Sequence dependence of the free energy of B-Z junction formation in deoxyoligonucleotides

The NaCl-induced transition from the right-handed B form to a hybrid form containing both left and right-handed DNA, joined by a B-Z junction, was investigated. Transition curves were constructed from circular dichroism spectra collected as a function of NaCl concentration for a series of 16 bp deoxyoligonucleotides. The sequence of the series (one strand of the duplex) was: 5'CGCGCGCGAMNGACTG, where C indicates m5dC, and -MN- was varied to include the possible Py:Py stacks: -CC-, -CT-, -TC- and -TT-. Transition curves for the conversion of all deoxyoligonucleotides were found to be biphasic. Singular value decomposition was used to analyze the experimental circular dichroism spectra obtained as a function of NaCl, and showed that the transition was not a simple two-state process, but rather required at least three species to account for the experimental data. A sequential three-state model, B<-->I<-->BZ, was derived and applied to analyze experimental transition curves. Non-linear least-squares analysis was used to evaluate the salt-dependent equilibrium constants for each step in the sequential reaction model. The results indicate that the free energy change for B-Z junction formation (delta Gj) depends on the dinucleotide sequence near the junction. At a Na activity of 5, delta Gj values ranging from +1.2 to +1.7 kcal mol-1 were determined, depending on the sequence near the junction. delta Gj was found to be strongly dependent on salt concentration, with its magnitude decreasing with increasing Na activity. In addition to studies on linear duplex molecules, the B to BZ transition was also investigated in "dumbbell" forms of selected sequences. In these molecules, the ends were covalently linked by a single-stranded T4 segment. These studies show that junction formation is energetically more costly in dumbbells than in their linear counterparts. A striking correlation was found between delta Gj and two independent conformational properties of the dinucleotide steps that were introduced into the linear duplex molecules. These are the free energy of unstacking and the estimated free energy change for the conversion of the dinucleotide from the B to the A conformation. The more stable against unstacking, or the more resistant to the B to A conversion, the sequence near the junction site is, the more costly is B-Z junction formation. These correlations reveal that the DNA sequence near the junction apparently must be pliable in order to accommodate the unusual structure of the junction.(ABSTRACT TRUNCATED AT 400 WORDS)