Oligonucleotides with novel, cationic backbone substituents: Aminoethylphosphonates

Abstract

Ollgonucleotide (2-amlnoethyl)phosphonates in which the backbone consisted of isomerically pure, alternating (2-aminoethyl)-phosphonate and phosphodiester linkages have been prepared and characterized. One of these single isomer oligonucleotides (Rp) formed a more stable duplex with ONA or RNA than its corresponding natural counterpart. Hybrid stability was more pH-dependent, but less salt-dependent than a natural duplex. The specificity of hybridization was examined by hybridization of an ollgonucleotide containing one (2-aminoethyl)phosphonate to oligonucleotides possessing mismatches in the region opposite to the amlnoethyl group. In contrast to oligonucleotides containing (amlnomethyl)-phosphonate linkages, ollgonucleotide (2-aminoethyl)phosphonates were completely stable to hydrolysis in aqueous solution. These oligonucleotides were resistant to nuclease activity but did not induce RNase H mediated cleavage of a complementary RNA strand. Incubation In a serum-contalnlng medium resulted In minimal degradation over 24 hours. Studies of cell uptake by flow cytometry and confocal microscopy demonstrated temperature dependent uptake and In-tracellular localization. (2-Amlnoethyl)phosphonates represent a novel approach to the Introduction of positive charges Into the backbone of oligonucleotides. © 1994 Oxford University Press.