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1hoq

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(New page: 200px<br /><applet load="1hoq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1hoq" /> '''CHIMERIC RNA/DNA HAIRPIN'''<br /> ==Overvie...)
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[[Image:1hoq.gif|left|200px]]<br /><applet load="1hoq" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1hoq" />
 
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'''CHIMERIC RNA/DNA HAIRPIN'''<br />
 
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==Overview==
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==CHIMERIC RNA/DNA HAIRPIN==
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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.
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<StructureSection load='1hoq' size='340' side='right'caption='[[1hoq]]' scene=''>
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== Structural highlights ==
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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>
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1HOQ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1HOQ OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=11691916 11691916]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1hoq" style="background-color:#fffaf0;"></div>
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[[Category: Denisov, A.Y.]]
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== References ==
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[[Category: Gehring, K.]]
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<references/>
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[[Category: dna]]
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__TOC__
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[[Category: hairpin]]
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</StructureSection>
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[[Category: rna]]
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[[Category: Large Structures]]
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[[Category: Denisov AY]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:50:52 2007''
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[[Category: Gehring K]]

Current revision

CHIMERIC RNA/DNA HAIRPIN

PDB ID 1hoq

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