Oligonucleotides with novel, cationic backbone substituents: aminoethylphosphonates.
Oligonucleotide (2-aminoethyl)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 DNA 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 oligonucleotide containing one (2-aminoethyl)phosphonate to oligonucleotides possessing mismatches in the region opposite to the aminoethyl group. In contrast to oligonucleotides containing (aminomethyl)-phosphonate linkages, oligonucleotide (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-containing medium resulted in minimal degradation over 24 hours. Studies of cell uptake by flow cytometry and confocal microscopy demonstrated temperature dependent uptake and intracellular localization. (2-Aminoethyl)phosphonates represent a novel approach to the introduction of positive charges into the backbone of oligonucleotides.
Fathi
R
R
PharmaGenics, Inc., Allendale, NJ 07401.
Huang
Q
Q
Coppola
G
G
Delaney
W
W
Teasdale
R
R
Krieg
A M
AM
Cook
A F
AF
D000615:Aminoethylphosphonic Acid / Q000031:analogs & derivatives* / Q000378:metabolism; D001402:B-Lymphocytes; D001483:Base Sequence; D001769:Blood; D002478:Cells, Cultured; D006801:Humans; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D009692:Nucleic Acid Heteroduplexes / Q000378:metabolism; D009693:Nucleic Acid Hybridization; D011089:Polydeoxyribonucleotides / Q000138:chemical synthesis* / Q000378:metabolism; D011131:Polyribonucleotides / Q000138:chemical synthesis / Q000378:metabolism; D016914:Ribonuclease H; D015719:Single-Strand Specific DNA and RNA Endonucleases
D009692:Nucleic Acid Heteroduplexes; D011089:Polydeoxyribonucleotides; D011131:Polyribonucleotides; D000615:Aminoethylphosphonic Acid; D016914:Ribonuclease H; D015719:Single-Strand Specific DNA and RNA Endonucleases