Nucleic-acid analogs with restricted conformational flexibility in the sugar-phosphate backbone ('Bicyclo-DNA') .6. Probing the influence of torsion angle gamma on DNA-duplex stability: Synthesis and properties of oligodeoxynucleotides containing [(3'S,5'S)-2'-deoxy-3','-ethano-beta-D-ribofuranosy]adenine and -thymine ('5'-epi-bicyclodeoxynucleosides')

The synthesis of the thymine- and adenine-containing 5'-epi-bicyclodeoxynucleosides 7 and 8 as well as of the corresponding building blocks 13 and 14 for oligonucleotide synthesis according to the phosphoramidite methodology is described. A conformational analysis of 7 and 8 by H-1-NMR spectroscopy, refined by molecular modeling, shows the preferred conformation of the furanose unit in these nucleosides to be of the 1'-exo/2'-endo type, The 5'-OH group on the carbocyclic ring prefers to be axially oriented, thus placing torsion angle gamma in the unusual -syn-clinal (-sc) range. These epi-bicyclodeoxynucleosides were successfully incorporated into DNA decamers. From UV/melting curves of such decamers with DNA and RNA complements, a duplex destabilization of -2 to -9 degrees per residue was observed. An oligonucleotide built completely from 5'-epi-bicyclothymidine shows no detectable affinity to its DNA or RNA complement anymore. CD Spectra of duplexes containing 5'-epi-bicyclodeoxynucleotide units are very similar to the natural reference systems, indicating no major structural changes. A molecular-dynamics simulation of a heptamer duplex containing one 5'-epibicyclothymidine residue in the center reveals a conformational change of its carbocyclic unit placing torsion angle gamma in the (for the free mononucleoside unfavorable) -anti-clinal (-ac) conformation in the duplex. The role of torsion angle gamma on DNA duplex stability is discussed.