Solution Structure of a DNA·RNA Hybrid Containing an -Anomeric Thymidine and Polarity Reversals: d(ATGG-3'-3'-
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- 作者：James M. Aramini and Markus W. Germann
- 刊名：Biochemistry
- 出版年：1999
- 出版时间：November 23, 1999
- 年：1999
- 卷：38
- 期：47
- 页码：15448 - 15458
- 全文大小：283K
- 年卷期：v.38,no.47(November 23, 1999)
- ISSN：1520-4995
文摘
We report the thermodynamic and structural properties of an 
-containing DNA·RNA nonamerhybrid duplex, d(ATGG-3'-3'-T-5'-5'-GCTC)·r(gagcaccau). The RNA strand corresponds to the core ofthe initiation sequence for the transcript of the erbB-2 oncogene. The tandem anomeric and polarity changesin the DNA strand result in a slight decrease in thermostability (
Tm = -2.8 
C) compared to theunmodified control hybrid. The three-dimensional solution structure determination of the -containingDNA·RNA hybrid, conducted via restrained molecular dynamics using interproton distance (nuclearOverhauser enhancement) and furanose ring torsion angle (J-based) restraints, converged to a final ensembleof structures from unique starting models. In agreement with hyperchromicity and circular dichroismdata, the final average structure derived from this ensemble is consistent with an overall A-like motiffeaturing Watson-Crick base pairing and base stacking across the entire sequence, albeit with localizedB-like traits within the DNA strand. Comparative pseudorotation analyses of the J-coupling data for thishybrid and its unmodified control reveal a surprising increase in S-puckering for two nucleotidesimmediately upstream of the 3'-3' linkage, and the associated narrowing of the minor groove in thisportion of the hybrid. Other structural perturbations are localized to and diagnostic of the central-nucleotide and juxtaposed polarity reversals. The structural information presented here has direct relevanceto the design of future antisense oligonucleotides composed of these modifications.
-containing DNA·RNA nonamerhybrid duplex, d(ATGG-3'-3'-T-5'-5'-GCTC)·r(gagcaccau). The RNA strand corresponds to the core ofthe initiation sequence for the transcript of the erbB-2 oncogene. The tandem anomeric and polarity changesin the DNA strand result in a slight decrease in thermostability (Tm = -2.8 C) compared to theunmodified control hybrid. The three-dimensional solution structure determination of the -containingDNA·RNA hybrid, conducted via restrained molecular dynamics using interproton distance (nuclearOverhauser enhancement) and furanose ring torsion angle (J-based) restraints, converged to a final ensembleof structures from unique starting models. In agreement with hyperchromicity and circular dichroismdata, the final average structure derived from this ensemble is consistent with an overall A-like motiffeaturing Watson-Crick base pairing and base stacking across the entire sequence, albeit with localizedB-like traits within the DNA strand. Comparative pseudorotation analyses of the J-coupling data for thishybrid and its unmodified control reveal a surprising increase in S-puckering for two nucleotidesimmediately upstream of the 3'-3' linkage, and the associated narrowing of the minor groove in thisportion of the hybrid. Other structural perturbations are localized to and diagnostic of the central-nucleotide and juxtaposed polarity reversals. The structural information presented here has direct relevanceto the design of future antisense oligonucleotides composed of these modifications.