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1eel

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STRUCTURE OF A COMPLEX BETWEEN THE DNA SEQUENCE DCGCGAATTCGCG AND BIS[PIPERIDINO-ETHYL]-FURAMIDINE

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Categories: Large Structures | Neidle S | Simpson IJ

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-[[Image:1eel.gif|left|200px]]<br /><applet load="1eel" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1eel, resolution 2.40&Aring;" />
-'''STRUCTURE OF A COMPLEX BETWEEN THE DNA SEQUENCE DCGCGAATTCGCG AND BIS[PIPERIDINO-ETHYL]-FURAMIDINE'''<br />
-==Overview==
+==STRUCTURE OF A COMPLEX BETWEEN THE DNA SEQUENCE DCGCGAATTCGCG AND BIS[PIPERIDINO-ETHYL]-FURAMIDINE==
-As part of an effort to develop a better understanding of the structural, and thermodynamic principles of DNA minor groove recognition, we have, investigated complexes of three diphenylfuran dications with the, d(CGCGAATTCGCG)(2) duplex. The parent compound, furamidine (DB75), has two, amidine substituents while DB244 has cyclopentyl amidine substituents and, DB226 has 3-pentyl amidines. The structure for the DB244-DNA complex is, reported here and is compared to the structure of the DB75 complex., Crystals were not obtained with DB226 but information from the DB75 and, DB244 structures as well as previous NMR results on DB226 indicate that, all three compounds bind in the minor groove at the AATT site of the, duplex. DB244 and DB75 penetrate to the floor of the groove and form, hydrogen bonds with T8 on one strand and T20 on the opposite strand while, DB226 forms a complex with fewer interactions. Binding studies by surface, plasmon resonance (SPR) yield -delta G degrees values in the order, DB244&gt;DB75&gt;DB226 that are relatively constant with temperature. The, equilibrium binding constants for DB244 are 10-20 times greater than that, for DB226. Isothermal titration calorimetric (ITC) experiments indicate, that, in contrast to delta G degrees, delta H degrees varies considerably, with temperature to yield large negative delta Cp degrees values. The, thermodynamic results, analyzed in terms of structures of the DNA, complexes, provide an explanation of why DB244 binds more strongly to DNA, than DB75, while DB266 binds more weakly. All three compounds have a major, contribution to binding from hydrophobic interactions but the hydrophobic, term is most favorable for DB244. DB244 also has strong contributions from, molecular interactions in its DNA complex and all of these factors combine, to give it the largest-delta G degrees for binding. Although the factors, that influence the energetics of minor groove interactions are varied and, complex, results from the literature coupled with those on the furan, derivatives indicate that there are some common characteristics for minor, groove recognition by unfused heterocyclic cations that can be used in, molecular design.
+<StructureSection load='1eel' size='340' side='right'caption='[[1eel]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1eel]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EEL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EEL FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D24:2,5-BIS-[4-[CYCLOPENTA-1,3-DIEN-5-YLAMINO-1-AMINOMETHYL]-PHEN-1-YL]FURAN'>D24</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=1eel FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eel OCA], [https://pdbe.org/1eel PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eel RCSB], [https://www.ebi.ac.uk/pdbsum/1eel PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eel ProSAT]</span></td></tr>
+</table>
-==About this Structure==
+==See Also==
-EEL is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with D24 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EEL OCA].
+*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-A thermodynamic and structural analysis of DNA minor-groove complex formation., Mazur S, Tanious FA, Ding D, Kumar A, Boykin DW, Simpson IJ, Neidle S, Wilson WD, J Mol Biol. 2000 Jul 7;300(2):321-37. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10873468 10873468]
+[[Category: Large Structures]]
-[[Category: Protein complex]]
+[[Category: Neidle S]]
-[[Category: Neidle, S.]]
+[[Category: Simpson IJ]]
-[[Category: Simpson, I.J.]]
-[[Category: D24]]
-[[Category: b-dna]]
-[[Category: bulky side-chains]]
-[[Category: minor groove binding ligand]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:08:20 2007''

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STRUCTURE OF A COMPLEX BETWEEN THE DNA SEQUENCE DCGCGAATTCGCG AND BIS[PIPERIDINO-ETHYL]-FURAMIDINE

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