Sequence-dependent mechanics of single DNA molecules

Atomic force microscope-based single-molecule force spectroscopy was employ ed to measure sequence-dependent mechanical properties of DNA by stretching individual DNA double strands attached between a gold surface and an AFM t ip. We discovered that in lambda-phage DNA the previously reported B-S tran sition, where 'S' represents an overstretched conformation, at 65 pN is fol lowed by a nonequilibrium melting transition at 150 pN. During this transit ion the DNA is split into single strands that fully recombine upon relaxati on, The sequence dependence was investigated in comparative studies with po ly(dG-dC) and poly(dA-dT) DNA. Both the B-S and the melting transition occu r at significantly lower forces in poly(dA-dT) compared to poly(dG-dC). We made use of the melting transition to prepare single poly(dG-dC) and poly(d A-dT) DNA strands that upon relaxation reannealed into hairpins as a result of their self-complementary sequence. The unzipping of these hairpins dire ctly revealed the base pair-unbinding forces for G-C to be 20 +/- 3 pN and for A-T to be 9 +/- 3 pN.