1ntq

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

1ntq is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ntq"

Categories: Large Structures | Barnes III TW | Krugh TR | Turner DH | Znosko BM

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1ntq.png|left|200px]]
-<!--
+==5'(dCCUCCUU)3':3'(rAGGAGGAAA)5'==
-The line below this paragraph, containing "STRUCTURE_1ntq", creates the "Structure Box" on the page.
+<StructureSection load='1ntq' size='340' side='right'caption='[[1ntq]]' 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'>[[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>
-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=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>
-{{STRUCTURE_1ntq|  PDB=1ntq  |  SCENE=  }}
+</table>
+<div style="background-color:#fffaf0;">
+== 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.
-===5'(dCCUCCUU)3':3'(rAGGAGGAAA)5'===
+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<ref>PMID:12785839</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12785839}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ntq" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12785839 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12785839}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NTQ OCA].
+[[Category: Barnes III TW]]
+[[Category: Krugh TR]]
-==Reference==
+[[Category: Turner DH]]
-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: Znosko BM]]
-[[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 Sun Jul 27 14:01:16 2008''

1ntq

From Proteopedia

Current revision

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

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox