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| - | [[Image:1bae.gif|left|200px]] | |
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| - | <!--
| + | ==STRUCTURE OF DNA (5'-D 5MCCTTTACC-3')2, NMR, 1 STRUCTURE== |
| - | The line below this paragraph, containing "STRUCTURE_1bae", creates the "Structure Box" on the page.
| + | <StructureSection load='1bae' size='340' side='right'caption='[[1bae]]' 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'>[[1bae]] is a 2 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=1BAE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BAE 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_1bae| PDB=1bae | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bae FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bae OCA], [https://pdbe.org/1bae PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bae RCSB], [https://www.ebi.ac.uk/pdbsum/1bae PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bae ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''STRUCTURE OF DNA (5'-D 5MCCTTTACC-3')2, NMR, 1 STRUCTURE'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Synthetic construct]] |
| - | BACKGROUND: Repetitive cytosine-rich DNA sequences have been identified in telomeres and centromeres of eukaryotic chromosomes. These sequences play a role in maintaining chromosome stability during replication and may be involved in chromosome pairing during meiosis. The C-rich repeats can fold into an 'i-motif' structure, in which two parallel-stranded duplexes with hemiprotonated C.C+ pairs are intercalated. Previous NMR studies of naturally occurring repeats have produced poor NMR spectra. This led us to investigate oligonucleotides, based on natural sequences, to produce higher quality spectra and thus provide further information as to the structure and possible biological function of the i-motif. RESULTS: NMR spectroscopy has shown that d(5mCCTTTACC) forms an i-motif dimer of symmetry-related and intercalated folded strands. The high-definition structure is computed on the basis of the build-up rates of 29 intraresidue and 35 interresidue nuclear Overhauser effect (NOE) connectivities. The i-motif core includes intercalated interstrand C.C+ pairs stacked in the order 2*.8/1.7*/1*.7/2.8* (where one strand is distinguished by an asterisk and the numbers relate to the base positions within the repeat). The TTTA sequences form two loops which span the two wide grooves on opposite sides of the i-motif core; the i-motif core is extended at both ends by the stacking of A6 onto C2.C8+. The lifetimes of pairs C2.C8+ and 5mC1.C7+ are 1 ms and 1 s, respectively, at 15 degrees C. Anomalous exchange properties of the T3 imino proton indicate hydrogen bonding to A6 N7 via a water bridge. The d(5mCCTTTTCC) deoxyoligonucleotide, in which position 6 is occupied by a thymidine instead of an adenine, also forms a symmetric i-motif dimer. However, in this structure the two TTTT loops are located on the same side of the i-motif core and the C.C+ pairs are formed by equivalent cytidines stacked in the order 8*.8/1.1*/7*.7/2.2*. CONCLUSIONS: Oligodeoxynucleotides containing two C-rich repeats can fold and dimerize into an i-motif. The change of folding topology resulting from the substitution of a single nucleoside emphasizes the influence of the loop residues on the i-motif structure formed by two folded strands.
| + | [[Category: Leroy JL]] |
| - | | + | [[Category: Nonin S]] |
| - | ==About this Structure== | + | [[Category: Tuan AP]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BAE OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Solution structure and base pair opening kinetics of the i-motif dimer of d(5mCCTTTACC): a noncanonical structure with possible roles in chromosome stability., Nonin S, Phan AT, Leroy JL, Structure. 1997 Sep 15;5(9):1231-46. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9331414 9331414]
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| - | [[Category: Leroy, J L.]]
| + | |
| - | [[Category: Nonin, S.]] | + | |
| - | [[Category: Tuan, A P.]] | + | |
| - | [[Category: Deoxyribonucleic acid]] | + | |
| - | [[Category: Dimer]] | + | |
| - | [[Category: Dna dimer of 5mcctttacc]] | + | |
| - | [[Category: I-motif]] | + | |
| - | [[Category: Nmr]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 11:16:26 2008''
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