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| <!--
| | ==The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2== |
| The line below this paragraph, containing "STRUCTURE_1l3m", creates the "Structure Box" on the page.
| | <StructureSection load='1l3m' size='340' side='right'caption='[[1l3m]]' 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'>[[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> |
| 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> |
| -->
| | <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> |
| {{STRUCTURE_1l3m| PDB=1l3m | SCENE= }}
| | <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> |
| | | </table> |
| '''The Solution Structure of [d(CGC)r(amamam)d(TTTGCG)]2'''
| | __TOC__ |
| | | </StructureSection> |
| | | [[Category: Large Structures]] |
| ==Overview== | | [[Category: Cheng JW]] |
| 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.
| | [[Category: Chou SH]] |
| | | [[Category: Hsu ST]] |
| ==About this Structure==
| | [[Category: Huang WC]] |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L3M OCA]. | | [[Category: Jain ML]] |
| | | [[Category: Tsao YP]] |
| ==Reference== | | [[Category: Wang LY]] |
| 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.]] | |
| [[Category: Chou, S H.]] | |
| [[Category: Hsu, S T.]] | |
| [[Category: Huang, W C.]] | |
| [[Category: Jain, M L.]] | |
| [[Category: Tsao, Y P.]] | |
| [[Category: Wang, L Y.]] | |
| [[Category: Dna/rna hybrid,chimeric duplex,2'o-methyl]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 23:30:09 2008''
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