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{{Seed}}
[[Image:1b0s.png|left|200px]]


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==BINDING OF AR-1-144, A TRI-IMIDAZOLE DNA MINOR GROOVE BINDER, TO CCGG SEQUENCE ANALYZED BY NMR SPECTROSCOPY==
The line below this paragraph, containing "STRUCTURE_1b0s", creates the "Structure Box" on the page.
<StructureSection load='1b0s' size='340' side='right'caption='[[1b0s]]' 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'>[[1b0s]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B0S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B0S 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AR1:(2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM'>AR1</scene></td></tr>
{{STRUCTURE_1b0s|  PDB=1b0s  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b0s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b0s OCA], [https://pdbe.org/1b0s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b0s RCSB], [https://www.ebi.ac.uk/pdbsum/1b0s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b0s ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The interactions of N-[2-(dimethylamino)ethyl]-1-methyl-4-[1-methyl-4-[4-formamido-1-meth ylimidazole-2-carboxamido]imidazole-2-carboxamido]imidazole-2-c arboxa mide (AR-1-144), a tri-imidazole polyamide minor groove binder, with DNA have been investigated by NMR and CD spectroscopy. A series of DNA oligonucleotides with a C/G-containing four-bp core, i.e. CCGG, CGCG, GGCC, and GCGC, have been titrated with AR-1-144 at different ratios. AR-1-144 favors the CCGG sequence. The flanking sequence of the CCGG core also influences the binding preference, with a C or T being favored on the 3'-side of the CCGG core. The three-dimensional structure of the symmetric 2:1 side-by-side complex of AR-1-144 and GAACCGGTTC, determined by NOE-constrained NMR refinement, reveals that each AR-1-144 binds to four base pairs, i.e. at C5-G6-G7-T8, with every amide-imidazole unit forming two potential hydrogen bonds with DNA. The same DNA binding preference of AR-1-144 was also confirmed by circular dichroism spectroscopy, indicating that the DNA binding preference of AR-1-144 is independent of concentration. The cooperative binding of an AR-1-144 homodimer to the (purine)CCGG(pyrimidine) core sequence appears to be weaker than that of the distamycin A homodimer to A/T sequences, most likely due to the diminished hydrophobic interactions between AR-1-144 and DNA. Our results are consistent with previous footprinting data and explain the binding pattern found in the crystal structure of a di-imidazole drug bound to CATGGCCATG.


===BINDING OF AR-1-144, A TRI-IMIDAZOLE DNA MINOR GROOVE BINDER, TO CCGG SEQUENCE ANALYZED BY NMR SPECTROSCOPY===
Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy.,Yang XL, Kaenzig C, Lee M, Wang AH Eur J Biochem. 1999 Aug;263(3):646-55. PMID:10469127<ref>PMID:10469127</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_10469127}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1b0s" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 10469127 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_10469127}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B0S OCA].
[[Category: Kaenzig C]]
 
[[Category: Lee M]]
==Reference==
[[Category: Wang AH-J]]
Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy., Yang XL, Kaenzig C, Lee M, Wang AH, Eur J Biochem. 1999 Aug;263(3):646-55. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10469127 10469127]
[[Category: Yang X-L]]
[[Category: Kaenzig, C.]]
[[Category: Lee, M.]]
[[Category: Wang, A H.J.]]
[[Category: Yang, X L.]]
[[Category: Anticancer drug]]
[[Category: Dna structure]]
[[Category: Drug design]]
[[Category: Sequence specific recognition]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 18:00:10 2008''

Latest revision as of 11:34, 22 November 2023

BINDING OF AR-1-144, A TRI-IMIDAZOLE DNA MINOR GROOVE BINDER, TO CCGG SEQUENCE ANALYZED BY NMR SPECTROSCOPY

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