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.
Subject(s)
Oligoribonucleotides/chemistry , Base Pairing , Chromatography, High Pressure Liquid , Models, Molecular , Nucleic Acid Conformation , Nucleic Acid Denaturation , Oligoribonucleotides/chemical synthesis , Oligoribonucleotides/metabolism , Pentoses , Ribose , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , TemperatureABSTRACT
[formula: see text] The D-beta-ribo, D-beta-xylo, L-alpha-lyxo, and L-alpha-arabino members of the pentopyranosyl (4'-->2') oligonucleotide family show efficient intersystem cross-pairing among each other. This family of configurationally isomeric and conformationally well-defined pairing systems offers an opportunity to study structural factors that determine cross-communication between informational oligonucleotide systems of different backbone structure.
Subject(s)
Base Pairing , Oligonucleotides/chemistry , Nucleic Acid ConformationABSTRACT
[formula: see text] The L-alpha-lyxopyranosyl (4'-->3') oligonucleotide system shows cooperative base-pairing in spite of containing only five instead of the usual six covalent bonds per repetitive backbone unit. In contrast, corresponding D-beta-ribofuranosyl (4'-->3') oligonucleotides do not show adenine-thymine pairing under comparable conditions. The difference in pairing behavior relates to the conformation of the two systems' vicinal 3',4'-phosphodiester substituents, which is diaxial in the lyxopyranosyl system and 3'-axial-4'-equatorial in the ribopyranosyl system.
