Studies on anti-human immunodeficiency virus oligonucleotides that have alternating methylphosphonate/phosphodiester linkages

Preliminary investigations of the physical properties of oligonucleotide an alogs that contain alternating methylphosphonate/phosphodiester linkages ar e described. An alternating oligo-2'-O-methylribonucleoside methylphosphona te, oligomer 1676, whose sequence is complementary to the upper hairpin reg ion of human immunodeficiency virus TAR RNA, has been synthesized. This 15- mer forms a very stable duplex with its complementary RNA target, whose mel ting temperature is 71 degrees C. Introduction of two mismatched bases redu ces the melting temperature by 16 degrees C. Similar results were obtained with the all-phosphodiester version of oligomer 1676, which demonstrates th at introduction of the methylphosphonate linkages does not significantly pe rturb the ability of the oligo-3'-O-methylribonucleoside methylphosphonate to bind to RNA. Unlike the phosphodiester oligomer, however, oligomer 1676 is completely resistant to hydrolysis by the 3'-exonuclease activity found in mammalian serum. The interactions between nuclease-resistant, 5'-psorale n-derivatized, alternating oligo-2'-deoxypyrimidine methylphosphonates and double-stranded DNA were also studied. A 15-mer that contains thymine, 5-me thylcytosine, and 5-propynyl-uracil forms a tripler with a polypurine tract found in the env gene of human immunodeficiency virus proviral DNA with an apparent dissociation constant of 400 nM at 22 degrees C. Maximal tripler formation by these oligomers is observed at approximately 2.5 mM magnesium, whereas maximal tripler formation by the corresponding all-phosphodiester oligomers occurs between 10 and 20 mM magnesium. This reduced magnesium dep endence most likely results from reduced charge repulsion between the backb ones of the methylphosphonate oligomer and purine strand of the target. The nuclease stability and ability of the methylphosphonate oligomers to form stable complexes with their target nucleic acids suggest that these oligome rs are potential candidates for use as antisense or antigene agents in cell culture (C) 2000 Elsevier Science Inc. All rights reserved.