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| - | [[Image:1nts.gif|left|200px]] | |
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| - | <!--
| + | ==5'(dCCPUPCPCPUPUP)3':3'(rAGGAGGAAA)5', where P=propynyl== |
| - | The line below this paragraph, containing "STRUCTURE_1nts", creates the "Structure Box" on the page.
| + | <StructureSection load='1nts' size='340' side='right'caption='[[1nts]]' 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'>[[1nts]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NTS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NTS 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=5PC:5(1-PROPYNYL)-2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>5PC</scene>, <scene name='pdbligand=PDU:5(1-PROPYNYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>PDU</scene></td></tr> |
| - | {{STRUCTURE_1nts| PDB=1nts | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nts OCA], [https://pdbe.org/1nts PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nts RCSB], [https://www.ebi.ac.uk/pdbsum/1nts PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nts ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''5'(dCCPUPCPCPUPUP)3':3'(rAGGAGGAAA)5', where P=propynyl'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Barnes III TW]] |
| - | The 1-propynylation at C5 of consecutive pyrimidines in DNA can enhance DNA:RNA hybrid stability at 37 degrees C by over 1 kcal/mol of substitution [Barnes, T. W., III; Turner, D. H. J. Am. Chem. Soc.2001, 123, 4107-4118]. To provide information on the structural consequences of propynylation, two-dimensional NMR spectroscopy was used to study the structures of several oligonucleotides. Intraresidue nuclear Overhauser effect spectroscopy cross peaks were observed at 30 degrees C and a 200 ms mixing time in the H6-H1' region for 5'(dC(P)C(P)U(P)C(P)C(P)U(P)U(P)) (ssPrODN) but not for 5'(dCCUCCUU) (ssODN), suggesting preorganization of the propynylated single strand. NMR structures of the duplexes 5'(dC(P)C(P)U(P)C(P)C(P)U(P)U(P))3':3'(rGAGGAGGAAAU)5' (PrODN:RNA), 5'(dCC(P)U(P)C(P)C(P)U(P)U(P))3':3'(rGAGGAGGAAAU)5' (sPrODN1:RNA), and 5'(dCCUCCUU)3':3'(rGAGGAGGAAAU)5' (ODN:RNA) indicate that their global structures are almost identical. The NMR data, however, suggest that the 5'-end of sPrODN1:RNA is more dynamic than that of PrODN:RNA. In the propynylated duplexes, the propyne group stacks on the aromatic ring of the 5'-base and extends into the major groove. The results suggest that the increased stability of the propynylated duplexes is caused by preorganization of the propynylated single strand and different interactions in the double strand. The propynyl group provides volume exclusion, enhanced stacking, and possibly different solvation.
| + | [[Category: Krugh TR]] |
| - | | + | [[Category: Turner DH]] |
| - | ==About this Structure== | + | [[Category: Znosko BM]] |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NTS OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | NMR studies of DNA single strands and DNA:RNA hybrids with and without 1-propynylation at C5 of oligopyrimidines., Znosko BM, Barnes TW 3rd, Krugh TR, Turner DH, J Am Chem Soc. 2003 May 21;125(20):6090-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12785839 12785839]
| + | |
| - | [[Category: III, T W.Barnes.]] | + | |
| - | [[Category: Krugh, T R.]]
| + | |
| - | [[Category: Turner, D H.]] | + | |
| - | [[Category: Znosko, B M.]] | + | |
| - | [[Category: Dna]] | + | |
| - | [[Category: Hybrid]] | + | |
| - | [[Category: Propynyl]] | + | |
| - | [[Category: Rna]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:58:15 2008''
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