Thermodynamics and kinetics of the B-S transition in base-modified DNA

Understanding changes in the mechanical properties of nucleic acids is important to understand many biological processes. DNA exhibits a conformational change from canonical B- to overstretched S-form, characterized by 70% elongation, at ∼60–70 pN. The structure of S-form DNA is still debated and also difficult to distinguish from force-induced melting and peeling of DNA. Here, we characterized the kinetics and thermodynamics of the B-S transition and also investigated the effect of base modifications on the transition using tricyclic cytosine tC, which forms hydrogen bonds with guanine and changes the base stacking properties of B-DNA. The B-S transition in 60 bp DNA occurs at ∼63.5 pN (at 1 M salt) and fraying of ∼20 bp precedes the cooperative B-to-S transition of the remaining ∼40 bp. The B-S transition force increases gradually with tC incorporation, whereas the extension and free energy of the transition decrease. We conclude that fewer bp undergo the cooperative B-S transition in tC-stabilized duplexes, due to more fraying of B-DNA at higher transition forces, consistent with the transition becoming faster. For the first time we characterize the kinetics of the cooperative B-to-S transition and it occurs significantly faster than the alternative melting transition, while the extension of B-DNA at the B-to-S transition barrier is almost half-way between B- and S-DNA, suggesting an elastic nature of this transition. By characterizing the free energies of tC-modified relative to unmodified oligos, we estimated that each tC stabilizes the duplex by ∼3 kBT. The approach of studying short synthetic oligonucleotides with modified bases opens up new opportunities for understanding the local structure of nucleic acids with base-pair resolution.