WATSON-CRICK BASE-PAIRING PROPERTIES OF BICYCLO-DNA

A series of sequences of the DNA analog bicyclo-DNA, 6-12 nucleotides in length and containing all four natural nucleobases, were prepared a nd their Watson-Crick pairing properties with complementary RNA and DN A, as well as in its own series, were analyzed by UV-melting curves an d CD-spectroscopy, The results can be summarized as follows: bicyclo-D NA forms stable Watson-Crick duplexes with complementary RNA and DNA, the duplexes with RNA generally being more stable than those with DNA, Pyrimidine-rich bicyclo-DNA sequences form duplexes of equal or sligh tly increased stability with DNA or RNA, whereas purine-rich sequences show decreased affinity to complementary DNA and RNA when compared wi th wild-type (DNA-DNA, DNA-RNA) duplexes, In its own system, bicyclo-D NA prefers antiparallel strand alignment and strongly discriminates fo r base mismatches, Duplexes are always inferior in stability compared with the natural ones, A detailed analysis of the thermodynamic proper ties was performed with the sequence 5'-GGATGGGAG-3'. 5'-CTCCCATCC-3' in both backbone systems, Comparison of the pairing enthalpy and entro py terms shows an enthalpic advantage for DNA association (Delta Delta H = -18 kcal . mol(-1)) and an entropic advantage for bicyclo-DNA ass ociation (Delta Delta S = 49 cal . K-1. mol(-1)), leading to a Delta D elta G(25 degrees C) of -3.4 kcal . mol(-1) in favor of the natural du plex, The salt dependence of T-m for this sequence is more pronounced in the case of bicyclo-DNA due to increased counter ion screening from the solvent, Furthermore bicyclo-DNA sequences are more stable toward s snake venom phosphodiesterase by a factor of 10-20, and show increas ed stability in fetal calf serum by a factor of 8 compared with DNA.