. Eng. 85, 47 (2007).
- P. Kovacic and R.S. Pozos, J. Recept. Signal Transduct. 27, 261 (2007).
- L. Ma, N.K. Sundlass, R.T. Raines, and Q. Cui, Biochemistry 50, 266 (2011).
- L.M. Pegrama, T. Wendorffa, R. Erdmanna, I. Shkela, D. Bellissimoa, D.J. Felitskya, and M.T. Record, Jr,Proc. Natl. Acad. Sci. U.S.A. 107, 7716 (2010).
- W.S. Kontur, M.W. Capp, T.J. Gries, R.M. Saecker, and M.T. Record, Jr,Biochemistry 49, 4361 (2010).
- P. Bernado, Proc. Natl. Acad. Sci. U.S.A. 102, 17002 (2005).
- M.G. Cacace, E.M. Landau, and J.J. Ramsden, Q. Rev. Biophys. 3, 241 (1997).
- R.L. Baldwin, Biophys. J. 71, 2056 (1996).
- P.H. von Hippel and K.Y. Wong, Science 145, 577 (1964).
- P. Kovacic, J. Electrostat. 66, 124 (2008).
- J.D. Smith, R.J. Saykally, and P.L. Geissler, J. Am. Chem. Soc. 129, 13847 (2007).
- N.C. Seeman, Nature (London) 421, 427 (2003).
- Y. Lu and J. Liu, Curr. Opin. Biotechnol. 17, 580 (2006).
- T. Liedl and F.C. Simmel, Nano Lett. 5, 1894 (2005).
- P.A. Wiggins, T. van der Heijden, F. Moreno-Herrero, A. Spakowitz, R. Phillips, J. Widom, C. Dekker, and P.C. Nelson, Nature Nanotechnol. 1, 137 (2006).
- Y. Santoso, C.M. Joyce, O. Potapova, L. Le Reste, J. Hohlbein, J.P. Torella, N.D.F. Grindley, and A.N. Kapanidis, Proc. Natl. Acad. Sci. U.S.A. 107, 715 (2010).
- A. Tsuji and K. Yoshikawa, J. Am. Chem. Soc. 132, 12464 (2010).
- S. Johansen, N. Megger, D. Bohme, R.K.O. Sigel, and J. Muller, Nature Chem. 2, 229 (2010).
- Y. Sannohe, M. Endo, Y. Katsuda, K. Hidaka, and H. Sugiyama, J. Am. Chem. Soc. 132, 16311 (2010).
- J. Geng, C. Zhao, J. Ren, and X. Qu, Chem. Commun. 46, 7187 (2010).
- S. Pal, P.K. Maiti, and B. Bagchi, J. Chem. Phys. 125, 234903 (2006).
- H.R. Drew and R.E. Dickerson, J. Mol. Biol. 151, 535 (1981).
- H. Ikeda, R. Fernandez, J.J. Barchi, Jr., X. Huang, and V.E. Marquez, Nucleic Acids Res. 26, 2237 (1998).
- F.J. Solis and M.O. de la Cruz, J. Chem. Phys. 112, 2030 (2000).
- A.G. Cherstvy, J. Chem. Phys. 123, 116101 (2005).
- M. Tsunoda, J. Kondo, N. Karino, Y. Ueno, A. Matsuda, and A. Takenaka, Biophys. Chem. 95, 227 (2002).
- K.J. McConnell and D.L. Beveridge, J. Mol. Biol. 304, 803 (2000).
- L. McFail-Isom, C.C. Sines, and L.D. Williams, Curr. Opin. Struct. Biol. 9, 298 (1999).
- N.V. Hud and M. Polak, Curr. Opin. Struct. Biol. 11, 293 (2001).
- M. Egli, Chem. Biol. 9, 277 (2002).
- V. Tereshko, G. Minasov, and M. Egli, J. Am. Chem. Soc. 121, 470 (1999).
- D. Watkins, S. Mohan, G.B. Koudelka, and L.D. Williams, J. Mol. Biol. 396, 1145 (2010).
- P. Varnal and K. Zakrzewska, Nucleic Acids Res. 32, 4269 (2004).
- Y. von Hansen, R.R. Netz, and M. Hinczewski, J. Chem. Phys. 132, 135103 (2010).
- X. Shui, L. McFail-Isom, G.G. Hu, and L.D. Williams, Biochemistry 37, 8341 (1998).
- V.P. Denisov and B. Halle, Proc. Natl. Acad. Sci. U.S.A. 97, 629 (2000).
- E. Stellwagen, Q. Dong, and N.C. Stellwagen, Biochemistry 46, 2050 (2007).
- R.C. DeMille, T.E. Cheatham, III, and V. Molinero, J. Phys. Chem. B 13, 132 (2011).
- X. Shen, B. Gu, S.A. Che, and F.S. Zhang, J. Chem. Phys. 135, 034509 (2011).
- M.A. Young, B. Jayaram, and D.L. Beveridge, J. Am. Chem. Soc. 119, 59 (1997).
