1fc8: Difference between revisions

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

OverviewOverview

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.

About this StructureAbout this Structure

1FC8 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Mar 20 11:07:13 2008

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OCA

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-[[Image:1fc8.gif|left|200px]]<br /><applet load="1fc8" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1fc8.gif|left|200px]]
-caption="1fc8" />
-'''NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC)'''<br />
+ {{Structure
+|PDB= 1fc8 |SIZE=350|CAPTION= <scene name='initialview01'>1fc8</scene>
+|SITE=
+|LIGAND=
+|ACTIVITY=
+|GENE=
+}}
+'''NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC)'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-FC8 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1FC8 OCA].
+FC8 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=1FC8 OCA].
 ==Reference==
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11457316 11457316]
+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:[http://www.ncbi.nlm.nih.gov/pubmed/11457316 11457316]
 [[Category: Protein complex]]
 [[Category: Gehring, K.]]
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 [[Category: rna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:37:10 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:07:13 2008''