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| | ==5'(dCCUCCUU)3':3'(rAGGAGGAAA)5'== | | ==5'(dCCUCCUU)3':3'(rAGGAGGAAA)5'== |
| - | <StructureSection load='1ntq' size='340' side='right' caption='[[1ntq]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''> | + | <StructureSection load='1ntq' size='340' side='right'caption='[[1ntq]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1ntq]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NTQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NTQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1ntq]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NTQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NTQ FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene></td></tr> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nts|1nts]], [[1ntt|1ntt]]</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=1ntq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ntq OCA], [https://pdbe.org/1ntq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ntq RCSB], [https://www.ebi.ac.uk/pdbsum/1ntq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ntq ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ntq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ntq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ntq RCSB], [http://www.ebi.ac.uk/pdbsum/1ntq PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 1ntq" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: III, T W.Barnes]] | + | [[Category: Large Structures]] |
| - | [[Category: Krugh, T R]] | + | [[Category: Barnes III TW]] |
| - | [[Category: Turner, D H]] | + | [[Category: Krugh TR]] |
| - | [[Category: Znosko, B M]] | + | [[Category: Turner DH]] |
| - | [[Category: Dna]] | + | [[Category: Znosko BM]] |
| - | [[Category: Dna-rna complex]]
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| - | [[Category: Hybrid]]
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| - | [[Category: Propynyl]]
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| - | [[Category: Rna]]
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| Structural highlights
Publication Abstract from PubMed
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.
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:12785839[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Znosko BM, Barnes TW 3rd, Krugh TR, Turner DH. NMR studies of DNA single strands and DNA:RNA hybrids with and without 1-propynylation at C5 of oligopyrimidines. J Am Chem Soc. 2003 May 21;125(20):6090-7. PMID:12785839 doi:10.1021/ja021285d
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