Synthesis and RNA-selective hybridization of α- l- ribo- and β- d- lyxo-configured oligonucleotides

Abstract

Three α- l-ribofuranosyl analogues of RNA nucleotides (α- l-RNA analogues) have been synthesized and incorporated into oligonucleotides using the phosphoramide approach on an automated DNA synthesizer. The 4′- C-hydroxymethyl-α- l-ribofuranosyl thymine monomer was furthermore synthesized. Relative to the unmodified duplexes, incorporation of a single α- l-RNA monomer into a DNA strand leads to reduced thermal stability of duplexes with DNA complements but unchanged thermal stability of duplexes with RNA complements, whereas incorporation of more than one α- l-RNA monomer lead to moderately decreased thermal stability also of duplexes with RNA complements. Efficient hybridization with an RNA complement and no melting transition with a DNA complement were observed with stereoregular chimeric oligonucleotides composed of a mixture of α- l-RNA and affinity enhancing α- l-LNA monomers (α- l- ribo-configured locked nucleic acid). Furthermore, duplexes formed between oligodeoxynucleotides containing an α- l-RNA monomer and complementary RNA were good substrates for Escherichia coli RNase H. RNA-selective hybridization was also achieved by the incorporation of 1-(4- C-hydroxymethyl-β- d-lyxofuranosyl)thymine monomers into a DNA strand, whereas stable duplexes were formed with both complementary DNA and RNA when these monomers were incorporated into an RNA strand.