J. Am. Chem. SOC.1992, 114, 6254-6255
6254
major interesting differences. These possibilities are under continuing investigation.
1
2
3
5 74 13
1
12 11 0
1
1 0 0
1
(I
7
8
0
16 16 1
0
0
1
1
0
Acknowledgment. R.D.E. is grateful to the NSF for generous support and to Professor Fred West and Dr.Christine Brzezowski for helpful suggestions and discussions. We also thank the referees and Professor Chuck Casey for helpful comments.
Supplementary Material Available: Tables of bonding and thermal parameters, positional coordinates, and synthetic and spectroscopicdetails for the reported compounds (37 pages); tables of observed and calculated structure factors (41 pages). Ordering information is given on any current masthead page.
Oligodeoxynucleotides That Contain 2’,5’’ Linkages: Synthesis and Hybridization Properties Joseph P. Dougherty, Carmelo J. Rizzo, and Ronald Breslow* Department of Chemistry, Columbia University New York, New York 10027 Received December 6, 1991 Would DNA be as useful a genetic material if the 3’-oxygen had been removed from RNA, forcing a 2’,5’’ link? Divergent predictions have been offered,’* but there was no experimental Our molecular evidence on the properties of 2’,5’’ modeling confirms that antiparallel Watson-Crick base pairing is possible, but in an open helix with poorer than normal base stacking. We have now prepared 16-mer oligodeoxynucleotides that contain one or more 2’,5’’ linkages. Such linkages prove to destabilize normal 3’,5” double helices. There is at best weak strand association, and that only at high salt concentrations, in isomeric DNA in which all links are 2’,5’’. We have described the synthesis of 1 and 2.9 Oligonucleotide synthesis was carried out on an Applied Biosystems Model 381A DNA synthesizer. The manufacturer’s cycles and reagents proved satisfactory for coupling using phosphoramidites 1 and 2. Since 0
F i i 1. Native polyacrylamide gel (201, 1X TBE). Oligomers 12,14, and 15 were 5’-end-labelled with y 3 * PATP and T4 polynucleotide kinase. The labeled oligomer (=hot”) (12 lanes 1-3, 15 lanes 7-9, 14 lanes 4-6 and 10-12,
