Cooperativity-Dependent Folding of Single-Stranded DNA

The folding of biological macromolecules is a fundamental process which we lack full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming non-specific secondary structures that are difficult to characterize with biophysical techniques. Here present helix-coil model for structure formation, where ssDNA bases organized two different types domains (compact free). contains parameters: the energy gain per base compact domain, $\epsilon$, cooperativity related interfacial between domains, $\gamma$. We tested ability quantify formation molecules mechanically stretched optical tweezers. reproduces experimental force-extension curves molecular lengths varying sodium magnesium concentrations. Salt-correction effects found be compatible those hybridization. predicts free average size zero force, finding good agreement predictions Mfold. envision could further extended investigate native RNA proteins.