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[[Image:1ho6.gif|left|200px]]


{{Structure
==CHIMERIC ARABINONUCLEIC ACID (ANA) HAIRPIN WITH ANA/RNA HYBRID STEM==
|PDB= 1ho6 |SIZE=350|CAPTION= <scene name='initialview01'>1ho6</scene>
<StructureSection load='1ho6' size='340' side='right'caption='[[1ho6]]' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CAR:CYTOSINE+ARABINOSE-5&#39;-PHOSPHATE'>CAR</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=GAO:GUANINE+ARABINOSE-5&#39;-PHOSPHATE'>GAO</scene>, <scene name='pdbligand=UAR:URACIL+ARABINOSE-5&#39;-PHOSPHATE'>UAR</scene>
<table><tr><td colspan='2'>[[1ho6]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HO6 FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAR:CYTOSINE+ARABINOSE-5-PHOSPHATE'>CAR</scene>, <scene name='pdbligand=GAO:GUANINE+ARABINOSE-5-PHOSPHATE'>GAO</scene>, <scene name='pdbligand=UAR:URACIL+ARABINOSE-5-PHOSPHATE'>UAR</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ho6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ho6 OCA], [https://pdbe.org/1ho6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ho6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ho6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ho6 ProSAT]</span></td></tr>
|RELATEDENTRY=[[1fc8|1FC8]], [[1hoq|1HOQ]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ho6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ho6 OCA], [http://www.ebi.ac.uk/pdbsum/1ho6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ho6 RCSB]</span>
<div style="background-color:#fffaf0;">
}}
== Publication Abstract from PubMed ==
 
'''CHIMERIC ARABINONUCLEIC ACID (ANA) HAIRPIN WITH ANA/RNA HYBRID STEM'''
 
 
==Overview==
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.
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.


==About this Structure==
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>
1HO6 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=1HO6 OCA].
 
==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: Protein complex]]
[[Category: Denisov, A Y.]]
[[Category: Gehring, K.]]
[[Category: arabinonucleic acid]]
[[Category: hairpin]]
[[Category: rna]]


''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:08:17 2008''
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ho6" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Denisov AY]]
[[Category: Gehring K]]

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