Base Pair Opening in a Deoxynucleotide Duplex Containing a cis-syn Thymine Cyclobutane Dimer Lesion

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• 作者：Belinda B. Wenke ; Leah N. Huiting ; Elisa B. Frankel ; Benjamin F. Lane ; Megan E. Nú?ez
• 刊名：Biochemistry
• 出版年：2013
• 出版时间：December 23, 2013
• 年：2013
• 卷：52
• 期：51
• 页码：9275-9285
• 全文大小：602K
• ISSN：1520-4995

文摘

The cis-syn thymine cyclobutane dimer is a DNA photoproduct implicated in skin cancer. We compared the stability of individual base pairs in thymine dimer-containing duplexes to undamaged parent 10-mer duplexes. UV melting thermodynamic measurements, CD spectroscopy, and 2D NOESY NMR spectroscopy confirm that the thymine dimer lesion is locally and moderately destabilizing within an overall B-form duplex conformation. We measured the rates of exchange of individual imino protons by NMR using magnetization transfer from water and determined the equilibrium constant for the opening of each base pair K<sub>opsub>. In the normal duplex K<sub>opsub> decreases from the frayed ends of the duplex toward the center, such that the central TA pair is the most stable with a K<sub>opsub> of 8 脳 10<sup>鈥?sup>. In contrast, base pair opening at the 5鈥睺 of the thymine dimer is facile. The 5鈥睺 of the dimer has the largest equilibrium constant (K<sub>opsub> = 3 脳 10<sup>鈥?sup>) in its duplex, considerably larger than even the frayed penultimate base pairs. Notably, base pairing by the 3鈥睺 of the dimer is much more stable than by the 5鈥睺, indicating that the predominant opening mechanism for the thymine dimer lesion is not likely to be flipping out into solution as a single unit. The dimer asymmetrically affects the stability of the duplex in its vicinity, destabilizing base pairing on its 5鈥?side more than on the 3鈥?side. The striking differences in base pair opening between parent and dimer duplexes occur independently of the duplex-single strand melting transitions.