ACYCLIC OLIGONUCLEOTIDES - POSSIBILITIES AND LIMITATIONS

Oligonucleotides containing acyclic nucleosides with a 3(S),5-dihydroxypentyl (1a-e) or 4(R)-methoxy-3(S),5-dihydroxypentyl (2a) side chain were prepared and their hybridization properties as well as their stability towards degradation with snake venom posphodiesterase were studied. Attachment of an acyclic nucleoside at the 3'-end of an oligonucleotide makes it extremely resistant against enzymatic breakdown. Whereas oligonucleotides consisting completely of acyclic 2'-deoxyadenosine analogues (1a or 2a) can still hybridize with an unmodified oligothymidylate, completely modified oligothymidylates or hetero-oligomers do not hybridize with their unmodified complementary oligonucleotide. This can be explained by the favourable enthalpy change on hybridization for the oligomers with adenine bases because of their higher degree of stacking and the ability to form T-A . T triplets. In base-pairing with the natural DNA-nucleosides (dA,dC,dG,T), the acyclic nucleoside analogues (1a-e) discriminate less compared to the natural 2'-deoxynucleosides. 9-(3(S),5-Dihydroxypentyl)hypoxanthine shows the least spreading in melting temperature on hybridization with the four natural 2'-deoxynucleosides. Because of their conformation flexibility, acyclic nucleosides can be considered as universal nucleoside for the design of probes with ambiguous positions.