(213e) Single Molecule Measurements of Non-Exponential DNA Hybridization Kinetics

We report single-molecule measurements of the spontaneous hybridization and dehybridization of 16 base pair DNA oligomers bridging between two microspheres, using a novel line optical tweezer instrument. Unlike similar measurements carried out at large pulling force, ours are conducted at essentially zero force (<25 fN), and should thus correspond to 'natural' equilibrium solution behavior. We find that the distribution of duplex lifetimes has an unusual, stretched exponential form (stretching exponent = 0.45) and a mean lifetime of several seconds. This is essentially in agreement with literature studies based on FCS (at lifetimes of milliseconds), and in apparent disagreement with nanopore based approaches. Overall, our results suggest that thermal dissociation of short duplex DNA passes through a number of distinct reaction pathways with different effective rate constants, despite being typically described using a two-state melting model. Moreover, by increasing the oligonucleotide density, we can examine the effects of cooperativity on the microsphere binding kinetics, finding that they become progressively more non-exponential. Our results can be reproduced with simple KMC/Gillespie-type models. The consequences for hybridization-based DNA sensors will be discussed.