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==Structure of a bis-naphthalene bound to a thymine-thymine DNA mismatch==
==Structure of a bis-naphthalene bound to a thymine-thymine DNA mismatch==
<StructureSection load='2llj' size='340' side='right' caption='[[2llj]], [[NMR_Ensembles_of_Models | 5 NMR models]]' scene=''>
<StructureSection load='2llj' size='340' side='right'caption='[[2llj]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2llj]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LLJ FirstGlance]. <br>
<table><tr><td colspan='2'>[[2llj]] 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=2LLJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LLJ FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLJ:6,22-DIOXA-3,9,19,25-TETRAAZONIAPENTACYCLO[25.5.3.3~11,17~.0~14,37~.0~30,34~]OCTATRIACONTA-1(33),11(38),12,14(37),15,17(36),27,29,31,34-DECAENE'>LLJ</scene></td></tr>
</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2llj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2llj OCA], [http://pdbe.org/2llj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2llj RCSB], [http://www.ebi.ac.uk/pdbsum/2llj PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLJ:6,22-DIOXA-3,9,19,25-TETRAAZONIAPENTACYCLO[25.5.3.3~11,17~.0~14,37~.0~30,34~]OCTATRIACONTA-1(33),11(38),12,14(37),15,17(36),27,29,31,34-DECAENE'>LLJ</scene></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=2llj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2llj OCA], [https://pdbe.org/2llj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2llj RCSB], [https://www.ebi.ac.uk/pdbsum/2llj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2llj ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The macrocyclic bis-naphthalene macrocycle (2,7-BisNP), belonging to the cyclobisintercalator family of DNA ligands, recognizes T-T mismatch sites in duplex DNA with high affinity and selectivity, as evidenced by thermal denaturation experiments and NMR titrations. The binding of this macrocycle to an 11-mer DNA oligonucleotide containing a T-T mismatch was studied using NMR spectroscopy and NMR-restrained molecular modeling. The ligand forms a single type of complex with the DNA, in which one of the naphthalene rings of the ligand occupies the place of one of the mismatched thymines, which is flipped out of the duplex. The second naphthalene unit of the ligand intercalates at the A-T base pair flanking the mismatch site, leading to encapsulation of its thymine residue via double stacking. The polyammonium linking chains of the macrocycle are located in the minor and the major grooves of the oligonucleotide and participate in the stabilization of the complex by formation of hydrogen bonds with the encapsulated thymine base and the mismatched thymine remaining inside the helix. The study highlights the uniqueness of this cyclobisintercalation binding mode and its importance for recognition of DNA lesion sites by small molecules.
Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch.,Jourdan M, Granzhan A, Guillot R, Dumy P, Teulade-Fichou MP Nucleic Acids Res. 2012 Jun;40(11):5115-28. Epub 2012 Feb 22. PMID:22362757<ref>PMID:22362757</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2llj" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Dumy, P]]
[[Category: Large Structures]]
[[Category: Granzhan, A]]
[[Category: Synthetic construct]]
[[Category: Guillot, R]]
[[Category: Dumy P]]
[[Category: Jourdan, M]]
[[Category: Granzhan A]]
[[Category: Teulade-Fichou, M]]
[[Category: Guillot R]]
[[Category: Bisintercalation]]
[[Category: Jourdan M]]
[[Category: Dna]]
[[Category: Teulade-Fichou M]]
[[Category: Dna thymine mismatch]]
[[Category: Macrocyle]]
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