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Physics Colloquium: "Soft" Physics of Large Molecules in Small Spaces - Properties of DNA in...

Thursday, October 9, 2014

3:30 PM-4:30 PM

Yeng-Long Chen, PhD, Academia Sinica

"Soft" Physics of Large Molecules in Small Spaces - Properties of DNA in Micro- and Nano-channels

A molecule that plays a central role in genetics is the DNA molecule. Although the DNA molecular structure has been solved, the molecular conformation and dynamics under physiological conditions (in a solution) and during biological processes such as transcription are not yet fully understood. Human DNA molecules have a double helix structure with widths of 2 nm and 3.4 nm (10 base pairs) per helical turn. With 3 billion base pairs, human DNA has a length of approximately a meter if fully stretched, yet it is stored in the cell nucleus, which has a size of approximately one
micron. The properties of DNA can vary widely as one examines its conformation and dynamics over six orders of magnitude change in length. As we seek to understand the physical properties of DNA, we must first ask, what is the length scale? what is the time scale?

I will introduce the classic approach pioneered by P. G. de Gennes and others, using scaling arguments to predict the qualitative changes of DNA conformation as the molecule becomes confined in a tube, a square channel, or slit. The confinement geometry was found to qualitatively change the DNA physical conformation. In a tube smaller than the DNA persistence length, a characteristic length for DNA stiffness, T. Odijk and others have predicted qualitatively changes to DNA conformation beyond the scaling arguments.

Recent experimental and simulation results have shown that the transition into the highly-stretched Odijk regime can be observed in nanochannels smaller than 70nm. Theoretical predications also expected that the DNA relaxation time, a characteristic time scale over which DNA segments fluctuates, should increase in smaller nanochannels. Surprisingly, measurements of the DNA relaxation time, was found to decrease for nanochannels smaller than 150nm. As it turns out, sufficiently small nanochannels can act as a "filter" that blocks long wavelength DNA relaxation modes.

In addition, strong confinement also affect DNA dynamics in an environment crowded by proteins or other nanoparticles, such as that found in a cell, a virus particle, or a nanochannel. It has been observed that crowding agents can help compact DNA molecules due to molecular entropy, known as depletion-induced attraction. I will also discuss how depletion effect can either cause the DNA size to swell or reduce in a nanochannel.

Non-technical: Suckjoon Jun and Andrew Write, Nature Reviews Microbiology
8, 600 (2010)
Technical: Y.-L. Chen, Y.H. Lin, J.F. Chang, and P.-K. Lin, Macromolecules
47, 1199 (2014)

Contact Information

Professor Jian-Min Yuan