X-Ray analyses of hybrid duplexes between antisense oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2′-O-methyluridine and their target RNAs

Incorporation of 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine ((N)Um) into oligonucleotides increases antisense properties such as RNA binding affinity, nuclease resistance and RNase H activity. The present X-ray studies on hybrid duplexes formed between antisense oligonucleotides containing (N)Um and their target RNAs have revealed the structural basis for such properties. The terminal ammonium groups of the aminohexyl chains interact with the phosphate oxygen anions. The 2'-O-methyl modification induces the ribose group to adopt the C3'-endo conformation. Comparisons with the structure of unmodified duplex show that the (N)Um incorporation narrows the minor grooves and alters their hydration structures. These structural changes are well correlated to the favorable properties for useful antisense molecules.