DNA recognition studied by molecular simulations
Seminar Room 1, Newton Institute
In order to fulfill its biological role DNA has to interact with other molecules, ranging from small ligands to protein complexes. In many cases these molecules intercalate, at least partially, into DNA. This intercalation can involve the conjugated rings of a drug, or the hydrophobic side chains of a protein. How different DNA binding molecules find their target sites, and what role intercalation plays in this mechanism, is still not understood. We try to answer these questions by analyzing the energetic and mechanistic aspects of recognition using molecular simulations at the atomic level. Results will be presented for binding a small drug, daunomycin, and for binding a protein, SRY, a mammalian transcription factor. We will show that daunomycin intercalates into DNA by a complex, multistep process, starting with an intermediate, minor groove bound state. In the case of SRY, the mechanism of DNA sequence specificity, via deformation of the double helix, will be discussed. References: A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA, R.Lavery et al. Nucl. Acids Res. (2010) 38(1): 299-313 Protein–DNA Recognition Triggered by a DNA Conformational Switch,
B. Bouvier et al, Angew. Chem. Int. Ed. 2011, 50, 6516 –6518 Multistep Drug Intercalation: Molecular Dynamics and Free Energy Studies of the Binding of Daunomycin to DNA, M. Wilhelm et al, JACS (2012), published on line.