1hoq: Difference between revisions

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-{{Seed}}
-[[Image:1hoq.png|left|200px]]
-<!--
+==CHIMERIC RNA/DNA HAIRPIN==
-The line below this paragraph, containing "STRUCTURE_1hoq", creates the "Structure Box" on the page.
+<StructureSection load='1hoq' size='340' side='right'caption='[[1hoq]]' 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'>[[1hoq]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HOQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HOQ 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=1hoq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hoq OCA], [https://pdbe.org/1hoq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hoq RCSB], [https://www.ebi.ac.uk/pdbsum/1hoq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hoq ProSAT]</span></td></tr>
-{{STRUCTURE_1hoq|  PDB=1hoq  |  SCENE=  }}
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hybrids of RNA and arabinonucleic acid (ANA) as well as the 2'-fluoro-ANA analog (2'F-ANA) were recently shown to be substrates of the enzyme RNase H. Although RNase H binds to double-stranded RNA, no cleavage occurs with such duplexes. Therefore, knowledge of the structure of ANA/RNA hybrids may prove helpful in the design of future antisense oligonucleotide analogs. In this study, we have determined the NMR solution structures of ANA/RNA and DNA/RNA hairpin duplexes and compared them to the recently published structure of a 2'F-ANA/RNA hairpin duplex. We demonstrate here that the sugars of RNA nucleotides of the ANA/RNA hairpin stem adopt the C3'-endo (north, A-form) conformation, whereas those of the ANA strand adopt a 'rigid' O4'-endo (east) sugar pucker. The DNA strand of the DNA/RNA hairpin stem is flexible, but the average DNA/RNA hairpin structural parameters are close to the ANA/RNA and 2'F-ANA/RNA hairpin parameters. The minor groove width of ANA/RNA, 2'F-ANA/RNA and DNA/RNA helices is 9.0 +/- 0.5 A, a value that is intermediate between that of A- and B-form duplexes. These results rationalize the ability of ANA/RNA and 2'F-ANA/RNA hybrids to elicit RNase H activity.
-===CHIMERIC RNA/DNA HAIRPIN===
+Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids.,Denisov AY, Noronha AM, Wilds CJ, Trempe JF, Pon RT, Gehring K, Damha MJ Nucleic Acids Res. 2001 Nov 1;29(21):4284-93. PMID:11691916<ref>PMID:11691916</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_11691916}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1hoq" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11691916 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11691916}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HOQ OCA].
+[[Category: Denisov AY]]
+[[Category: Gehring K]]
-==Reference==
-Solution structure of an arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2'-fluoro-ANA/RNA and DNA/RNA hybrids., Denisov AY, Noronha AM, Wilds CJ, Trempe JF, Pon RT, Gehring K, Damha MJ, Nucleic Acids Res. 2001 Nov 1;29(21):4284-93. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11691916 11691916]
-[[Category: Denisov, A Y.]]
-[[Category: Gehring, K.]]
-[[Category: Dna]]
-[[Category: Hairpin]]
-[[Category: Rna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 08:28:28 2008''