Exploring the motional dynamics of end-grafted DNA oligonucleotides by in situ electrochemical atomic force microscopy

We introduce herein the use of atomic-force electrochemical microscopy (AFM-SECM) to simultaneously probe locally the conformation and motional dynamics of nanometer-sized single-stranded (ss) and double-stranded (ds) DNA oligonucleotides end-tethered to electrode surfaces. The ss-DNA system studied here consists of a low-density monolayer of (dT)(20) oligonucleotides, 5'-thiol end-tethered onto a flat gold surface via a C-6 alkyl linker and bearing at their free 3'-end a redox ferrocene label. It is shown that, as a result of the flexibility of the relatively long C-6 linker, hinge motion, rather than elastic deformation of the DNA chain, is the major component of the dynamics of both the (dT)(20) strand and its post-hybridized (dT-dA)(20) duplex. DNA chain elasticity is nevertheless sufficiently contributing to the overall dynamics to result in similar to 4 times slower dynamics for (dT-dA)(20) than for (dT)(20). Taking advantage of this dissimilar dynamical behavior of ss- and ds-DNA, it is demonstrated that hybridization can be easily locally detected at the scale of similar to 200 molecules by AFM-SECM.