Watson-Crick hybridization

DNA as a polyelectrolyte in saline solution presents a unique chemistry and physics in terms of the complementary self pairing, known biologically as Watson-Crick hybridization. The free energies of association in solution are well studied and form the basis for the normal molecular recognition process. This process is fundamentally altered by the presence of a solid interface. 

Clearly, the antisense concept derives from an understanding of nucleic acid structure and function and depends on Watson-Crick hybridization (18). Thus, arguably, the demonstration that nucleic acid hybridization is... 

ASON are sequences of usually 17-30 bases of single-stranded DNA that hybridize to specific genes or their mRNA products by Watson-Crick base pairing and disrupt their function. In the case of AS-ODN (antisense oligodeoxyribonucleotides) cellular RNAseH is able to bind to the DNA-RNA duplex and hydrolyze the RNA, resulting in increased transcript turnover. Modifications to the deoxy moiety at the 2 -sugar position prohibits RNAse H action. 

Egholm M., Buchardt O., Christensen L., Behrens C., Ereier S.M., Driver D.A., Berg, R. H., Kim, S.K., Nor-DEN B., Nielsen, P.E. PNA hybridizes to complementary oligonucleotides obeying the Watson—Crick hydrogen-bonding rules. Nature 1993, 365 566-568. 

Previous work has suggested that aminoglycoside specificity may occur in nucleic acid forms that display features characteristic of an A-type conformation (RNA triplex, DNA-RNA hybrid duplex,RNA duplex, DNA triplex, A-form DNA duplex, and DNA tetraplex ), rather than in naturally occurring RNA. However, conflicting results have been reported regarding the conformation of the triplex and of the Watson-Crick duplex within these triplexes. Both... 

Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA, et al. PNA Hybridizes to Complementary Oligonucleotides Obeying the Watson-Crick Hydrogen Bonding Rules. Nature 1993 365 566-8. 

The noncontributing base pairs are the most disruptive to the hybridization, whereas the Watson-Crick base pairs act as the most positive contributors as originally shown by Ikuta et al. [S. Ikuta, K. Takagj, R. B. Wallace, and K. Itakura, Nucleic Acids Res. 15,797 (1987)]. 

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