Modeling DNA Replication Intermediates

While there is now available a great deal of information on double stranded DNA from X-ray crytallography, high resolution NMR and computer modeling, very little is known about structures that are representative of the DNA core of replication intermediates. DNA replication occurs at a single strand/double strand junction and bulged out intermediates near the junction can lead to frameshift mutations. The single stranded domains are particularly challenging. Our interest is focused on strategies for modeling the DNA of these types of replication intermediates. Modeling such structures presents special problems in addressing the multiple minimum problem and in treating the electrostatic component of the force field. We are testing a number of search strategies for locating low energy structures of these types and we are also investigating two different distance dependent dielectric functions in the coulombic term of the force field. We are studying both unmodified DNA and DNA damaged by aromatic amines, carcinogens present in the environment in tobacco smoke, barbecued meats and automobile exhaust. The nature of the structure adopted by the carcinogen modified DNA at the replication fork plays a key role in determining whether the carcinogen will cause a mutation during replication that can initiate the carcinogenic process. In the present work results are presented for unmodified DNA in the NarI mutational hotspot sequence. Interestingly, we find that a slipped bulged mutagenic intermediate is much more stable relative to its normally extended counterpart when the guanine mutational hotspot is syn instead of anti. This suggests that carcinogens such as 2-(acetyl)aminofluorene which induce the syn conformation enhance mutagenesis at the hotspot by stabilizing a slipped intermediate in the syn orientation.