Effective computational strategies for determining structures of carcinogen-damaged DNA

To determine three-dimensional conformations of DNA damaged by environmenta l chemical carcinogens, effective molecular mechanics search techniques hav e been developed to deal with the large system sizes and computational dema nds. First, extensive surveys of the potential energy surface are carried o ut by energy minimization. These search strategies rely on (1) using the re duced variable domain of torsion-angle (rather than Cartesian) space, (2) b uilding larger units (about 12 base pairs) on the basis of structures of sm all modified subunits, and (3) employing penalty functions to search for se lected hydrogen bonding patterns and to incorporate interproton distance bo unds when available from experimental high-resolution nuclear magnetic reso nance (NMR) studies. Second, molecular dynamics simulations with solvent ca n subsequently be employed to probe conformational features in the presence of polymerase enzyme responsible for DNA replication, using structures com puted in the energy minimization searches as initial coordinates. A key str ucture-function relationship involving mirror-image molecules with very dif fering experimentally determined tumorigenic potencies has been deduced: th e members of the pairs align oppositely when bound to DNA, making it likely that their treatment by replication and repair enzymes differ. This opposi te orientation phenomenon, first predicted computationally (Singh et al., 1 991), has been observed in experimental high-resolution NMR studies combine d with our molecular mechanics computations in a number of different exampl es and has recently been confirmed experimentally in other laboratories as well (reviewed in Geacintov et al., 1997), Elucidation of this conformation al feature has paved the way to uncovering the structural origin underlying very different biological outcomes stemming from chemically identical but mirror-image molecules. (C) 1999 Academic Press.