- Y.H. Cheng, N. Korolev, and L. Nordenskiold, Nucleic Acids Res. 34, 686 (2006).
- J.F. Swisher, L.J. Su, M. Brenowitz, V.E. Anderson, and A.M. Pyle, J. Mol. Biol. 315, 297 (2002).
- G. Minasov, V. Tereshko, and M. Egli, J. Mol. Biol. 291, 83 (1999).
- Y.Q. Li, Q.R. Huang, T.F. Shi, and L.J. An, J. Chem. Phys. 125, 044902 (2006).
- B. Gu, F.S. Zhang, Z.P. Wang, and H.Y. Zhou, Phys. Rev. Lett. 100, 088104 (2008).
- B. Jayaram, J. Am. Chem. Soc. 120, 10629 (1998).
- A. Noy, A. Perez, C.A. Laughton, and M. Orozco, Nucleic Acids Res. 35, 3330 (2007).
- J.M. Vargason, K. Henderson, and P.S. Ho, Proc. Natl. Acad. Sci. U.S.A. 98, 7265 (2001).
- M. Moradi, V. Babin, C. Roland, and C. Sagui, Nucleic Acids Res. 41, 33 (2013).
- T.E. Cheatham III, M.F. Crowley, T. Fox, and P.A. Kollman, Proc. Natl. Acad. Sci. U.S.A. 94, 9626 (1997).
- J. Alejandre and R.M. Lynden-Bell, Mol. Phys. 105, 3029 (2007).
- T. Head-Gordon and R.M. Lynden-Bell, J. Chem. Phys. 128, 104506 (2008).
- S. Chatterjee, P.G. Debenedetti, F.H. Stillinger, and R.M. Lynden-Bell, J. Chem. Phys. 128, 124511 (2008).
- R.M. Lynden-Bell and P.G. Debenedetti, J. Phys. Chem. B 109, 6527 (2005).
- K. Toukan and A. Rahman, Phys. Rev. B 31, 2643 (1985).
- B.I. Schweitzer, T. Mikita, G.W. Kellogg, K.H. Gardner, and G.P. Beardsley, Biochemistry 33, 11460 (1994).
- K. Heinzinger, Phys. B 131, 196 (1985).
- D.S. Cerutti, C.F. Wong, and J.A. McCammon, Biopolymers 70, 391 (2003).
- N. Korolev and L. Nordenskiold, Biopolymers 86, 409 (2007).
- A.P. Lyubartsev and A. Laaksonen, J. Chem. Phys. 111, 11207 (1999).
- L. van Dam, A.P. Lyubartsev, A. Laaksonen, and L. Nordenskiold, J. Phys. Chem. B 102, 51 (1998).
- Z. Wang, W. Zhang, C. Wu, H. Lei, P. Ciplak, and Y. Duan, J. Comput. Chem. 27, 196 (2006).
- W. Yu, C.F. Wong, and J. Zhang, J. Phys. Chem. 100, 15280 (1996).
- W.D. Cornell, P. Cieplak, C.I. Bayly, I. Gould, K.M. Merz, Jr, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman, J. Am. Chem. Soc. 117, 5179 (1995).
- A. Perez, I. Marchan, D. Svozil, J. Sponer, T.E. Cheatham III, C.A. Laughton, and M. Orozco, Biophys. J. 92, 3817 (2007).
- L. Dai, Y. Mu, L. Nordenskiold, and J.R.C. van der Maarel1, Phys. Rev. Lett. 100, 118301 (2008).
- N.V. Prabhu, M. Panda, Q. Yang, and K.A. Sharp, J. Comput. Chem. 29, 1113 (2008).
- A.P. Lyubartsev and A. Laaksonen, Comput. Phys. Commun. 128, 565 (2000).
- R. Lohikoski, J. Timonen, and A. Laaksonen, Chem. Phys. Lett. 407, 1 (2005).
- M. Tuckerman and B.J. Berne, J. Chem. Phys. 97, 1989 (1992).
- D. Fincham, Mol. Simul. 13, 1 (1994).
- E. Stofer and R. Lavery, Biopolymers 34, 337 (1994).
- R.E. Dickerson, Nucleic Acids Res. 17, 1797 (1989).
- C.G. Kalodimos, Science 305, 386 (2004).
- S.N. Timasheff, Adv. Protein Chem. 51, 355 (1998).
- G. Karlstrom, Phys. Chem. Chem. Phys. 5, 3238 (2003).
- A.N. Real and R.J. Greenall, J. Mol. Model. 6, 654 (2000).
- D. Jose and D. Porschke, Nucleic Acids Res. 32, 2251 (2004).
- D. Jose and D. Porschke, J. Am. Chem. Soc. 127, 16120 (2005).
- M. Rueda, J. Am. Chem. Soc. 125, 8007 (2003).
- T.E. Cheatham III and P.A. Kollman, Structure 5, 1297 (1997).