Use of Cross-Links To Study the Conformational Dynamics of Triplex DNA
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- 作者：Robert J. Cain and Gary D. Glick
- 刊名：Biochemistry
- 出版年：1998
- 出版时间：February 3, 1998
- 年：1998
- 卷：37
- 期：5
- 页码：1456 - 1464
- 全文大小：138K
- 年卷期：v.37,no.5(February 3, 1998)
- ISSN：1520-4995
文摘
The conformational dynamics of a 34-base-longpyrimidine·purine-pyrimidine motif intramolecular DNA triple helix possessing three cytosine residues in theHoogsteen strand (1) and a disulfidecross-linked analog (2) were studied by two-dimensionalexchange and NOE spectroscopy and by measuringbase-catalyzed imino proton exchange rates. Under acidicconditions that stabilize triplexes containingHoogsteen strand cytosines (pH 6.0 and 1 
C), sequences 1and 2 exhibit a small and identical degree ofconformational heterogeneity. However, at a higher temperature (pH6.0 and 37 C), 1 exhibits muchmore extensive conformational heterogeneity than 2. Theexchange times for Watson-Crick imino protonsare ~1 h for both triplexes. However, the Hoogsteen base-pairlifetimes of 1 could not be measuredbecause this sequence is conformationally labile under the alkalineconditions necessary to conduct theseexperiments. Because of the extraordinary pH stability conferredby the cross-link, it is possible to estimatethe base-pair lifetimes for 2. The lifetimes of theHoogsteen base pairs range from about 3 to 370 ms,and in all cases are shorter than that of the Watson-Crick base paircontained in the same triplet. Theseexperiments represent the first measurement of base-pair lifetimeswithin Hoogsteen triplets. The abilityto measure individual base-pair lifetimes may prove useful in studiesthat attempt to modulate triplexproperties through rational design.
C), sequences 1and 2 exhibit a small and identical degree ofconformational heterogeneity. However, at a higher temperature (pH6.0 and 37 C), 1 exhibits muchmore extensive conformational heterogeneity than 2. Theexchange times for Watson-Crick imino protonsare ~1 h for both triplexes. However, the Hoogsteen base-pairlifetimes of 1 could not be measuredbecause this sequence is conformationally labile under the alkalineconditions necessary to conduct theseexperiments. Because of the extraordinary pH stability conferredby the cross-link, it is possible to estimatethe base-pair lifetimes for 2. The lifetimes of theHoogsteen base pairs range from about 3 to 370 ms,and in all cases are shorter than that of the Watson-Crick base paircontained in the same triplet. Theseexperiments represent the first measurement of base-pair lifetimeswithin Hoogsteen triplets. The abilityto measure individual base-pair lifetimes may prove useful in studiesthat attempt to modulate triplexproperties through rational design.