Synthesis and thermodynamic and biophysical properties of tricyclo-DNA

The DNA analogue tricyclo-DNA, built from conformationally rigid nucleoside analogues that were linked via tertiary phosphodiester functions, can effi ciently be synthesized from the corresponding phosphoramidites by conventio nal solid-phase cyanoethyl phosphoramidite chemistry, 5'-End phosphorylated tricyclo-DNA sequences are chemically stable in aqueous, pH-neutral media at temperatures from 0 to 90 degrees C. Tricyclo-DNA sequences resist enzym atic hydrolysis by the 3'-exonuclease snake venom phosphodiesterase. Homoba sic adenine- and thymine-containing tricyclo-DNA octa- and nonamers are ext raordinarily stable AT base-pairing systems, not only in their own series b ut also with complementary DNA and RNA. Base mismatch formation is strongly destabilized. As in bicyclo-DNA, the tricyclo-DNA purine sequences prefere ntially accept a complementary strand on the Hoogsteen face of the base, A thermodynamic analysis reveals entropic benefits in the case of hetero-back bone duplex formation (tricyclo-DNA/DNA duplexes) and both an enthalpic and entropic benefit fur duplex formation in the pure tricyclo-DNA series comp ared to natural DNA, Stability of tricyclo-DNA duplex formation depends mor e strongly on monovalent salt concentration compared to natural DNA. Homopy rimidine DNA sequences containing tricyclothymidine residues form triplexes with complementary double-stranded DNA, Triple-helix stability depends on the sequence composition and can be higher when compared to that of natural DNA. The use of one tricyclothymidine residue in the center of the self-co mplementary dodecamer duplex (d(CGCGAATtCGCG), t = tricyclothymidine) stron gly stabilizes its monomolecular hairpin loop structure relative to that of the corresponding pure DNA dodecamer (Delta T-m = +20 degrees C), indicati ng (tetra)loop-stabilizing properties of this rigid nucleoside analogue.