Based on the above and on the remarkable properties of the
2'-O,4'-C-methylene bridged LNA monomers it was decided to synthesise
oligonucleotides comprising one or more
2'-O,4'-C-methylene-.beta.-D-xylofuranosyl nucleotide monomer(s) as the
first stereoisomer of LNA modified oligonucleotides. Modelling clearly
indicated the xylo-LNA monomers to be locked in an N-type furanose
conformation. Whereas the parent 2'-deoxy-.beta.-D-xylofuranosyl
nucleosides were shown to adopt mainly an N-type furanose conformation,
the furanose ring of the 2'-deoxy-.beta.-D-xylofuranosyl monomers present
in xylo-DNA were shown by conformational analysis and computer modelling
to prefer an S-type conformation thereby minimising steric repulsion
between the nucleobase and the 3'-O-phopshate group (Seela, F.; Womer,
Rosemeyer, H. Helv. Chem. Acta 1994, 77, 883). As no report on the
hybridisation properties and binding mode of xylo-configurated
oligonucleotides in an RNA context was believed to exist, it was the aim
to synthesise 2'-O,4'-C-methylene-.beta.-D-xylofuranosyl nucleotide
monomer and to study the thermal stability of oligonucleotides comprising
this monomer. The results showed that fully modified or almost fully
modified Xylo-LNA is useful for high-affinity targeting of complementary
nucleic acids. When taking into consideration the inverted
stereochemistry at C-3' this is a surprising fact. It is likely that
Xylo-LNA monomers, in a sequence context of Xylo-DNA monomers, should
have an affinity-increasing effect.