In by admin

Name Mr. Paul Orndorff
Organization or Institution University of South Florida
Presentation Type Poster
Topic Computational Chemistry

Flexibility of Lesion Containing DNA


Paul Orndorff Arjan van der Vaart

Author Institution(s)

University of South Florida


Ionization radiation damages DNA by oxidizing bases, and these distortions can be removed by variety of glycosylases resulting in an apyrimidinic (AP) site. Subsequent AP endonucleases cut out the remaining nucleotide creating a lesion in the strand. This nick in the phosphodiester backbone causes considerable flexibility which has been linked to an increased affinity for repair enzymes. The flexibility and behavior of a control, single strand AP site and an AP site with a lesion were investigated by molecular dynamic simulations. Global bending angles as high as 110° and 80° are found for a lesioned and single strand AP system respectfully. Total hydrogen bonds in each system decrease over simulation time. Hydrogen bonding between the AP system’s base pairs significantly lessen over simulation time. Results are as expected for each type of damage, and implications for repair will be discussed.