Structure of a DNA Duplex That Contains -Anomeric Nucleotides and 3'-3' and 5'-5' Phosphodiester Linkages: Coexistence of Parallel a
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- 作者：James M. Aramini ; Bernd W. Kalisch ; Richard T. Pon ; Johann H. van de Sande ; and Markus W. Germann
- 刊名：Biochemistry
- 出版年：1996
- 出版时间：July 23, 1996
- 年：1996
- 卷：35
- 期：29
- 页码：9355 - 9365
- 全文大小：541K
- 年卷期：v.35,no.29(July 23, 1996)
- ISSN：1520-4995
文摘
We report a comparative spectroscopic study of a novelself-complementary duplex decamer,d(GCGAAT-3'-3'-(
T)-5'-5'-CGC)2, in which an -anomericnucleotide has been inserted into the sequencein a parallel orientation via 3'-3' and 5'-5' phosphodiester bonds,and its unmodified B-DNA analog,d(GCGAATTCGC)2. Plots of the hyperchromicity andcircular dichroism of these oligonucleotides arevirtually identical, indicating that the overall base stacking andhandedness are preserved in the duplex.Thermodynamic parameters extracted from UV melting experimentsshow that the duplex is only slightlyless stable than the control. A near complete set of1H and 31P nuclear magnetic resonance(NMR)assignments were obtained for both duplexes using classical one- andtwo-dimensional approaches. Severallines of evidence, in particular, imino 1H,31P, nuclear Overhauser enhancement, and deoxyriboseringproton spin-spin coupling data, convincingly demonstrate that theoverall structural integrity of the and control duplexes are quite comparable, with any perturbations inthe former localized to the regionsof the construct encompassing the -nucleotide and the uniquebackbone linkages. Specifically, the duplex exhibits normal Watson-Crick type base pairing, it remainsantiparallel except at the invertednucleotide, all bases are in the anti orientation, and the sugar ringpuckering is predominantly "S"-type.However, the J-coupling information for the-nucleotide and the neighboring (3') cytidine arenotablydifferent, and reflect a decrease in the amplitude of the sugar puckerin T7, and a significant shift in theconformational equilibrium of the furanose ring in C8 toward the"N"-type pucker. The feasibility ofsynthesizing oligodeoxynucleotides containing a combination of sugars and short parallel strandedsegments, their propensity for forming stable duplexes, and thestructural insights into such complexesreported here are of potential importance in the area of antisensetherapy.
T)-5'-5'-CGC)2, in which an -anomericnucleotide has been inserted into the sequencein a parallel orientation via 3'-3' and 5'-5' phosphodiester bonds,and its unmodified B-DNA analog,d(GCGAATTCGC)2. Plots of the hyperchromicity andcircular dichroism of these oligonucleotides arevirtually identical, indicating that the overall base stacking andhandedness are preserved in the duplex.Thermodynamic parameters extracted from UV melting experimentsshow that the duplex is only slightlyless stable than the control. A near complete set of1H and 31P nuclear magnetic resonance(NMR)assignments were obtained for both duplexes using classical one- andtwo-dimensional approaches. Severallines of evidence, in particular, imino 1H,31P, nuclear Overhauser enhancement, and deoxyriboseringproton spin-spin coupling data, convincingly demonstrate that theoverall structural integrity of the and control duplexes are quite comparable, with any perturbations inthe former localized to the regionsof the construct encompassing the -nucleotide and the uniquebackbone linkages. Specifically, the duplex exhibits normal Watson-Crick type base pairing, it remainsantiparallel except at the invertednucleotide, all bases are in the anti orientation, and the sugar ringpuckering is predominantly "S"-type.However, the J-coupling information for the-nucleotide and the neighboring (3') cytidine arenotablydifferent, and reflect a decrease in the amplitude of the sugar puckerin T7, and a significant shift in theconformational equilibrium of the furanose ring in C8 toward the"N"-type pucker. The feasibility ofsynthesizing oligodeoxynucleotides containing a combination of sugars and short parallel strandedsegments, their propensity for forming stable duplexes, and thestructural insights into such complexesreported here are of potential importance in the area of antisensetherapy.