286D

X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE

Summary for 286D

• Entry DOI: 10.2210/pdb286d/pdb
• Descriptor: DNA (5'-D(*CP*CP*IP*IP*IP*CP*CP*CP*GP*G)-3') (2 entities in total)
• Functional Keywords: b-dna, double helix, modified, dna
• Total number of polymer chains: 2
• Total formula weight: 6003.88

Authors

Shatzky-Schwartz, M.,Shakked, Z.,Luisi, B.F. (deposition date: 1996-09-16, release date: 1997-05-08, Last modification date: 2024-04-03)

Primary citation

Shatzky-Schwartz, M.,Arbuckle, N.D.,Eisenstein, M.,Rabinovich, D.,Bareket-Samish, A.,Haran, T.E.,Luisi, B.F.,Shakked, Z.
X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature.
J.Mol.Biol., 267:595-623, 1997

PubMed Abstract: DNA containing short periodic stretches of adenine residues (known as A-tracts), which are aligned with the helical repeat, exhibit a pronounced macroscopic curvature. This property is thought to arise from the cumulative effects of a distinctive structure of the A-tract. It has also been observed by gel electrophoresis that macroscopic curvature is largely retained when inosine bases are introduced singly into A-tracts but decreases abruptly for pure I-tracts. The structural basis of this effect is unknown. Here we describe X-ray and gel electrophoretic analyses of several oligomers incorporating adenine or inosine bases or both. We find that macroscopic curvature is correlated with a distinctive base-stacking geometry characterized by propeller twisting of the base-pairs. Regions of alternating adenine and inosine bases display large propeller twisting comparable to that of pure A-tracts, whereas the values observed for pure I-tracts are significantly smaller. We also observe in the crystal structures that propeller twist leads to close cross-strand contacts between amino groups from adenine and cytosine bases, indicating an attractive NH-N interaction, which is analogous to the NH-O interaction proposed for A-tracts. This interaction also occurs between adenine bases across an A-T step and may explain in part the different behavior of A-T versus T-A steps in the context of A-tract-induced curvature. We also note that hydration patterns may contribute to propeller-twisted conformation. Based on the present data and other structural and biophysical studies, we propose that DNA macroscopic curvature is related to the structural invariance of A-tract and A-tract-like regions conferred by high propeller twist, cross-strand interactions and characteristic hydration. The implications of these findings to the mechanism of DNA bending are discussed.

PubMed: 9126841
DOI: 10.1006/jmbi.1996.0878

Experimental method

X-RAY DIFFRACTION (2.5 Å)