Structure of a DNA duplex that contains alpha-anomeric nucleotides and 3'-3' and 5'-5' phosphodiester linkages: Coexistence of parallel and antiparallel DNA

被引:30
作者
Aramini, JM
Kalisch, BW
Pon, RT
vandeSande, JH
Germann, MW
机构
[1] THOMAS JEFFERSON UNIV, KIMMEL CANC INST, DEPT PHARMACOL, PHILADELPHIA, PA 19107 USA
[2] UNIV CALGARY, DEPT MED BIOCHEM, CALGARY, AB T2N 4N1, CANADA
关键词
D O I
10.1021/bi960612p
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
We report a comparative spectroscopic study of a novel self-complementary duplex decamer, d(GCGAAT-3'-3'-(alpha T)-5'-5'-CGC)(2), in which an alpha-anomeric nucleotide has been inserted into the sequence in a parallel orientation via 3'-3' and 5'-5' phosphodiester bonds, and its unmodified B-DNA analog, d(GCGAATTCGC)(2). Plots of the hyperchromicity and circular dichroism of these oligonucleotides are virtually identical, indicating that the overall base stacking and handedness are preserved in the alpha duplex. Thermodynamic parameters extracted from UV melting experiments show that the alpha duplex is only slightly less stable than the control. A near complete set of H-1 and P-31 nuclear magnetic resonance (NMR) assignments were obtained for both duplexes using classical one- and two-dimensional approaches. Several lines of evidence, in particular, imino H-1, P-31, nuclear Overhauser enhancement, and deoxyribose ring proton spin-spin coupling data, convincingly demonstrate that the overall structural integrity of the alpha and control duplexes are quite comparable, with any perturbations in the former localized to the regions of the construct encompassing the alpha-nucleotide and the unique backbone linkages. Specifically, the alpha duplex exhibits normal Watson-Crick type base pairing, it remains antiparallel except at the inverted nucleotide, all bases are in the anti orientation, and the sugar ring puckering is predominantly ''S''-type. However, the J-coupling information for the alpha-nucleotide and the neighboring (3') cytidine are notably different, and reflect a decrease in the amplitude of the sugar pucker in alpha T7, and a significant shift in the conformational equilibrium of the furanose ring in C8 toward the ''N''-type pucker. The feasibility of synthesizing oligodeoxynucleotides containing a combination of alpha sugars and short parallel stranded segments, their propensity for forming stable duplexes, and the structural insights into such complexes reported here are of potential importance in the area of antisense therapy.
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页码:9355 / 9365
页数:11
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共 60 条
[1]  
[Anonymous], 1980, BIOPHYS CHEM
[2]   MLEV-17-BASED TWO-DIMENSIONAL HOMONUCLEAR MAGNETIZATION TRANSFER SPECTROSCOPY [J].
BAX, A ;
DAVIS, DG .
JOURNAL OF MAGNETIC RESONANCE, 1985, 65 (02) :355-360
[3]   COMPARATIVE ACTIVITY OF ALPHA-ANOMERIC AND BETA-ANOMERIC OLIGONUCLEOTIDES ON RABBIT BETA-GLOBIN SYNTHESIS - INHIBITORY EFFECT OF CAP TARGETED ALPHA-OLIGONUCLEOTIDES [J].
BERTRAND, JR ;
IMBACH, JL ;
PAOLETTI, C ;
MALVY, C .
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 1989, 164 (01) :311-318
[4]   CHIMERIC ALPHA-BETA OLIGONUCLEOTIDES AS ANTISENSE INHIBITORS OF REVERSE TRANSCRIPTION [J].
BOIZIAU, C ;
DEBART, F ;
RAYNER, B ;
IMBACH, JL ;
TOULME, JJ .
FEBS LETTERS, 1995, 361 (01) :41-45
[5]   INHIBITION OF TRANSLATION INITIATION BY ANTISENSE OLIGONUCLEOTIDES VIA AN RNASE-H INDEPENDENT MECHANISM [J].
BOIZIAU, C ;
KURFURST, R ;
CAZENAVE, C ;
ROIG, V ;
THUONG, NT ;
TOULME, JJ .
NUCLEIC ACIDS RESEARCH, 1991, 19 (05) :1113-1119
[6]   MECHANISMS OF THE INHIBITION OF REVERSE TRANSCRIPTION BY ANTISENSE OLIGONUCLEOTIDES [J].
BOIZIAU, C ;
THUONG, NT ;
TOULME, JJ .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1992, 89 (02) :768-772
[7]  
BORGIAS BA, 1989, METHOD ENZYMOL, V176, P169
[8]  
Chaconas G, 1980, Methods Enzymol, V65, P75
[9]  
CHEN CW, 1984, PHOSPHORUS 31 NMR PR, P233
[10]   PROGRESS TOWARD OLIGONUCLEOTIDE THERAPEUTICS - PHARMACODYNAMIC PROPERTIES [J].
CROOKE, ST .
FASEB JOURNAL, 1993, 7 (06) :533-539