Jody M. Lingbeck, Mark G. Kubinec, Kate McAteer, and Michael A. Kennedy
Battelle Pacific Northwest Laboratory, Richland, Washington, 99352
We have observed interesting patterns of secondary structure and dynamics in DNA that may help understand interactions between DNA and proteins and between DNA and certain carcinogens. In one case, we have observed unusually slow, large amplitude base motion at the TpA step in DNA that contains TnAn (where n = 22) segments. The TnAn segment represents a family of restriction sites in which cleavage occurs at the TpA step. We observe the expected increase in linewidths due to base motion in intermediate exchange when going from 500 MHz to 750 MHz. The unusual dynamics is accompanied by striking anomalies in base stacking at the TpA step. The structure/dynamics observed at TpA steps may be important for protein recognition and enzymatic cleavage in these restrictionsites. We have investigated the effect of N6-methylation on the structure and dynamics and find that methylation abolishes the unusual dynamics and induces changes in the base stacking. Such anomalous base dynamics appears to only occur at TpA steps. We will report on our efforts to establish rules for how sequence context affects base dynamics in TpA steps. In a second case, we have observed variations in minor groove width in poly:G segments of DNA that are typically associated with B' DNA in poly:A regions. A screening of seven sequences containing G inserts into poly:A segments reveals that guanine can be accomodated into a narrow minor groove structure. We will report details of the structure that allow this to occur. This observation appears to explain patterns of benzo[a]pyrene diol epoxide adduct formation in poly:G regions of DNA.