title: Pentopyranosyl oligonucleotide systems. Part 11: Systems with shortened backbones: (D)-beta-ribopyranosyl-(4'-->3')- and (L)-alpha-lyxopyranosyl-(4'-->3')-oligonucleotides.
abstract: The (L)-alpha-lyxopyranosyl-(4'-->3')-oligonucleotide system-a member of a pentopyranosyl oligonucleotide family containing a shortened backbone-is capable of cooperative base-pairing and of cross-pairing with DNA and RNA. In contrast, corresponding (D)-beta-ribopyransoyl-(4'-->3')-oligonucleotides 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 bridges can assume an antiperiplanar conformation. An additional structural feature that seems relevant to the cross-pairing capability of the (L)-alpha-lyxopyranosyl-(4'-->3')-oligonucleotide system is its (small) backbone/basepair axes inclination. An inclination which is similar to that in B-DNA seems to be a prerequisite for an oligonucleotide system's capability to cross-pair with DNA.
authors.affiliation: The Skaggs Institute for Chemical Biology at The Scripps Research Institute (TSRI), 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
authors.forename: H
authors.initials: H
authors.lastname: Wippo
authors.forename: F
authors.initials: F
authors.lastname: Reck
authors.forename: R
authors.initials: R
authors.lastname: Kudick
authors.forename: M
authors.initials: M
authors.lastname: Ramaseshan
authors.forename: G
authors.initials: G
authors.lastname: Ceulemans
authors.forename: M
authors.initials: M
authors.lastname: Bolli
authors.forename: R
authors.initials: R
authors.lastname: Krishnamurthy
authors.forename: A
authors.initials: A
authors.lastname: Eschenmoser
mesh_terms: D020029:Base Pairing; D002851:Chromatography, High Pressure Liquid; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism; D010429:Pentoses; D012266:Ribose; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013696:Temperature
chemical_list: D009843:Oligoribonucleotides; D010429:Pentoses; C043333:lyxose; D012266:Ribose