1qe7
From Proteopedia
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| - | [[Image:1qe7.gif|left|200px]]<br /><applet load="1qe7" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1qe7" /> | ||
| - | '''SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA'''<br /> | ||
| - | == | + | ==SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA== |
| + | <StructureSection load='1qe7' size='340' side='right'caption='[[1qe7]]' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1qe7]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QE7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QE7 FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=1qe7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qe7 OCA], [https://pdbe.org/1qe7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qe7 RCSB], [https://www.ebi.ac.uk/pdbsum/1qe7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qe7 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
Three-dimensional (3D) structure of a hairpin DNA d-CTAGAGGATCCTTTUGGATCCT (22mer; abbreviated as U4-hairpin), which has a uracil nucleotide unit at the fourth position from the 5' end of the tetra-loop has been solved by NMR spectroscopy. The(1)H resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimisation procedures have been used to describe the 3D structure of the U4 hairpin. This study establishes that the stem of the hairpin adopts a right handed B-DNA conformation while the T(12)and U(15)nucleotide stack upon 3' and 5' ends of the stem, respectively. Further, T(14)stacks upon both T(12)and U(15)while T(13)partially stacks upon T(14). Very weak stacking interaction is observed between T(13)and T(12). All the individual nucleotide bases adopt ' anti ' conformation with respect to their sugar moiety. The turning phosphate in the loop is located between T(13)and T(14). The stereochemistry of U(15)mimics the situation where uracil would stack in a B-DNA conformation. This could be the reason as to why the U4-hairpin is found to be the best substrate for its interaction with uracil DNA glycosylase (UDG) compared to the other substrates in which the uracil is at the first, second and third positions of the tetra-loop from its 5' end, as reported previously. | Three-dimensional (3D) structure of a hairpin DNA d-CTAGAGGATCCTTTUGGATCCT (22mer; abbreviated as U4-hairpin), which has a uracil nucleotide unit at the fourth position from the 5' end of the tetra-loop has been solved by NMR spectroscopy. The(1)H resonances of this hairpin have been assigned almost completely. NMR restrained molecular dynamics and energy minimisation procedures have been used to describe the 3D structure of the U4 hairpin. This study establishes that the stem of the hairpin adopts a right handed B-DNA conformation while the T(12)and U(15)nucleotide stack upon 3' and 5' ends of the stem, respectively. Further, T(14)stacks upon both T(12)and U(15)while T(13)partially stacks upon T(14). Very weak stacking interaction is observed between T(13)and T(12). All the individual nucleotide bases adopt ' anti ' conformation with respect to their sugar moiety. The turning phosphate in the loop is located between T(13)and T(14). The stereochemistry of U(15)mimics the situation where uracil would stack in a B-DNA conformation. This could be the reason as to why the U4-hairpin is found to be the best substrate for its interaction with uracil DNA glycosylase (UDG) compared to the other substrates in which the uracil is at the first, second and third positions of the tetra-loop from its 5' end, as reported previously. | ||
| - | + | Structural characterisation of a uracil containing hairpin DNA by NMR and molecular dynamics.,Ghosh M, Kumar NV, Varshney U, Chary KV Nucleic Acids Res. 1999 Oct 1;27(19):3938-44. PMID:10481034<ref>PMID:10481034</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: | + | <div class="pdbe-citations 1qe7" style="background-color:#fffaf0;"></div> |
| - | [[Category: Chary | + | == References == |
| - | [[Category: Ghosh | + | <references/> |
| - | + | __TOC__ | |
| - | + | </StructureSection> | |
| - | + | [[Category: Large Structures]] | |
| - | + | [[Category: Chary KVR]] | |
| - | + | [[Category: Ghosh M]] | |
| - | + | ||
Current revision
SOLUTION STRUCTURE OF A URACIL CONTAINING HAIRPIN DNA
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