Hydrogen Bonding or Stacking Interactions in Differentiating Duplex Stability in Oligonucleotides Containing Synthetic Nucleoside Probes for Alkylated DNA

Oligonucleotides that hybridize to modified DNA are useful chemical tools to probe the noncovalent interactions that stabilize DNA duplexes. In an effort to better understand the interactions that influence the specificity of hybridization probes for O⁶‐alkylguanine lesions, we examined a series of synthetic nucleoside analogues (BIM, Benzi, and Peri) with respect to their ability to stabilize duplex DNA comprised of native or damaged DNA oligonucleotides. The base‐modified nucleoside analogues contained systematically varied hydrogen‐bonding and π‐stacking properties. The nucleoside probes were incorporated into DNA and paired opposite canonical bases (A, T, C, or G), O⁶‐methylguanine (O⁶‐MeG), O⁶‐benzylguanine (O⁶‐BnG), or a stable abasic site analogue (tetrahydrofuran, THF). On the basis of the free energy of duplex formation, the highest degree of stabilization was observed when Peri was paired opposite O⁶‐MeG. The thermodynamic data suggest that the smaller probes stabilize DNA duplexes more through hydrogen bonding, whereas the larger probes, with a greater capacity to π stack, contribute to duplex stabilization more on the basis of base stacking. These results demonstrate that increased helix stability could be achieved when BIM, Benzi, or Peri were paired opposite damage‐containing DNA rather than unmodified DNA (that is, O⁶‐MeG rather than G). This knowledge is expected to be useful in the design and development of nucleoside analogues for uses in DNA‐based technologies.