Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

DNA Damage Probed By Molecular Dynamics Simulations

Loss of a nucleic acid base is a common form of cellular DNA damage, and each resulting "abasic" site is potentially mutagenic or cytotoxic. Abasic sites are specifically detected and cleaved by the major human apurinic/apyrimidinic endonuclease, Ape1, triggering the action of other base excision repair proteins. We are studying the means by which Ape1 and abasic DNA recognize one another, by studying various chemical forms of abasic damage in DNA in solution as well as the dynamical structure of the DNA:Ape1 complex. Our results to date from MD simulations on DNA duplexes that contain either apurinic or apyrimidinic sites indicate that the abasic site does not form a rigid hole or gap in the DNA, but instead induces a local destabilization. The apurinic site (i.e., when a pyrimidine is opposite the missing base) shows an especially large conformational range, including conformations where an unpaired cytosine hydrogen bonds with a neighboring thymine (see figure). The observed increased mobility of the bases around the abasic lesion and the greater conformational range of the DNA backbone are structural/dynamic features involved in abasic site recognition, and, in fact, the simulations show that abasic DNA achieves more easily the contortions recently observed in the DNA:Ape1 co-complex structure. Additional MD simulations of additional abasic site analogs (involving replacement of the natural nucleoside by an ethyl or propyl linkage) will be presented, and preliminary analysis suggests that these linkages are more flexible than the natural abasic site and may be more easily strained into an activated substrate, explaining an experimental result.

References and Footnotes

  1. D.M. Wilson, III and D. Barsky. The major human abasic endonuclease ape1. Formation, consequences, and repair of abasic lesions in DNA. [Review article] Mutation Res. In Press. 2001.
  2. D. Barsky and M.E. Colvin. Guanine-cytosine base pairs in parallel-stranded DNA: An ab initio study of the keto-amino wobble pair versus the enol-imino minor tautomer pair. J. Phys. Chem. A. 104: 8570?8576, 2000
  3. .
  4. D. Barsky, N. Foloppe, S. Ahmadia, D.M. Wilson, III, and A.D. MacKerell, Jr. New insights into the structure of abasic DNA from molecular dynamics simulations. Nucleic Acids Res. 28(13): 2613?2626, 2000.
  5. L.H. Nguyen, D. Barsky, J.P. Erzberger, and D.M. Wilson, III. Mapping the protein-DNA interface and the metal binding site of the major human apurinic/apyriminic endonuclease. J. Mol. Biol. 298:447?459, 2000.

This work has been done at LLNL under the auspices of the U.S. Depart-ment of Energy Energy by University of California, Lawrence Livermore National. Lab, contract W-7405-ENG-48, and is supported by an NIH grant (CA79056).

Daniel Barsky

Biology and Biotechnology Research Program
University of California/Lawrence Livermore National Lab
P.O. Box 808, L-448,
7000 East Avenue, Livermore, CA 94550
Email: barsky@llnl.gov WWW: http://compbio.llnl.gov/barsky