ACYCLIC OLIGONUCLEOTIDES - POSSIBILITIES AND LIMITATIONS

Oligonucleotides containing acyclic nucleosides with a 3(S),5-dihydrox ypentyl (1a-e) or 4(R)-methoxy-3(S),5-dihydroxypentyl (2a) side chain were prepared and their hybridization properties as well as their stab ility towards degradation with snake venom posphodiesterase were studi ed. Attachment of an acyclic nucleoside at the 3'-end of an oligonucle otide makes it extremely resistant against enzymatic breakdown. Wherea s oligonucleotides consisting completely of acyclic 2'-deoxyadenosine analogues (1a or 2a) can still hybridize with an unmodified oligothymi dylate, completely modified oligothymidylates or hetero-oligomers do n ot hybridize with their unmodified complementary oligonucleotide. This can be explained by the favourable enthalpy change on hybridization f or the oligomers with adenine bases because of their higher degree of stacking and the ability to form T-A . T triplets. In base-pairing wit h the natural DNA-nucleosides (dA,dC,dG,T), the acyclic nucleoside ana logues (1a-e) discriminate less compared to the natural 2'-deoxynucleo sides. 9-(3(S),5-Dihydroxypentyl)hypoxanthine shows the least spreadin g in melting temperature on hybridization with the four natural 2'-deo xynucleosides. Because of their conformation flexibility, acyclic nucl eosides can be considered as universal nucleoside for the design of pr obes with ambiguous positions.