This article describes how classical molecular simulation methods are being used to gain a molecular-level understanding of the interaction mechanisms responsible for DNA–ligand recognition, and that govern the response of DNA to ligand binding. Case studies using a variety of different ligands—including small pharmaceutical drugs, proteins and lipids—are used to illustrate the power of modern molecular dynamics simulation methods for understanding how we may control the function and structure of DNA.
LevyG. C., CraikD. J., KumarA., and LondonR. E.1983. Biopolymers, 22, 2703–2726, Kollman, P., Keepers, J. W. and Weiner, P. 1982. Biopolymers, 21, 2345-2376.
2.
BeveridgeD.L., SwaminathanS., RavishankarG., WithkaJ.M., and SrinivasanJ.1993. In Water and Biological Molecules, ed. WesthofE., pp 165–225New York/London: Macmillan.
3.
BeveridgeD.L., and RavishankarG.1994. Curr. Opin. Struct. Biol., 4, 246–55.
4.
MillerJ.L., CheathamT.E.III, and KollmanP.A.1999. In Oxford Handbook of Nucleic Acid Structure, ed. NeidleS., pp 95–115. Oxford University Press.
5.
CheathamT.E.III, MillerJ.L., FoxT., DardenT.A., and KollmanP.A.1995. J. Am. Chem. Soc., 117, 4193–4194.
6.
RealA. N., and GreenallR. J.2004. J. Biomol. Struct. Dyn., 21, 469–487.
7.
WrightJ. D., NoskovS. Y., and LimC.2002. Nucleic Acids Res., 30, 1563–1574
8.
CheathamT. E., and YoungM. A.2000. Biopolymers, 56, 232–256.
CollinsJ. G., ShieldsT. P., and BartonJ. K.1994. J. Am. Chem. Soc., 116, 9840–9846.
51.
HiortC., NordenB., and RodgerA.1990. J. Am. Chem. Soc., 112, 1971–1982.
52.
HaworthI. S., ElcockA. H., RodgerA., and RichardsW. G., 1991. J. Biomol. Struct. Dyn., 9, 553–569
53.
SchlagE. W., SheuS. Y., YangD. Y., SelzleH. L., and LinS. H.2000. Proc.Natl.Acad.Sci.U.S.A., 97, 1068–1072.
54.
CogganZ. M., HaworthI. S., BatesP. J., RobinsonA., and RodgerA.1999. Inorg. Chem., 38, 4486–4497.
55.
HannonM., MeistermannI., IsaacC. J., RodgerA., MorenoV., PrietoM. J., SlettenE., and MoldrheimE.2001. J. Inorg. Biochem., 86, 56–56.
56.
MeistermannI., MorenoV., PrietoM. J., MoldrheimE., SlettenE., KhalidS., RodgerP. M., PeberdyJ. C., IsaacC. J., RodgerA., and HannonM. J.2002. Proc. Nat. Acad. Sci., 99, 5069–5074.
57.
MeistermannI., RodgerA., HannonM. J., MorenoV., PrietoM. J., SlettenE., and MoldrheimE., 2001. J. Inorg. Biochem., 86, 335–335.
58.
MoldrheimE., HannonM. J., MeistermannI., RodgerA., and SlettenE.2002. J. Biol. Inorg. Chem., 7, 770–780.
59.
ZambleD. B., and LippardS. J.1999. In Cisplatin: Chemistry and Biochemistry of a Leading Anticancer Drug, LippertB., ed., pp. 73–110, Verlag Helvetica Chimica Acta, Zürich.
60.
FouchetM. H., GuittetE., CognetJ. A. H., KozelkaJ., GauthierC., LeBretM., ZimmermannK., and ChottardJ. C.1997. J. Biol. Inorg. Chem., 2, 83–92.
61.
ScheeffE. D., BriggsJ. M., and HowellS. B.1999. Molec. Pharmacol., 56, 633–643.
62.
KozelkaJ., SavinelliR., BerthierG., FlamentJ. P., and LaveryR.1993. J. Comp. Chem., 14, 45–53.
63.
BruhnS. L., PilP. M., EssigmanJ. M., HousmanD. E., and LippardS. J.1992. Proc. Natl Acad. Sci. USA, 89, 2307–2311.
64.
PayetD., HillischA., LoweN., DiekmannS., and TraversA.1999. J. Mol. Biol, 294, 79–91.
65.
TakaharaP.M., FrederickC.A., and LippardS.J.1996. Nature (Lond), 377, 649–652.
66.
Elizondo-RiojasM. A., and KozelkaJ.2001. J. Mol. Biol, 314, 1227–1243.
67.
FoloppeN., and MacKerellA. D.2000. J. Comput. Chem., 21, 86–104.
68.
CheathamT. E., CieplakP., and KollmanP. A.1999. J. Biomol. Struct. Dyn., 16, 845–862.
69.
StockerU., and van GunsterenW. F.2000. Proteins-Structure Function and Genetics, 40, 145–153.
70.
RoxstromG., VelazquezI., PaulinoM., and TapiaO.1998. J. Phys. Chem. B, 102, 1828–1832.
71.
DauraX., OlivaB., QuerolE., AvilesF. X., and TapiaO.1996. Proteins-Structure Function and Genetics, 25, 89–103.
72.
TsuiV., RadhakrishnanI., WrightP. E., and CaseD. A.2000. J. Mol. Biol, 302, 1101–1117.
73.
MarcoE., Garcia-NietoR., and GagoF.2003. J. Mol. Biol, 328, 9–32.
74.
WibowoF.R., RauchC., TriebM., WellenzohnB., and LiedlK.R.2004. Biopolymers, 73, 668–681.
75.
OtwinowskiZ., SchevitzR. W., ZhangR. G., LawsonC. L., JoachimiakA., MarmorsteinR. Q., LuisiB. F., and SiglerP. B.1988. Nature (Lond), 335.321–329.
76.
MulliganR.1993. Science, 260, 926–932.
77.
FelgnerP.L., GadekT.R., HolmM., RomanR., ChanH.W., WenzM., NorthrpJ.P., RingoldG.M., and DanielsonM.1987. Proc. Natl. Acad. Sci., 84, 7413–7417.
78.
BandyopadhyayS., TarekM., and KleinM. L.1999. J. Phys. Chem. B, 103, 10075–10080.
