1bjd: Difference between revisions

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[[Image:1bjd.png|left|200px]]


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==SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING SINGLE G*T MISMATCHES USING RELAXATION MATRIX ANALYSIS AND RESTRAINED MOLECULAR DYNAMICS, NMR, 1 STRUCTURE==
The line below this paragraph, containing "STRUCTURE_1bjd", creates the "Structure Box" on the page.
<StructureSection load='1bjd' size='340' side='right'caption='[[1bjd]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1bjd]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BJD FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bjd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bjd OCA], [https://pdbe.org/1bjd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bjd RCSB], [https://www.ebi.ac.uk/pdbsum/1bjd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bjd ProSAT]</span></td></tr>
{{STRUCTURE_1bjd|  PDB=1bjd  |  SCENE=  }}
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The three-dimensional solution structure of the self-complementary DNA dodecamer (CGT_GACGT_TACG above GCAT_TGCAG_TGC] which contains the thermodynamically destabilizing [TG_A above AT_T] motif was determined using two-dimensional NMR spectroscopy and simulated annealing protocols. Relaxation matrix analysis methods were used to yield accurate NOE derived distance restraints. Scalar coupling constants for the sugar protons were determined by quantitative simulations of DQF-COSY cross-peaks and used to determine sugar pucker populations. Twenty refined structures starting from random geometries converged to an average pairwise root mean square deviation of 0.49 A. Back calculated NOEs give Rc and Rx factors of 0.38 and 0.088, respectively. The final structure shows that each of the single G@T mismatches form a wobble pair with two hydrogen bonds where the guanine projects into the minor groove and the thymine projects into the major groove. The incorporation of the destabilizing [TG_A above AT_T] motif has little effect on the backbone torsion angles and helical parameters compared to standard B-form duplexes, which may explain why G.T mismatches are among the most commonly observed in DNA. The structure shows that perturbations caused by a G.T mismatch extend only to its neighboring Watson-Crick base pair, thus providing a structural basis for the applicability of the nearest-neighbor model to the thermodynamics of internal G.T mismatches.


===SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING SINGLE G*T MISMATCHES USING RELAXATION MATRIX ANALYSIS AND RESTRAINED MOLECULAR DYNAMICS, NMR, 1 STRUCTURE===
NMR solution structure of a DNA dodecamer containing single G.T mismatches.,Allawi HT, SantaLucia J Jr Nucleic Acids Res. 1998 Nov 1;26(21):4925-34. PMID:9776755<ref>PMID:9776755</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_9776755}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1bjd" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 9776755 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_9776755}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BJD OCA].
[[Category: Allawi HT]]
 
[[Category: Santalucia Junior J]]
==Reference==
NMR solution structure of a DNA dodecamer containing single G.T mismatches., Allawi HT, SantaLucia J Jr, Nucleic Acids Res. 1998 Nov 1;26(21):4925-34. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9776755 9776755]
[[Category: Allawi, H T.]]
[[Category: Junior, J Santalucia.]]
[[Category: Deoxyribonucleic acid]]
[[Category: Dna]]
[[Category: G*t mismatch]]
[[Category: Nmr]]
 
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