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Base flipping induced by the base pair analogues of deoxyadenosine and deoxycytidine derivatives tethering a phenyl or naphthyl group was explored to study the dynamics and energetics of unusual conformation observed during DNA repair and DNA and RNA modification processes. The results for the base flipping which occurred in competition with base pair formation could be applied to study the base flipping conformation under the equilibrium with base pairing.

The adenosine derivative of deoxyadenosine by an amide linker (X) incorporated in a DNA stand promoted the site-selective hydrolysis of the complementary RNA in the presence of MgCl(sub 2). Natural ribozymes catalyzes the site-selective RNA cleavage reaction by utilizing metal ions and nucleotide bases as catalysts, in which the nucleotide subject to be cleaved generally is located in an unpaired region involving the tertiary interactions.

Complementary nucleotides can self-assemble in water in the presence of appreciated cations, forming a duplex through stacking of bases and hydrogen bonding. Duplexes with dangling ends are widely used to estimate the energy of the stacking interaction as the energy contribution from the dangling end results from the stacking interaction between the dangling end residue and the bases of the neighboring base pair.