Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session P2: Nanopore World: from Single-Molecules to Bionanotechnology Prospects |
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Sponsoring Units: DBP Chair: Liviu Movileanu, Syracuse University Room: Colorado Convention Center Four Seasons 4 |
Wednesday, March 7, 2007 11:15AM - 11:51AM |
P2.00001: Towards DNA Sequencing using Solid-State Nanopores Invited Speaker: 10 Years ago John Kasianowicz and coworkers invented the concept of using ionic conductance as a mechanism for scanning a DNA molecule for genetic information. Their proposal has since led to the creation of an exciting field of nanopore biophysics. I will discuss our current effort in combining the SBH (sequencing-by-hybridization) concept and solid-state nanopores for fast DNA sequencing. [Preview Abstract] |
Wednesday, March 7, 2007 11:51AM - 12:27PM |
P2.00002: Entropic springs in single-molecule polymer partitioning into protein nano-pores Invited Speaker: The capture and release of single polyethylene glycol molecules by the alpha-Hemolysin pore are observed as time-resolved reversible steps in ion conductance. The capture on-rate, inferred from the step frequency, decreases monotonically with polymer size. However, the polymer residence time shows a cross-over behavior, first increasing and then decreasing with molecular weight (\textit{Phys. Rev. Lett.}, 2006, \textbf{97}:018301). Our interpretation is that in case of polymers which are too large to be accommodated within the pore, the out-of-the-pore part of the molecule pulls on the trapped part thus acting as an entropic spring. [Preview Abstract] |
Wednesday, March 7, 2007 12:27PM - 1:03PM |
P2.00003: Forces on DNA in a solid-state nanopore Invited Speaker: Amongst the variety of roles for nanopores in biology, an important one is enabling polymer transport, for example in gene transfer between bacteria and transport of RNA through the nuclear membrane. Recently, this has inspired the use of protein and solid-state nanopores as single-molecule sensors for the detection and structural analysis of DNA and RNA by voltage-driven translocation. The magnitude of the force involved is of fundamental importance in understanding and exploiting this translocation mechanism. Furthermore, solid-state nanopores can be seen as a model system for biological nanopores. We will discuss the forces acting on single DNA strands electrophoretically driven through a solid-state nanopore. The force was directly measured using optical tweezers [1]. The force depends linearly on the applied voltage for a wide range of salt concentrations (0.02M -- 1M KCl) and nanopore diameters (6 nm -- 80 nm). Interestingly, we find for small nanopores with a diameter less than 15 nm that the force on the DNA is independent of the salt concentrations. However, the force decreases significantly in the larger nanopores. We will qualitatively discuss our results using the Poisson-Boltzmann and Navier-Stokes equations for a simple geometry. The influence of hydrodynamic coupling between the nanopore walls and the DNA molecule is of crucial importance to understand the force on a DNA molecule in nanopores. [1] U. F. Keyser et al. Nature Physics 2, 473 (2006) [Preview Abstract] |
Wednesday, March 7, 2007 1:03PM - 1:39PM |
P2.00004: Molecular Tweezers: Using the Electric Field in a Synthetic Nanopore to Disrupt Biomolecular Binding Forces Invited Speaker: The forces binding proteins to DNA in an aqueous solution are vital to biology, but inadequately understood. In particular, restriction enzymes like EcoRI are extraordinarily sequence-specific and yet the complex with DNA is very stable. To stringently test these forces, we use the electric field inside a synthetic nanometer-diameter pore in a thin membrane to pull on double-stranded DNA bound to EcoRI and BamHI, introducing a shear between the enzyme and their respective cognate sites in DNA. We observe a sharp threshold near 1nN in the force required to disrupt the binding in the complex, which is in stark contrast with previous measurements of the force (10pN) accomplished by unzipping the DNA molecule at a constant loading rates (1nN/sec). This force, acting over a distance corresponding to the separation between bases, coincidentally corresponds to the free energy of formation for the EcoRI-DNA complex. Using molecular dynamics, we interpret the measurements and elucidate the binding with atomic precision. [Preview Abstract] |
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