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| - | [[Image:1rme.gif|left|200px]] | |
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| - | <!--
| + | ==DNA (5'-D(MCYP*CP*TP*CP*C)-3') tetramer, NMR, 1 structure== |
| - | The line below this paragraph, containing "STRUCTURE_1rme", creates the "Structure Box" on the page.
| + | <StructureSection load='1rme' size='340' side='right'caption='[[1rme]]' 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'>[[1rme]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RME 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=MCY:5-METHYL-2-DEOXYCYTIDINE'>MCY</scene></td></tr> |
| - | {{STRUCTURE_1rme| PDB=1rme | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rme OCA], [https://pdbe.org/1rme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rme RCSB], [https://www.ebi.ac.uk/pdbsum/1rme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rme ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''DNA (5'-D(5MCP*CP*TP*CP*C)-3') TETRAMER, NMR, 1 STRUCTURE'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Synthetic construct]] |
| - | At slightly acidic pH, protonation of C-rich oligomers results in the formation of a four-stranded structure composed of two parallel duplexes in a head to tail orientation with their hemi-protonated C.C+ pairs intercalated in a so-called i-motif. In all cases reported previously the duplexes are identical. The tetramer formed by the d(5mCCTCC) oligomer is different. The structure is computed on the basis of 55 inter-residue distances derived from NOESY cross-peaks measured at short mixing times. It consists of two intercalated non-equivalent symmetrical duplexes. The base stacking order is C5* C1 C4* C2 (T3*) T3 C2* C4 C1* C5, but the thymidine bases (T3*) of one duplex are looped out and lie in the wide grooves of the tetramer. The thymidine bases T3 stack as a symmetrical T.T pair between the sequentially adjacent C2.C2+ pair and the C2*.C2*+ pair of the other duplex. Numerous exchange cross-peaks provide evidence for duplex interconversion. The interconversion rate is 1.4 s-1 at 0 degree C and the activation energy is 94 kJ/mol. The opening of the T3.T3 pair, the closing of the T3*.T3 pair, and the opening of the C2*.C2*+ pair occur simultaneously with the duplex interconversion. This suggests that the concerted opening and closing of the thymidine bases drive the duplex interconversion. Opening of the C4.C4+ and C4*.C4*+ pairs, and dissociation of the tetramer are not part of the interconversion since they occur at much slower rates. Duplex interconversion within the [d(5mCCTCC)]4 tetramer provides the first structural and kinetics characterization of broken symmetry in a biopolymer. The tetramer formed by d(5mCCUCC) adopts a similar structure, but the rate of duplex interconversion is faster: 40 s-1 at 0 degree C. At 32 degrees C, interconversion is fast on the NMR time scale.
| + | [[Category: Leroy J-L]] |
| - | | + | [[Category: Nonin S]] |
| - | ==About this Structure==
| + | |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RME OCA]. | + | |
| - | | + | |
| - | ==Reference== | + | |
| - | Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer., Nonin S, Leroy JL, J Mol Biol. 1996 Aug 23;261(3):399-414. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8780782 8780782]
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| - | [[Category: Leroy, J L.]] | + | |
| - | [[Category: Nonin, S.]] | + | |
| - | [[Category: Deoxyribonucleic acid]] | + | |
| - | [[Category: I-motif]] | + | |
| - | [[Category: Tetramer]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:40:09 2008''
| + | |
