title: Watson-Crick base-pairing properties of bicyclo-DNA.
abstract: 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'x 5'-CTCCCATCC-3' in both backbone systems. Comparison of the pairing enthalpy and entropy terms shows an enthalpic advantage for DNA association (delta deltaH = -18 kcal x (mol)-1)) and an entropic advantage for bicyclo-DNA association (delta deltaS = 49 cal x K(-1) x mol(-1), leading to a delta deltaG 25 degrees C of -3.4 kcal x mol(-1) in favor of the natural duplex. The salt dependence of Tm 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.
authors.affiliation: Department of Chemistry and Biochemistry, University of Bern, Switzerland.
authors.forename: M
authors.initials: M
authors.lastname: Bolli
authors.forename: H U
authors.initials: HU
authors.lastname: Trafelet
authors.forename: C
authors.initials: C
authors.lastname: Leumann
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004355:Drug Stability; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry; D010727:Phosphoric Diester Hydrolases / Q000378:metabolism; D011687:Purines / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry; D018075:RNA, Complementary / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D009692:Nucleic Acid Heteroduplexes; D011687:Purines; D011743:Pyrimidines; D018075:RNA, Complementary; D004247:DNA; D010727:Phosphoric Diester Hydrolases