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1fc8

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NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC)

Structural highlights

1fc8 is a 1 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

The first structure of a 2'-deoxy-2'-fluoro-D-arabinose nucleic acid (2'F-ANA)/RNA duplex is presented. We report the structural characterization by NMR spectroscopy of a small hybrid hairpin, r(GGAC)d(TTCG)2'F-a(GTCC), containing a 2'F-ANA/RNA stem and a four-residue DNA loop. Complete (1)H, (13)C, (19)F, and (31)P resonance assignments, scalar coupling constants, and NOE constraints were obtained from homonuclear and heteronuclear 2D spectra. In the chimeric duplex, the RNA strand adopts a classic A-form structure having C3' endo sugar puckers. The 2'F-ANA strand is neither A-form nor B-form and contains O4' endo sugar puckers. This contrasts strongly with the dynamic sugar conformations previously observed in the DNA strands of DNA/RNA hybrid duplexes. Structural parameters for the duplex, such as minor groove width, x-displacement, and inclination, were intermediate between those of A-form and B-form duplexes and similar to those of DNA/RNA duplexes. These results rationalize the enhanced stability of 2'F-ANA/RNA duplexes and their ability to elicit RNase H activity. The results are relevant for the design of new antisense drugs based on sugar-modified nucleic acids.

NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes.,Trempe JF, Wilds CJ, Denisov AY, Pon RT, Damha MJ, Gehring K J Am Chem Soc. 2001 May 30;123(21):4896-903. PMID:11457316^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Trempe JF, Wilds CJ, Denisov AY, Pon RT, Damha MJ, Gehring K. NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes. J Am Chem Soc. 2001 May 30;123(21):4896-903. PMID:11457316

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/1fc8"

Categories: Large Structures | Gehring K | Trempe J-F

@@ Line 1: / Line 1: @@
 ==NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC)==
-<StructureSection load='1fc8' size='340' side='right'caption='[[1fc8]], [[NMR_Ensembles_of_Models | 5 NMR models]]' scene=''>
+<StructureSection load='1fc8' size='340' side='right'caption='[[1fc8]]' scene=''>
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1fc8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FC8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FC8 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=TAF:2-DEOXY-2-FLUORO-ARABINO-FURANOSYL+THYMINE-5-PHOSPHATE'>TAF</scene></td></tr>
+</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=TAF:2-DEOXY-2-FLUORO-ARABINO-FURANOSYL+THYMINE-5-PHOSPHATE'>TAF</scene></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=1fc8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fc8 OCA], [https://pdbe.org/1fc8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fc8 RCSB], [https://www.ebi.ac.uk/pdbsum/1fc8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fc8 ProSAT]</span></td></tr>
 </table>
@@ Line 21: / Line 22: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Gehring, K]]
+[[Category: Gehring K]]
-[[Category: Trempe, J F]]
+[[Category: Trempe J-F]]
-[[Category: 2'f-arabinonucleic acid]]
-[[Category: Dna]]
-[[Category: Hairpin]]
-[[Category: Hybrid duplex]]
-[[Category: Rna]]
-[[Category: Rna-dna chimera complex]]

1fc8

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Current revision

NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC)

Structural highlights

Publication Abstract from PubMed

References

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