Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG

A double-helical B-DNA dodecamer has been analyzed by single crystal x-ray diffraction methods and refined independently in four variants: sequence CGCGAATTCGCG at 20 degrees C and at 16 K, and CGCGAATTBrCGCG in 60% methylpentanediol at 20 and at 7 degrees C. The first three forms show a 14-19 degre...

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Bibliographic Details
Published in:The Journal of biological chemistry 1982-12, Vol.257 (24), p.14686-14707
Main Authors: Fratini, A V, Kopka, M L, Drew, H R, Dickerson, R E
Format: Article
Language:English
Subjects:
DNA
Models, Molecular
Nucleic Acid Conformation
Oligodeoxyribonucleotides
Oligonucleotides
X-Ray Diffraction
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Summary:A double-helical B-DNA dodecamer has been analyzed by single crystal x-ray diffraction methods and refined independently in four variants: sequence CGCGAATTCGCG at 20 degrees C and at 16 K, and CGCGAATTBrCGCG in 60% methylpentanediol at 20 and at 7 degrees C. The first three forms show a 14-19 degrees bend in overall helix axis, but the fourth is straight and unbent. Detailed comparisons of the various forms have led to a better understanding of helix geometry and bending. Structural principles can be understood best if organized under four headings: 1) intrinsic geometry of the sugar rings, 2) stacking and relative motion of base pairs, 3) geometry of the connecting phosphate backbone, and 4) mechanics of bending in B-DNA. The observed bending is neither completely localized nor smooth and continuous, but an intermediate compromise that can be termed "annealed kinking."
ISSN:0021-9258
1083-351X
DOI:10.1016/S0021-9258(18)33335-0