(121e) Fundamental Mechanisms of DNA Self-Assembly

DNA is becoming increasingly more common as a building block for controlling the assembly of nanostructured materials.  The predictable self-assembly of small DNA oligomers attached to building blocks such as nanoparticles leads to the reversible formation of structures with long-range order.  Despite the proven effectiveness of DNA-directed self-assembly, the mechanisms underlying the hybridization of such DNA oligomers have, until recently, been largely unknown, even for naked strands in the bulk.  Prior work using Transition Path Sampling and a coarse-grained DNA model shed some insight into possible key intermediates in the pathways of bulk hybridization [1] and surface hybridization [2].  Recently, the same model was used with Forward Flux Sampling and Langevin dynamics to determine the effect of salt concentration, supercooling, and oligomer length on the rate of bulk hybridization [3].  A general mechanism for DNA oligomer bulk hybridization was also proposed.   In the present work, we expand on our previous results to examine the effect of geometry, as well as the effect of salt concentration, degree of supercooling, and sequence length and composition on hybridization rate.  So doing allows us to construct a more complete description of the mechanism of DNA oligomer hybridization.  This new understanding provides design principles that can be used by experimentalists to rationally design non-equilibrium kinetically-limited systems.  

1. Sambriski, E. J.,  Schwartz, D. C., and J. J. de Pablo. “Uncovering Pathways in DNA Oligonucleotide Hybridization via Transition State Analysis.” PNAS, 106, No. 43 (October 2009): 18125-30.

2.  Hoefert, M. J., Sambriski, E. J., and J. J. de Pablo. “Molecular Pathways in DNA-DNA Hybridization of Surface-bound Oligonucleotides.” Soft Matter 7, No. 2 (2011): 560.

3.  Hinckley, D. M., Freeman, G. S., and J. J. De Pablo.  A Mechanism of DNA Oligonucleotide Renaturation.  In preparation.