7cls: Difference between revisions

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==Solution structure of an intramolecular G-quadruplex containing a duplex bulge==

== Structural highlights ==

<table><tr><td colspan='2'>Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CLS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CLS FirstGlance]. <br>

<table><tr><td colspan='2'>[[7cls]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CLS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CLS FirstGlance]. <br>

</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7cls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cls OCA], [http://pdbe.org/7cls PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cls RCSB], [http://www.ebi.ac.uk/pdbsum/7cls PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cls ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Beyond the consensus definition of G-quadruplex-forming motifs with tracts of continuous guanines, G-quadruplexes harboring bulges in the G-tetrad core are prevalent in the human genome. Here, we study the incorporation of a duplex hairpin within a bulge of a G-quadruplex. The NMR solution structure of a G-quadruplex containing a duplex bulge was resolved, revealing the structural details of the junction between the duplex bulge and the G-quadruplex. Unexpectedly, instead of an orthogonal connection the duplex stem was observed to stack below the G-quadruplex forming a unique quadruplex-duplex junction. Breaking up of the immediate base pair step at the junction, coupled with a narrowing of the duplex groove within the context of the bulge, led to a progressive transition between the quadruplex and duplex segments. This study revealed that a duplex bulge can be formed at various positions of a G-quadruplex scaffold. In contrast to a non-structured bulge, the stability of a G-quadruplex slightly increases with an increase in the duplex bulge size. A G-quadruplex structure containing a duplex bulge of up to 33 nt in size was shown to form, which was much larger than the previously reported 7-nt bulge. With G-quadruplexes containing duplex bulges representing new structural motifs with potential biological significance, our findings would broaden the definition of potential G-quadruplex-forming sequences.

Duplex formation in a G-quadruplex bulge.,Ngoc Nguyen TQ, Lim KW, Phan AT Nucleic Acids Res. 2020 Sep 22. pii: 5909921. doi: 10.1093/nar/gkaa738. PMID:32960213<ref>PMID:32960213</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Lim KW]]

[[Category: Lim, K W]]

[[Category: Nguyen ~~TQN~~]]

[[Category: Nguyen, T Q.N]]

[[Category: Phan AT]]

[[Category: Phan, A T]]

[[Category: Bulge]]

[[Category: Dna]]

[[Category: G-quadruplex]]

[[Category: Quadruplex-duplex hybrid]]

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@@ Line 1: / Line 1: @@
 ==Solution structure of an intramolecular G-quadruplex containing a duplex bulge==
-<StructureSection load='7cls' size='340' side='right'caption='[[7cls]]' scene=''>
+<StructureSection load='7cls' size='340' side='right'caption='[[7cls]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CLS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CLS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7cls]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CLS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7CLS FirstGlance]. <br>
 </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7cls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cls OCA], [http://pdbe.org/7cls PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7cls RCSB], [http://www.ebi.ac.uk/pdbsum/7cls PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7cls ProSAT]</span></td></tr>
 </table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Beyond the consensus definition of G-quadruplex-forming motifs with tracts of continuous guanines, G-quadruplexes harboring bulges in the G-tetrad core are prevalent in the human genome. Here, we study the incorporation of a duplex hairpin within a bulge of a G-quadruplex. The NMR solution structure of a G-quadruplex containing a duplex bulge was resolved, revealing the structural details of the junction between the duplex bulge and the G-quadruplex. Unexpectedly, instead of an orthogonal connection the duplex stem was observed to stack below the G-quadruplex forming a unique quadruplex-duplex junction. Breaking up of the immediate base pair step at the junction, coupled with a narrowing of the duplex groove within the context of the bulge, led to a progressive transition between the quadruplex and duplex segments. This study revealed that a duplex bulge can be formed at various positions of a G-quadruplex scaffold. In contrast to a non-structured bulge, the stability of a G-quadruplex slightly increases with an increase in the duplex bulge size. A G-quadruplex structure containing a duplex bulge of up to 33 nt in size was shown to form, which was much larger than the previously reported 7-nt bulge. With G-quadruplexes containing duplex bulges representing new structural motifs with potential biological significance, our findings would broaden the definition of potential G-quadruplex-forming sequences.
+Duplex formation in a G-quadruplex bulge.,Ngoc Nguyen TQ, Lim KW, Phan AT Nucleic Acids Res. 2020 Sep 22. pii: 5909921. doi: 10.1093/nar/gkaa738. PMID:32960213<ref>PMID:32960213</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 7cls" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Lim KW]]
+[[Category: Lim, K W]]
-[[Category: Nguyen TQN]]
+[[Category: Nguyen, T Q.N]]
-[[Category: Phan AT]]
+[[Category: Phan, A T]]
+[[Category: Bulge]]
+[[Category: Dna]]
+[[Category: G-quadruplex]]
+[[Category: Quadruplex-duplex hybrid]]