Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session H34: DNA and Protein Analysis with Nanofluidics |
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Sponsoring Units: DBP Chair: Bob Austin, Princeton University Room: Colorado Convention Center 404 |
Tuesday, March 6, 2007 8:00AM - 8:36AM |
H34.00001: Single Molecule Manipulation and Analysis in Nanofluidic Systems Invited Speaker: We have used simple small-scale structures to isolate and manipulate individual biomolecules in order to observe there activity and identity. Nanofluidic devices with dimensions, smaller than a relevant molecular length scale, have been used to sort or control the confirmation of long biopolymers such as DNA. Structurally-derived entropic and frictional forces balanced against the forces resulting from applied fields can elongate and controllably move a selected molecule. This can be used for measuring the length of the DNA or presenting it in an oriented manner for analysis. We have also employed metallic apertures a few tens of nanometers in diameter to confine a region of optical excitation to a volume on the order of 10$^{-20}$ liters, which allows the observation of single molecule motion and binding activity at meaningful rates and concentrations. This approach enables measuring the motility of proteins and binding of individual molecules in lipid layers and cell membranes. Small fluid channels have also been used to isolate individual optically detected molecules for evaluation in flowing systems. The measurement of mobility and detection of discrete molecular binding events can be done at the individual molecule level in such fluid systems. [Preview Abstract] |
Tuesday, March 6, 2007 8:36AM - 8:48AM |
H34.00002: Single-molecule manipulation of genomic DNA in extensional flow for haplotyping applications Rebecca Dylla-Spears, Lydia Sohn, Susan Muller We have developed a method amenable to haplotyping and manipulation of single molecules of double-stranded genomic DNA. Fluorescent polystyrene beads that are surface-functionalized with site-specific probes are incubated with fluorescently labeled double-stranded lambda-DNA. The solution is introduced into a microfluidic cross slot where the DNA molecules are trapped and elongated at the stagnation point of the planar extensional flow. The degree of elongation can be controlled using the flow strength in the device, as demonstrated by Perkins, Smith, and Chu (Science 1997). Beads bound along the stretched DNA may be directly observed and their locations along the backbone determined using fluorescence microscopy. [Preview Abstract] |
Tuesday, March 6, 2007 8:48AM - 9:00AM |
H34.00003: A Single--Step Photolithographic Interface for Cell-Free Gene Circuits and Active Biochips Amnon Buxboim, Maya Bar-Dagan, Veronica Frydman, David Zbaida, Margherita Morpurgo, Roy Bar-Ziv We developed a biochip platform technology suitable for controlled cell-free gene expression at the micron scale. A new hybrid molecule, ``daisy,'' was designed and synthesized to form in a single step a bio-compatible lithographic interface on silicon dioxide. A protocol was formulated for immobilization of linear DNA molecules thousands of base pairs long on daisy-coated surfaces to submicron spatial resolution and up to high densities. On-chip protein synthesis can be obtained with dynamic range of up to four orders of magnitude and minimal nonspecific activity. En route to on-chip artificial gene circuits, a simple two-stage gene cascade was built in which the protein synthesized at the first location diffuses to regulate the synthesis of another protein at a second location. The current approach opens possibilities for laboratories not proficient in surface chemistry to design active biochips based on cell-free gene expression with applications in artificial systems and synthetic biology. [Preview Abstract] |
Tuesday, March 6, 2007 9:00AM - 9:12AM |
H34.00004: Mode Transition of RNA Trap by Electric and Hydraulic Force Field in Microfluidic Taper Shape Channel Yuzuru Takamura, Kunimitsu Ueno, Wako Nagasaka, Yuichi Tomizawa, Eiichi Tamiya We have discovered a phenomenon of accumulation of DNA near the constricted position of a microfluidic chip with taper shaped channel when both hydro pressure and electric field are applied in opposite directions. However, RNA has not been able to trap so far, unlike huge and uniformly double stranded DNA molecules, RNAs are smaller in size and single stranded with complicated conformation like blocks in lysed cell solution. In this paper, we will report not only large but also small RNA (100$\sim $10b) are successfully trapped in relatively large microfluidic taper shape channel (width $>$10um). RNA are trapped in circular motion near the constricted position of taper shape channel, and the position and shape of the trapped RNA are controlled and make mode transition by changing the hydraulic and the electric force. Using this technique, smaller size molecule can be trapped in larger micro fluidic structure compared to the trap using dielectrophoresis. This technique is expected to establish easy and practical device as a direct total RNA extraction tool from living cells or tissues. [Preview Abstract] |
Tuesday, March 6, 2007 9:12AM - 9:24AM |
