Pentopyranosyl oligonucleotide systems. Part 11: Systems with shortened backbones: (D)-beta-ribopyranosyl-(4 '-> 3 ')- and (L)-alpha-lyxopyranosyl-(4'-> 3 ')-oligonucleotides

The (L)-alpha -lyxopyranosyl-(4 ' -->3 ')-oligonucleotide system-a member o f a pentopyranosyl oligonucleotide family containing a shortened backbone-i s capable of cooperative base-pairing and of cross-pairing with DNA and RNA . In contrast, corresponding (D)-beta -ribopyransoyl-(4 ' -->3 ')-oligonucl eotides do not show base-pairing under similar conditions. We conclude that oligonucleotide systems can violate the 'six-bonds-per-backbone-unit' rule by having five bonds instead, if their vicinally bound phosphodiester brid ges can assume an antiperiplanar conformation. An additional structural fea ture that seems relevant to the cross-pairing capability of the (L)-alpha - lyxopyranosyl-(4 ' -->3 ')-oligonucleotide system is its (small) backbone/b asepair axes inclination. An inclination which is similar to that in B-DNA seems to be a prerequisite for an oligonucleotide system's capability to cr oss-pair with DNA. (C) 2001 Elsevier Science Ltd. All rights reserved.