Xylo-Configured oligonucleotides (XNA, xylo nucleic acid): synthesis of conformationally restricted derivatives and hybridization towards DNA and RNA complements

Xylo-Configured oligonucleotides (XNA) containing a novel conformationally restricted 2′-deoxy-2′-fluoro-β- -xylofuranosyl nucleotide monomer, a novel conformationally locked 2′-amino-2′-deoxy-2′-N,4′-C-methylene-β- -xylofuranosyl nucleotide monomer, and a known 2′-deoxy-β- -xylofuranosyl nucleotide monomer (XNA monomers) have been synthesized and their hybridization towards DNA and RNA complements studied. Thermal denaturation studies of nine-mer mixed-base sequences composed of a mixture of XNA monomers and DNA monomers revealed preferential hybridization towards RNA complements relative to DNA complements. For 14-mer homo-thymine XNAs containing thirteen XNA monomers, stable complexes towards single-stranded DNA and RNA were formed at pH 7. Gel-shift experiments revealed these complexes to involve at least two XNA strands per DNA or RNA target strand.