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[[Image:1l0r.gif|left|200px]]


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==NMR Solution Structure of Nogalamycin Intercalation Between Co-Axially Stacked Hairpins==
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<StructureSection load='1l0r' size='340' side='right'caption='[[1l0r]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1l0r]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L0R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L0R FirstGlance]. <br>
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</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NGP:NOGALAMYCIN+(PROTONATED+FORM)'>NGP</scene></td></tr>
{{STRUCTURE_1l0r| PDB=1l0r  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l0r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l0r OCA], [https://pdbe.org/1l0r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l0r RCSB], [https://www.ebi.ac.uk/pdbsum/1l0r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l0r ProSAT]</span></td></tr>
 
</table>
'''NMR Solution Structure of Nogalamycin Intercalation Between Co-Axially Stacked Hairpins'''
<div style="background-color:#fffaf0;">
 
== Publication Abstract from PubMed ==
 
==Overview==
Two DNA hairpin motifs (5'-GCGAAGC-3' and 5'-ACGA AGT-3'), both stabilized by a 5'-GAA loop, have been used to design novel intramolecular double hairpin structures (5'-GCGAAGCACGAAGT-3' and 5'-ACGAAGTGCG AAGC-3') in which coaxial stacking of the two hairpin components generates a double-stranded stem region effectively with a single-strand break in the middle of the sequence at either the TG or CA step between unconnected 3' and 5' terminal bases. We have investigated by NMR the conformation and dynamics of the DNA at the strand break site. We show that mutual stacking significantly enhances the stability of each hairpin. Further, the anthracycline antibiotic nogalamycin binds cleanly to the 5'-TG (5'-CA) site formed by the mutually stacked hairpins despite the break in the sugar-phosphate backbone on one strand. The complex resembles the structure of nogalamycin-DNA complexes with the drug bound at 5'-TG sites in intact duplex sequences, with pi-stacking interactions probably the single dominant stabilizing interaction.
Two DNA hairpin motifs (5'-GCGAAGC-3' and 5'-ACGA AGT-3'), both stabilized by a 5'-GAA loop, have been used to design novel intramolecular double hairpin structures (5'-GCGAAGCACGAAGT-3' and 5'-ACGAAGTGCG AAGC-3') in which coaxial stacking of the two hairpin components generates a double-stranded stem region effectively with a single-strand break in the middle of the sequence at either the TG or CA step between unconnected 3' and 5' terminal bases. We have investigated by NMR the conformation and dynamics of the DNA at the strand break site. We show that mutual stacking significantly enhances the stability of each hairpin. Further, the anthracycline antibiotic nogalamycin binds cleanly to the 5'-TG (5'-CA) site formed by the mutually stacked hairpins despite the break in the sugar-phosphate backbone on one strand. The complex resembles the structure of nogalamycin-DNA complexes with the drug bound at 5'-TG sites in intact duplex sequences, with pi-stacking interactions probably the single dominant stabilizing interaction.


==About this Structure==
Drug recognition of a DNA single strand break: nogalamycin intercalation between coaxially stacked hairpins.,Williams HE, Colgrave ML, Searle MS Eur J Biochem. 2002 Mar;269(6):1726-33. PMID:11895443<ref>PMID:11895443</ref>
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L0R OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Drug recognition of a DNA single strand break: nogalamycin intercalation between coaxially stacked hairpins., Williams HE, Colgrave ML, Searle MS, Eur J Biochem. 2002 Mar;269(6):1726-33. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11895443 11895443]
</div>
[[Category: Colgrave, M L.]]
<div class="pdbe-citations 1l0r" style="background-color:#fffaf0;"></div>
[[Category: Searle, M S.]]
== References ==
[[Category: Williams, H E.L.]]
<references/>
[[Category: Drug-dna recognition]]
__TOC__
[[Category: Gaa loop]]
</StructureSection>
[[Category: Nogalamycin intercalation]]
[[Category: Large Structures]]
[[Category: Single strand break]]
[[Category: Colgrave ML]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 23:24:46 2008''
[[Category: Searle MS]]
[[Category: Williams HEL]]
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