Force-induced unfolding of human telomeric G-quadruplex: A steered molecular dynamics simulation study

Biochemical and Biophysical Research Communications

Volumn 379, Issue 1, 2009, Pages 70-75

  Li, Hui ^a,b   Cao, En hua ^b   Gisler, Thomas ^a  

^a UNIVERSITY OF KONSTANZ   (Germany)

^b INSTITUTE OF BIOPHYSICS   (China)

Author keywords

G quadruplex; Intermediate state; Single molecule force spectrum; Steered molecular dynamics simulation; Unfolding

Indexed keywords

DNA; GUANINE QUADRUPLEX; NUCLEIC ACID BASE; SUGAR PHOSPHATE;

ARTICLE; ENERGY; FORCE; GENE SEQUENCE; HUMAN; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROCESSING; SIMULATION; STRETCHING; TELOMERE;

BASE SEQUENCE; COMPUTER SIMULATION; DNA; G-QUADRUPLEXES; HUMANS; MECHANICAL PROCESSES; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; TELOMERE;

EID: 58149288068     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2008.12.006     Document Type: Article

References (29)

1. Gellert M., Lipsett M.N., and Davies D.R. Helix formation by guanylic acid. Proc. Natl. Acad. Sci. USA 48 (1962) 2013-2018
2. Shafer R.H., and Smirnov I. Biological aspects of DNA/RNA quadruplexes. Biopolymers 56 (2000) 209-227
3. Neidle S., and Read M.A. G-quadruplexes as therapeutic targets. Biopolymers 56 (2000) 195-208
4. Lane A.N., Chaires J.B., Gray R.D., and Trent J.O. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res. 36 (2008) 5482-5515
5. Mergny J.L., De Cian A., Ghelab A., Sacca B., and Lacroix L. Kinetics of tetramolecular quadruplexes. Nucleic Acids Res. 33 (2005) 81-94
6. 2+: stability, heat, and hydration. J. Am. Chem. Soc. 123 (2001) 10799-10804
7. Olsen C.M., Gmeiner W.H., and Marky L.A. Unfolding of G-quadruplexes: energetic, and ion and water contributions of G-quartet stacking. J. Phys. Chem. B 110 (2006) 6962-6969
8. +-induced folding of models of human telomeric DNA into G-quadruplex structures. Nucleic Acids Res. 36 (2008) 4191-4203
9. 4 containing the human telomeric repeat: evidence for A-tetrad formation from NMR and molecular dynamics simulations. Org. Biomol. Chem. 1 (2003) 1650-1656
10. Cavallari M., Calzolari A., Garbesi A., and Di Felice R. Stability and migration of metal ions in G4-wires by molecular dynamics simulations. J. Phys. Chem. B 110 (2006) 26337-26348
11. Stefl R., Cheatham T.E., Spackova N., Fadrna E., Berger I., Koca J., and Sponer J. Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophys. J. 85 (2003) 1787-1804
12. Fadrna E., Spackova N., Stefl R., Koca J., Cheatham T.E., and Sponer J. Molecular dynamics simulations of guanine quadruplex loops: advances and force field limitations. Biophys. J. 87 (2004) 227-242
13. Rueda M., Luque F.J., and Orozco M. G-quadruplexes can maintain their structure in the gas phase. J. Am. Chem. Soc. 128 (2006) 3608-3619
14. Sotomayor M., and Schulten K. Single-molecule experiments in vitro and in silico. Science 316 (2007) 1144-1148
15. Grater F., Shen J.H., Jiang H.L., Gautel M., and Grubmüller H. Mechanically induced titin kinase activation studied by force-probe molecular dynamics simulations. Biophys. J. 88 (2005) 790-804
16. Zlatanova J., and van Holde K. Single-molecule biology: what is it and how does it work?. Mol. Cell 24 (2006) 317-329
17. Jarzynski C. Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 78 (1997) 2690-2693
18. Hummer G., and Szabo A. Free energy reconstruction from nonequilibrium single-molecule pulling experiments. Proc. Natl. Acad. Sci. USA 98 (2001) 3658-3661
19. Van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., and Berendsen H.J.C. GROMACS: fast, flexible, and free. J. Comp. Chem. 26 (2005) 1701-1718
20. Sorin E.J., and Pande V.S. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys. J. 88 (2005) 2472-2493
21. Mahoney M.W., and Jorgensen L.W. A five-site model for liquid water the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys. 112 (2000) 8910-8922
22. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Nola A.D., and Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
23. Hess B., Bekker H., Berendsen H.J.C., and Fraaije J.G.E.M. LINCS: a linear constraint solver for molecular simulations. J. Comp. Chem. 18 (1997) 1463-1472
24. Darden T., York D., and Pedersen L. Particle mesh Ewald-an N·Log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
25. Parkinson G.N., Lee M.P.H., and Neidle S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417 (2002) 876-880
26. Ferrenberg A.M., and Swendsen R.H. Optimized Monte Carlo data analysis. Phys. Rev. Lett. 63 (1989) 1195-1198
27. Gardiner C.W. Handbook of Stochastic Methods (1990), Springer
28. Mashimo T., and Sugiyama H. Folding pathways of human telomeric hybrid G-quadruplex structure. Nucleic Acids Symp. Ser. 51 (2007) 239-240
29. Neuman K.C., and Nagy A. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat. Methods 5 (2008) 491-505