H34.00005: The Physics of Nanoconfined DNA: Varying Temperature and Ionic Conditions Walter Reisner, Anders Kristensen, Jonas Tegenfeldt, Henrik Flyvbjerg, Niels B. Larsen Top-down approaches to nanotechnology have the potential to revolutionize biology by making possible the construction of chip-based devices with nanoscale features that can not only detect, separate and analyze single DNA molecules by size but also--it is hoped in the future--actually sequence at the single molecule level. Using electron beam lithography we have fabricated nanochannel devices in fused silica with dimensions on order of 100x100nm and lengths of 100s of micrometers. Both dsDNA and ssDNA molecules, imaged via fluorescence microscopy, are observed to stretch out in these effectively one dimensional systems. We present measurements of the DNA extension as a function of ionic strength. We also demonstrate how the DNA melting transition can be probed in real time by heating the nanochannel extended DNA. [Preview Abstract] |
Tuesday, March 6, 2007 9:24AM - 9:36AM |
H34.00006: Modeling DNA Separation in Entropic Trap Device Alex Vaughn, Yongmei Wang DNA electrophoresis in the entropic trap device fabricated by Craighead and coworkers has some interesting properties that allow long chains to be separated; moreover, their results showed that long chains had higher mobility than short chains, a counter-intuitive result. The mechanism by which the device works is not well understood. This study seeks therefore to understand the device's mechanism more thoroughly with a desire to provide the knowledge necessary to optimize the separation of long chains of DNA. The study uses dynamic Monte Carlo simulations on a simple-cubic lattice to model the separation of DNA. The simulation algorithm was first tested by confirming the chain length independence of the electrophoretic mobility of DNA in bulk solution, a well-known experimental fact. When DNA chains are constrained in a slit channel, the electrophoretic mobility is still independent of chain length. If DNA-wall interactions are added to the model, then the mobility decreases with the chain length for short chains and reaches a plateau for long chains. In a channel with entropic traps, the mobility is found to increase with the chain length, consistent with experimental results by Craighead and coworkers. We also found that a better separation was achieved when the trap was made deeper. [Preview Abstract] |
Tuesday, March 6, 2007 9:36AM - 9:48AM |
H34.00007: Imaging Biological Systems using Dielectric Near-Field Microscopy Keith Brown, David Issadore, Tom Hunt, Robert Westervelt We have developed a dielectric spectrometer for use on biological systems. The spectrum of dielectric response to RF electric fields is analogous to color as an optical response. Measurement of the dielectric spectrum from $\sim $ 10 kHz to $\sim $ 3 GHz will reveal information about the structure and conditions of protein solutions, protein crystals and biological tissues. We designed and built a system to test biological samples in a microfluidic chamber mounted on a circuit board. The apparatus measures the RF dielectric spectrum directly, or by analyzing the pulse response in the time domain. We have constructed several versions of the hardware for sensitive capacitive measurements, including two types of capacitive bridges, and a transmission line, incorporating precision electronics and local generation of pulses.~ A goal is to scale the system down and implement many dielectric spectrometers as an array of pixels on a CMOS chip for dielectric near-field microscopy of biological samples. This work made possible by NSEC NSF grant PHY-0117795 and the NCI MIT-Harvard CCNE. [Preview Abstract] |
Tuesday, March 6, 2007 9:48AM - 10:00AM |
H34.00008: Fundamental limits of detection with nanowire FET chem/bio sensors in subthreshold and linear regimes Xuan Gao, Gengfeng Zheng, Charles Lieber Nanowire field effect transistors (NW-FETs) have been demonstrated to be powerful sensors for the detection of biological and chemical species, and thus understanding and pushing their intrinsic sensitivity limits could have a significant impact on a broad-range of applications of these devices. We report studies of the response of silicon-NW-FET sensors as the devices are tuned from linear to subthreshold regimes by electrochemical gating. Conductance versus solution pH data show that operation in the subthreshold regime can increase both the percentage change in conductance and the signal to noise ratio of the device by over ten times compared to the linear regime. We also demonstrate that operating in the subthreshold regime yields improvement in the detection limit for the cancer marker protein PSA with detection down to $\sim $1.5 fM for a device with $\sim $0.75 pM detection limit in the linear regime. Analysis of these results shows that the sensitivity improvement is due to the more effective surface charge gating resulting from the reduced screening by carriers. In addition, the effect of NW diameters and the intrinsic charge detection limit for using NW-FET devices will be described. Our work shows that optimization of NW-FET structure and operating conditions can provide a significant enhancement as well as a fundamental understanding of the sensitivity limits for nano-FET sensors. [Preview Abstract] |
Tuesday, March 6, 2007 10:00AM - 10:12AM |
