5uzf: Difference between revisions

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'''Unreleased structure'''


The entry 5uzf is ON HOLD
==Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A6-DNA structure==
<StructureSection load='5uzf' size='340' side='right'caption='[[5uzf]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5uzf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UZF FirstGlance]. <br>
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5uzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzf OCA], [https://pdbe.org/5uzf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uzf RCSB], [https://www.ebi.ac.uk/pdbsum/5uzf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzf ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated ( approximately 0.02-0.4%) and short-lived (lifetimes approximately 0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A*T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking ( approximately 9 degrees ); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair.


Authors: Sathyamoorthy, B, Shi, H, Xue, Y, Al-Hashimi, HM
Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.,Sathyamoorthy B, Shi H, Zhou H, Xue Y, Rangadurai A, Merriman DK, Al-Hashimi HM Nucleic Acids Res. 2017 Mar 21. doi: 10.1093/nar/gkx186. PMID:28369571<ref>PMID:28369571</ref>


Description: Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A -A6-DNA structure
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Sathyamoorthy, B, Shi, H, Xue, Y, Al-Hashimi, Hm]]
<div class="pdbe-citations 5uzf" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Al-Hashimi HM]]
[[Category: Sathyamoorthy B]]
[[Category: Shi H]]
[[Category: Xue Y]]
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