title: Thermodynamic and structural analysis of DNA damage architectures related to replication.
abstract: Damaged DNA, generated by the abstraction of one of five hydrogen atoms from the 2'-deoxyribose ring of the nucleic acid, can contain a variety of lesions, some of which compromise physiological processes. Recently, DNA damage, resulting from the formation of a C3'-thymidinyl radical in DNA oligomers, was found to be dependent on nucleic acid structure. Architectures relevant to DNA replication were observed to generate larger amounts of strand-break and 1-(2'-deoxy- β -D-threo-pentofuranosyl)thymidine formation than that observed for duplex DNA. To understand how this damage can affect the integrity of DNA, the impact of C3'-thymidinyl radical derived lesions on DNA stability and structure was characterized using biophysical methods. DNA architectures evaluated include duplex DNA (dsDNA), single 3' or 5'-overhangs (OvHgs), and forks. Thermal melting analysis and differential scanning calorimetry measurements indicate that an individual 3'-OvHg is more destabilizing than a 5'-OvHg. The presence of a terminal 3' or 5' phosphate decreases the ΔG 25 to the same extent, while the effect of the phosphate at the ss-dsDNA junction of OvHgs is dependent on sequence. Additionally, the effect of 1-(2'-deoxy- β -D-threo-pentofuranosyl)thymidine is found to depend on DNA architecture and proximity to the 3' end of the damaged strand.
authors.affiliation: Department of Chemistry, College of Natural Sciences and Mathematics, The University of Toledo, Toledo, OH 43606-3390, USA.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Amato
authors.forename: Christopher N
authors.initials: CN
authors.lastname: Mwai
authors.forename: Timothy C
authors.initials: TC
authors.lastname: Mueser
authors.forename: Amanda C
authors.initials: AC
authors.lastname: Bryant-Friedrich