Design, synthesis, and analysis of disulfide cross-linked DNA duplexes

The design, synthesis, and analysis of analogs of d(CGCGAATTCGCG)(2) possessing one or two intrahelical disulfide cross-links is reported. The cross-linked oligomers were prepared by first synthesizing duplexes where the 3'- and 5'-terminal bases of the parent sequence were replaced with N-3-thioethylthymidine. Following deprotection and purification, air oxidation afforded the desired cross-linked constructs in high yield. Analysis of both the oxidized (disulfide cross-linked) and reduced (thiol modified) duplexes by UV, circular dichroism, and NMR spectroscopies along with susceptibility to EcoRI cleavage indicates that the modifications are not structurally perturbing. Optical thermal denaturation and differential scanning calorimetry measurements suggest that introducing disulfide cross-link(s) into d(CGCGAATTCGCG)(2) does, however, cause two fundamental changes. First, the cross-link(s) increase the thermal stability of the modified duplexes by changing the molecularity of denaturation without an increase in enthalpy. Second, the disulfide cross-link traps one of the conformations of the conformationally heterogeneous parent molecule resulting in a conformationally homogeneous system. Both of these features are themselves unique and will be important for further applications of disulfide cross-linked oligomers such as these in studies of nucleic acid structure and function.