285d
From Proteopedia
(New page: 200px<br /><applet load="285d" size="350" color="white" frame="true" align="right" spinBox="true" caption="285d, resolution 2.500Å" /> '''X-RAY AND SOLUTION ...) |
|||
| Line 4: | Line 4: | ||
==Overview== | ==Overview== | ||
| - | DNA containing short periodic stretches of adenine residues (known as | + | 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. |
==About this Structure== | ==About this Structure== | ||
| Line 12: | Line 12: | ||
X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature., Shatzky-Schwartz M, Arbuckle ND, Eisenstein M, Rabinovich D, Bareket-Samish A, Haran TE, Luisi BF, Shakked Z, J Mol Biol. 1997 Apr 4;267(3):595-623. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9126841 9126841] | X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature., Shatzky-Schwartz M, Arbuckle ND, Eisenstein M, Rabinovich D, Bareket-Samish A, Haran TE, Luisi BF, Shakked Z, J Mol Biol. 1997 Apr 4;267(3):595-623. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9126841 9126841] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Luisi, B | + | [[Category: Luisi, B F.]] |
[[Category: Shakked, Z.]] | [[Category: Shakked, Z.]] | ||
[[Category: Shatzky-Schwartz, M.]] | [[Category: Shatzky-Schwartz, M.]] | ||
| Line 19: | Line 19: | ||
[[Category: modified]] | [[Category: modified]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:22:08 2008'' |
Revision as of 14:22, 21 February 2008
|
X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE
Overview
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.
About this Structure
285D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature., Shatzky-Schwartz M, Arbuckle ND, Eisenstein M, Rabinovich D, Bareket-Samish A, Haran TE, Luisi BF, Shakked Z, J Mol Biol. 1997 Apr 4;267(3):595-623. PMID:9126841
Page seeded by OCA on Thu Feb 21 16:22:08 2008
