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 and their Watson-Crick pairing properties with complementary RNA and DNA, as well as in its own series, were analyzed by UV-melting curves and CD-spectroscopy, The results can be summarized as follows: bicyclo-DNA 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 slightly increased stability with DNA or RNA, whereas purine-rich sequences show decreased affinity to complementary DNA and RNA when compared with wild-type (DNA-DNA, DNA-RNA) duplexes, In its own system, bicyclo-DNA prefers antiparallel strand alignment and strongly discriminates for base mismatches, Duplexes are always inferior in stability compared with the natural ones, A detailed analysis of the thermodynamic properties was performed with the sequence 5'-GGATGGGAG-3'. 5'-CTCCCATCC-3' in both backbone systems, Comparison of the pairing enthalpy and entropy terms shows an enthalpic advantage for DNA association (Delta Delta H = -18 kcal . mol(-1)) and an entropic advantage for bicyclo-DNA association (Delta Delta S = 49 cal . K-1. mol(-1)), leading to a Delta Delta G(25 degrees C) of -3.4 kcal . mol(-1) in favor of the natural duplex, 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 towards snake venom phosphodiesterase by a factor of 10-20, and show increased stability in fetal calf serum by a factor of 8 compared with DNA.