2lby: Difference between revisions

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-[[Image:2lby.png|left|200px]]
-<!--
+==G-quadruplex structure formed at the 5'-end of NHEIII_1 element in human c-MYC promoter==
-The line below this paragraph, containing "STRUCTURE_2lby", creates the "Structure Box" on the page.
+<StructureSection load='2lby' size='340' side='right'caption='[[2lby]]' 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'>[[2lby]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LBY 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>
--->
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lby OCA], [https://pdbe.org/2lby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lby RCSB], [https://www.ebi.ac.uk/pdbsum/2lby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lby ProSAT]</span></td></tr>
-{{STRUCTURE_2lby|  PDB=2lby  |  SCENE=  }}
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We studied the structures and stabilities of G-quadruplexes formed in Myc1234, the region containing the four consecutive 5' runs of guanines of c-MYC promoter NHE III(1,) which have recently been shown to form in a supercoiled plasmid system in aqueous solution. We determined the NMR solution structure of the 1:2:1 parallel-stranded loop isomer, one of the two major loop isomers formed in Myc1234 in K(+) solution. This major loop isomer, although sharing the same folding structure, appears to be markedly less stable than the major loop isomer formed in the single-stranded c-MYC NHE III(1) oligonucleotide, the Myc2345 G-quadruplex. Our NMR structures indicated that the different thermostabilities of the two 1:2:1 parallel c-MYC G-quadruplexes are likely caused by the different base conformations of the single nucleotide loops. The observation of the formation of the Myc1234 G-quadruplex in the supercoiled plasmid thus points to the potential role of supercoiling in the G-quadruplex formation in promoter sequences. We also performed a systematic thermodynamic analysis of modified c-MYC NHE III(1) sequences, which provided quantitative measure of the contributions of various loop sequences to the thermostabilities of parallel-stranded G-quadruplexes. This information is important for understanding the equilibrium of promoter G-quadruplex loop isomers and for their drug targeting.
-===Myc G-quadruplex formed at the 5'-end of NHEIII element===
+c-MYC promoter G-quadruplex formed at the 5'-end of NHE III1 element: insights into biological relevance and parallel-stranded G-quadruplex stability.,Mathad RI, Hatzakis E, Dai J, Yang D Nucleic Acids Res. 2011 Nov 1;39(20):9023-33. Epub 2011 Jul 27. PMID:21795379<ref>PMID:21795379</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_21795379}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2lby" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 21795379 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21795379}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2lby]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LBY OCA].
+[[Category: Hatzakis E]]
+[[Category: Mathad R]]
-==Reference==
+[[Category: Yang D]]
-<ref group="xtra">PMID:021795379</ref><references group="xtra"/>
-[[Category: Hatzakis, E.]]
-[[Category: Mathad, R.]]
-[[Category: Yang, D.]]
-[[Category: C-myc]]
-[[Category: Dna]]
-[[Category: G-quadruplex]]