Biophysical Society Thematic Meeting - October 25-30, 2015

Polymers and Self Assembly: From Biology to Nanomaterials Poster Session I

16-POS Board 16 Spontaneous Nucleation of DNA Nanotubes of Defined Circumference John E. Devany 1 , Deborah K. Fygenson 1,2 . 1 Physics Dept., University of California, Santa Barbara, CA, USA, 2 Biomolecular Science & Engineering Program, University of California, Santa Barbara, CA, USA. Nanotubes are an important structural primitive in both cell biology and DNA nanotechnology. Like cellular “microtubules”, DNA nanotubes can grow to lengths that are thousands of times their diameter (~10 nm) without exceeding their persistence length (~10 µm), and thus truly bridge the molecular and material scales. DNA nanotubes are accordingly being investigated for a variety of applications: as templates for nanowires, pathways for molecular locomotion and rigidifying elements in active gels. To optimize quality, simplify placement, guide sequence design and rationalize solution conditions for such applications, fundamental understanding of and control over DNA nanotube self-assembly kinetics is needed. We studied the homogeneous (unseeded) nucleation of HX-tiled DNA nanotubes. The HX-tiling scheme, pioneered by Reif and co-workers, provides a versatile means for assembling DNA nanotubes with a defined number of double helices in circumference. Using sequence sets with binding domains of uniform strength that form nanotubes with either six, eight or ten helices in circumference, we looked for a dependence of nucleation rate on helix number. We detected nanotube nucleation and growth from the increase in fluorescence of a Cy3 molecule that occurs when the DNA to which it is covalently attached becomes double-stranded. We used a real-time PCR machine (Stratagene Mx3005P) to measure fluorescence following an abrupt change in temperature across the melting temperature and verify the rigid, linear nature of the assemblies that result by fluorescence microscopy. We find that nucleation of our DNA nanotubes proceeds in a single step (i.e., without meta-stable intermediates) and at a rate that scales with strand concentration to the 4th power, independent of helix number. The tetramer nature of the critical nucleus suggested by these results is further supported by a similar study on ribbon-forming subsets of the same strands.

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