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The Structure of a Stable Intermediate in the A <--> B DNA Helix Transition

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Specialty Science
Date 2000 Feb 26
PMID 10688897
Citations 38
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Abstract

The DNA dodecamer CATGGGCCCATG in a crystal structure of resolution 1.3 A has a conformation intermediate between A and B DNA. This trapping of a stable intermediate suggests that the A and B DNA families are not discrete, as previously believed. The structure supports a base-centered rather than a backbone-centered mechanism for the A <--> B transition mediated by guanine tracts. Interconversion between A and B DNA provides another means for regulating protein-DNA recognition.

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References
1.
Sprous D, Young M, Beveridge D . Molecular dynamics studies of axis bending in d(G5-(GA4T4C)2-C5) and d(G5-(GT4A4C)2-C5): effects of sequence polarity on DNA curvature. J Mol Biol. 1999; 285(4):1623-32. DOI: 10.1006/jmbi.1998.2241. View

2.
Berman H . Crystal studies of B-DNA: the answers and the questions. Biopolymers. 1997; 44(1):23-44. DOI: 10.1002/(SICI)1097-0282(1997)44:1<23::AID-BIP3>3.0.CO;2-1. View

3.
Merritt E . Expanding the model: anisotropic displacement parameters in protein structure refinement. Acta Crystallogr D Biol Crystallogr. 1999; 55(Pt 6):1109-17. DOI: 10.1107/s0907444999003789. View

4.
Foloppe N, MacKerell Jr A . Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA. Biophys J. 1999; 76(6):3206-18. PMC: 1300289. DOI: 10.1016/S0006-3495(99)77472-2. View

5.
Ivanov V, MINCHENKOVA L, Schyolkina A, Poletayev A . Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism. Biopolymers. 1973; 12(1):89-110. DOI: 10.1002/bip.1973.360120109. View