Date: November 27, 2009 -
Time: 4:15 pm -

Stanford University
APPLIED PHYSICS/PHYSICS COLLOQUIUM

Tuesday, October 27, 2009
4:15 p.m. on campus in Hewlett Teaching Center, Rm. 201
Refreshments in the Physics Lobby at 4:00 p.m.

Taekjip Ha
Department of Physics, University of Illinois

"Revisiting the Double Helix"

Properties of DNA double helix have been studied for over 60 years. Yet as more sensitive tools become available, fundamental assumptions in our understanding of these properties are being challenged. One such question is over the flexibility of DNA Looping or bending of DNA on short length scales is essential for many cellular processes but it is highly controversial exactly how flexible the DNA is when it becomes much shorter than its so-called persistent length. Using a new, single-molecule based method, we found that DNA of lengths as short as 50 base pairs can form a circle more than 108 times faster than theoretical predictions, suggesting perhaps it is not so surprising that DNA is found in sharply bent forms when bound to various proteins.

Another question concerns the physical principles governing the reversible, helix-coil transitions of DNA between the double helix and single strands. Using porous nanocontainers, we were able to measure repeated helix-coil transitions between the same pair of DNA strands at the single molecule level, and determined the transition rates as a function of single base pair mismatch position. Surprisingly, we found that the rate of double helix formation shows an abrupt 100 fold change depending on whether there are 7 or more contiguous base pairs or not, with fundamental and practical implications.