1ntq

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[[Image:1ntq.gif|left|200px]]
[[Image:1ntq.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 1ntq |SIZE=350|CAPTION= <scene name='initialview01'>1ntq</scene>
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The line below this paragraph, containing "STRUCTURE_1ntq", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DU:2&#39;-DEOXYURIDINE-5&#39;-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>
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|ACTIVITY=
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|GENE=
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|DOMAIN=
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{{STRUCTURE_1ntq| PDB=1ntq | SCENE= }}
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|RELATEDENTRY=[[1nts|1NTS]], [[1ntt|1NTT]]
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|RESOURCES=<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.ebi.ac.uk/pdbsum/1ntq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ntq RCSB]</span>
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'''5'(dCCUCCUU)3':3'(rAGGAGGAAA)5''''
'''5'(dCCUCCUU)3':3'(rAGGAGGAAA)5''''
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==About this Structure==
==About this Structure==
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1NTQ is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NTQ OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NTQ OCA].
==Reference==
==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]
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]
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[[Category: Protein complex]]
 
[[Category: III, T W.Barnes.]]
[[Category: III, T W.Barnes.]]
[[Category: Krugh, T R.]]
[[Category: Krugh, T R.]]
[[Category: Turner, D H.]]
[[Category: Turner, D H.]]
[[Category: Znosko, B M.]]
[[Category: Znosko, B M.]]
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[[Category: dna]]
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[[Category: Dna]]
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[[Category: hybrid]]
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[[Category: Hybrid]]
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[[Category: propynyl]]
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[[Category: Propynyl]]
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[[Category: rna]]
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[[Category: Rna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:58:06 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:35:26 2008''
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Revision as of 23:58, 2 May 2008

Image:1ntq.gif

Template:STRUCTURE 1ntq

5'(dCCUCCUU)3':3'(rAGGAGGAAA)5'


Overview

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.

About this Structure

Full crystallographic information is available from 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:12785839 Page seeded by OCA on Sat May 3 02:58:06 2008

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