H34.00009: Modeling PCR in Natural Convection Systems Kevin Dorfman, Ehud Yariv, Guy Ben Dov Polymerase chain reaction (PCR) is a biochemical protocol for making many copies of a DNA template by thermal cycling between a hot temperature (where the strands are separated) and a cool temperature (where primers are annealed). In natural convection PCR, the requisite thermal cycling is provided by a buoyancy-driven circulating flow of the carrying buffer between a lower hot plate (at the denaturing temperature) and an upper cold plate (at the annealing temperature). We present a multi-component convection-diffusion-reaction model for natural convection-driven PCR when both primers and PCR enzyme are in excess. The evolution of the DNA population achieves a stationary state, wherein the problem is recast as an eigenvalue problem for computing the exponential amplification rate. With a realistic choice of parameters, the model predicts a doubling time on the order of two minutes, in agreement with experiments and much slower than the fluid cycling time. In contrast to what might be expected, the doubling time increases monotonically with the diffusion coefficient. [Preview Abstract] |
Tuesday, March 6, 2007 10:12AM - 10:24AM |
H34.00010: Tethered DNA molecules stretched by an electric field: A Molecular Dynamics Study. Gary Slater, Martin Bertrand It has been predicted by Long, Ajdari and Viovy (Phys. Rev. Lett., 1996, 76:3858) that the mechanical force necessary to stall a DNA molecule during electrophoresis is substantially smaller than the sum of the electrical forces applied on all of its monomers. In fact, it should be proportional to its hydrodynamic friction coefficient, which may vary with the molecular conformation. We have tested this prediction using coarse-grained Molecular Dynamics simulations in which we explicitly included the polymer, the solvent, the counterions and the salt. Our results show that the above prediction is indeed valid. In fact, our data demonstrate that there is a universal linear relationship between the stall force and the product of the electrical field and the radius of gyration of the polyelectrolyte. This remarkable relationship holds even when the electric forces stretch the DNA molecule near full extension. We thus conclude that an electrophoretic field is equivalent to a fluid flow, as suggested by Long, Ajdari and Viovy. This has profound implications for the development of a theoretical framework that can explain the electrophoresis of hybrid DNA-protein molecules. [Preview Abstract] |
Tuesday, March 6, 2007 10:24AM - 10:36AM |
H34.00011: Electrical Noise Characterization of Noble Gas Ion Beam Fabricated Nanopore Detectors Ryan Rollings, Bradley Ledden, Eric Krueger, Greg Salamo, Jiali Li, John Chervinsky, Jene Golovchenko Nanopores fabricated with low energy noble gas ion beams in a silicon nitride membrane can be employed as the fundamental element of single biomolecule detection and characterization devices. The effect of morphology, annealing, and physical surface treatments are systematically studied to determine their effect on the electrical noise characteristics of the nanopore when used as part of a nanofluidic detector. Atomic Force Microscopy (AFM) is used to measure the morphology of the region near the pore, while X-ray Photoelectron Spectroscopy (XPS) and Rutherford Backscattering (RBS) are used to measure the change in the surface composition with annealing as well as initial depth profiles of imbedded ions. We qualitatively discuss the underlying physical processes that contribute to the electrical noise characteristics of the pore in comparison with our measurements and present optimized conditions for fabricating the quietest pores. [Preview Abstract] |
Tuesday, March 6, 2007 10:36AM - 10:48AM |
H34.00012: Self-trapping and stretching of DNA using single nano-height micropillar Po-Keng Lin, Chi-Cheng Fu, Y.-L. Chen, W. S. Fann We propose a novel method to trapping ds-DNA molecules in 30-100nm slit-like nanochannel with single micropillar. In this environment the DNA molecules unusually extend around obstacles such as pillars or walls. The DNA molecules appear to have quasi-one dimensional dynamics even though the confinement is quasi-two dimensional. The trapping process can occur only when the channel height below the Kuhn length of ds-DNA. We experimentally observe the Brownian motions of the DNA using wide-field fluorescence microscopy. The static and dynamic scaling with DNA length (9.4$\sim $166 kbps) and channel height (30$\sim $240nm) have been analyzed and compared with the experimental results of DNA confined in the square nanochannels in the literatures (W. Reisner et al., Phys. Rev. Lett. 94 196101 (2005)). This micro/nano fluidic device can be applied to study the multi-step biochemical reactions in confinements such as DNA folding induced by protein and restriction mapping of DNA in the future. [Preview Abstract] |
Tuesday, March 6, 2007 10:48AM - 11:00AM |
H34.00013: Spatial Detection of Submicron Particles with Integrated Circuit Charge Sensors David Issadore, Tom Hunt, Robert Westervelt Using a standard MOSIS 0.35 micron Integrated Circuit process, we have built a position sensor for use in all-electrical feedback traps for submicron particles. The device has four transistors in a square, with floating gates that capacitively detect a charged particle in a microfluidic chamber above. The four transistors form the front ends of two independent differential amplifiers that report the x and y position of the particle. Future work towards integration of dielectrophoretic feedback forces for an all-electrical ``Anti-Brownian motion'' trap will be discussed. [Preview Abstract] |
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