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1l3m

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[[Image:1l3m.gif|left|200px]]
 
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==The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2==
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The line below this paragraph, containing "STRUCTURE_1l3m", creates the "Structure Box" on the page.
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<StructureSection load='1l3m' size='340' side='right'caption='[[1l3m]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1l3m]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L3M FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene></td></tr>
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{{STRUCTURE_1l3m| PDB=1l3m | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1l3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l3m OCA], [https://pdbe.org/1l3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l3m RCSB], [https://www.ebi.ac.uk/pdbsum/1l3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l3m ProSAT]</span></td></tr>
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</table>
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'''The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Cheng JW]]
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The solution structure and hydration of a DNA.RNA hybrid chimeric duplex [d(CGC)r(amamam)d(TTTGCG)]2 in which the RNA adenines were substituted by 2'-O-methylated riboadenines was determined using two-dimensional NMR, simulated annealing, and restrained molecular dynamics. Only DNA residue 7T in the 2'-OMe-RNA.DNA junction adopted an O4'-endo sugar conformation, while the other DNA residues including 3C in the DNA.2'-OMe-RNA junction, adopted C1'-exo or C2'-endo conformations. The observed NOE intensity of 2'-O-methyl group to H1' proton of 4am at the DNA.2'-OMe-RNA junction is much weaker than those of 5am and 6am. The 2'-O-methyl group of 4am was found to orient towards the minor groove in the trans domain while the 2'-O-methyl groups of 5am and 6am were found to be in the gauche (+) domain. In contrast to the long-lived water molecules found close to the RNA adenine H2 and H1' protons and the methyl group of 7T in the RNA-DNA junction of [d(CGC)r(aaa)d(TTTGCG)]2, there were no long-lived water molecules found in [d(CGC)r(amamam)d(TTTGCG)]2. This is probably due to the hydrophobic enviroment created by the 2'-O-methylated riboadenines in the minor groove or due to the wider minor groove width in the middle of the structure. In addition, the 2'-O-methylation of riboadenines in pure chimeric duplex increses its melting temperature from 48.5 degrees C to 51.9 degrees C. The characteristic structural features and hydration patterns of this chimeric duplex provide a molecular basis for further therapeutic applications of DNA.RNA hybrid and chimeric duplexes with 2'-modified RNA residues.
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[[Category: Chou SH]]
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[[Category: Hsu ST]]
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==About this Structure==
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[[Category: Huang WC]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L3M OCA].
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[[Category: Jain ML]]
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[[Category: Tsao YP]]
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==Reference==
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[[Category: Wang LY]]
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The solution structure of [d(CGC)r(amamam)d(TTTGCG)]2., Tsao YP, Wang LY, Hsu ST, Jain ML, Chou SH, Huang C, Cheng JW, J Biomol NMR. 2001 Nov;21(3):209-20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11775738 11775738]
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[[Category: Cheng, J W.]]
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[[Category: Chou, S H.]]
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[[Category: Hsu, S T.]]
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[[Category: Huang, W C.]]
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[[Category: Jain, M L.]]
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[[Category: Tsao, Y P.]]
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[[Category: Wang, L Y.]]
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[[Category: Dna/rna hybrid,chimeric duplex,2'o-methyl]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 23:30:09 2008''
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Current revision

The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2

PDB ID 1l3m

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