Nucleic Acids Research, Vol 24, Issue 23 4660-4667, Copyright © 1996 by Oxford University Press
M Bolli, HU Trafelet and C Leumann
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.
ARTICLES
Watson-Crick base-pairing properties of bicyclo-DNA
Department of Chemistry and Biochemistry, University of Bern, Switzerland.
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