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| - | [[Image:1sy8.gif|left|200px]] | |
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| - | <!--
| + | ==Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spec and restrained molecular dynamics== |
| - | The line below this paragraph, containing "STRUCTURE_1sy8", creates the "Structure Box" on the page.
| + | <StructureSection load='1sy8' size='340' side='right'caption='[[1sy8]]' 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'>[[1sy8]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SY8 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sy8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sy8 OCA], [https://pdbe.org/1sy8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sy8 RCSB], [https://www.ebi.ac.uk/pdbsum/1sy8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sy8 ProSAT]</span></td></tr> |
| - | {{STRUCTURE_1sy8| PDB=1sy8 | SCENE= }}
| + | </table> |
| - | | + | __TOC__ |
| - | '''Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spec and restrained molecular dynamics'''
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | | + | [[Category: Awasthi P]] |
| - | ==Overview== | + | [[Category: Barthwal R]] |
| - | The 5' d-TpG 3' element is a part of DNA sequences involved in regulation of gene expression and is also a site for intercalation of several anticancer drugs. Solution conformation of DNA duplex d-TGATCA containing this element has been investigated by two-dimensional NMR spectroscopy. Using a total of 12 torsional angles and 121 distance constraints, structural refinement has been carried out by restrained molecular dynamics (rMDs) in vacuum up to 100 ps. The structure is characterized by a large positive roll at TpG/CpA base pair step and large negative propeller twist for AT and TA base pairs. The backbone torsional angle, gamma(O5'-C5'-C4'-C3'), of T1 residue adopts a trans-conformation which is corroborated by short intra nucleotide T1H6-T1H5' (3.7A) distance in nuclear overhauser effect spectroscopy (NOESY) spectra while the backbone torsional angle, beta(P-O5'-C5'-C4'), exists in trans as well as gauche state for T1 and C5 residues. There is evidence of significant flexibility of the sugar-phosphate backbone with rapid inter-conversion between two different conformers at TpG/CpA base pair step. The base sequence dependent variations and local structural heterogeneity have important implications in specific recognition of DNA by ligands.
| + | [[Category: Narang M]] |
| - | | + | [[Category: Sharma U]] |
| - | ==About this Structure== | + | [[Category: Srivastava N]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SY8 OCA]. | + | |
| - | | + | |
| - | ==Reference== | + | |
| - | Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics., Barthwal R, Awasthi P, Monica, Kaur M, Sharma U, Srivastava N, Barthwal SK, Govil G, J Struct Biol. 2004 Oct;148(1):34-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15363786 15363786]
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| - | [[Category: Awasthi, P.]] | + | |
| - | [[Category: Barthwal, R.]] | + | |
| - | [[Category: Narang, M.]] | + | |
| - | [[Category: Sharma, U.]] | + | |
| - | [[Category: Srivastava, N.]] | + | |
| - | [[Category: 2d-nmr of d-tgatca]] | + | |
| - | [[Category: Dna flexibility]] | + | |
| - | [[Category: Restrained molecular dynamic]] | + | |
| - | [[Category: Sequence related conformation]] | + | |
| - | [[Category: Tpg/cpa basepair step]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 09:16:24 2008''
| + | |
