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Nucleic Acids Research, 1989, Vol. 17, No. 18 7253-7262
© 1989

CHEMISTRY

Number and distribution of methyiphosphonate linkages in oligodeoxynucleotides affect exo- and endonuclease sensitivity and ability to form RNase H substrates

Robin S. Quartin, Christine L. Brakel1 and G. Wetmur*,

Department of Microbiology, Box 1124, Mount Sinai School of Medicine New York, NY 10029, USA 1Enzo Biochem Inc. 325 Hudson St., New York, NY 10013. USA

*To whom correspondence should be addressed

Received June 26, 1989. Revised August 15, 1989. Accepted August 15, 1989.

Oligodeoxynucleotides with different arrangements of methylphosphonate linkages were examined for nuclease sensitivity in vitro, stability in tissue culture, and ability to form RNase H-sensitive substrates with complementary RNA. After nuclease treatment, resistance was demonstrated by the ability to alter the electrophoretic mobility of a labeled complementary phosphodiester oligodeoxynucleotide. Both 5'- and 3'-exonuclease activities were retarded by methylphosphonate linkages. Methylphosphonate-containing oligodeoxynucleotides with 1 –5 adjacent phosphodiester linkages were tested as substrates for the endonucleases DNase I and DNase II. The results indicated that a span of three or fewer contiguous internal phosphodiester linkages led to the greatest resistance to endonuclease. However, in serum-supplemented culture medium half-lives of these oligodeoxynucleotides were independent of the number of contiguous phosphodiester linkages. Methylphosphonate-containing oligodeoxynucleotides were hybridized to RNA runoff transcripts and tested as substrates for RNase H. The results indicated that a span of three internal phosphodiester linkages in the oligodeoxynucleotide was necessary and sufficient to direct cleavage of the RNA in the duplex


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