Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session N26: Focus Session: DNA and Protein Analysis with Micro and Nano Fluidics |
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Sponsoring Units: DBP DFD Chair: Steven Quake, Stanford University Room: Baltimore Convention Center 323 |
Wednesday, March 15, 2006 8:00AM - 8:12AM |
N26.00001: Formation of bi-nanopores in silicon chips Sang Ryul Park, Hongbo Peng, X. S. Ling Solid-state nanopores are holes with diameter and length on the order of 20 nm or smaller embedded in an insulating solid membrane. These nanopores have been shown to allow linear translocation of DNA molecules in buffer conditions and can be used as an electronic device for detecting and characterizing nucleic acids and proteins. Here we report a novel method of fabricating bi-nanopores in silicon chips using feedback electrochemical etching. The simplicity and low-cost of our approach, taking advantage of the well-known anisotropic etching behavior of silicon in alkaline solutions, bring solid-state nanopores closer to industrial-scale applications. [Preview Abstract] |
Wednesday, March 15, 2006 8:12AM - 8:24AM |
N26.00002: Fabrication of nanopores in wax using laser-induced shrinking Shanshan Wu, Sang Ryul Park, X. S. Ling We developed a simple laser heating induced shrinking technique for making plastic nanopore bio-sensing devices. Our technique is capable of shrinking thermoplastic pores of diameters up to several hundred micrometers to a few nanometers. We have made nanopore devices by applying this technique to Apiezon W wax (thermoplastics) micropores. Our DNA translocation experiments with$\,48\,\,kilobasepairs\,(kbp)$double-stranded $\lambda \,$DNA ($\lambda \,$dsDNA) have yielded convincing results of the functionality of these devices as biomolecular nanosensors. [Preview Abstract] |
Wednesday, March 15, 2006 8:24AM - 8:36AM |
N26.00003: Ion Valence and Solution Temperature Effects on DNA Translocations in Solid-State Nanopores James Uplinger, Daniel Fologea, Jiali Li Solid-state nanopore device provides a sensitive and robust environment for single DNA analysis. When a nanopore is the only partition between two reservoirs filled with an ionic solution and electrical conduction is established any DNA molecule translocation through the nanopore will partially block the open pore current. The current blockage and dwell time depends on both the external parameters, such as applied voltage, ionic strength and on characteristics of the DNA molecule itself, such as the charge and geometry. The properties of the molecule can be modulated by interactions with the ionic solution, and these will produce modifications of the current blockage and translocation time. Here we report on how the DNA translocation signature is modified when: (1) salts of varied valences are used and concentration of the surrounding solution changes; (2) the temperature of ionic solution changes. The mobility and diffusion coefficient of DNA molecule at above conditions are estimated. [Preview Abstract] |
Wednesday, March 15, 2006 8:36AM - 9:12AM |
N26.00004: DNA in nanofluidic devices Invited Speaker: Nanochannels with a channel cross-section of around 100 nm x 100 nm or less are emerging as a powerful new technique for single-molecule DNA analysis. In these nanochannels, DNA is linearized to a constant fraction of its contour length, and thus spatial locations measured by fluorescence microscopy can be directly related to genomic locations. Because the stretching in nanochannels is caused by lateral confinement, molecules are free to undergo longitudinal fluctuations. Hence, time-averaging over a single molecule is meaningful, and a high resolution can be achieved even using few molecules. We will present how DNA imaging in nanochannels can be applied to common tasks in molecular biology that go beyond simple sizing. In particular, we will discuss the genomic identification of human DNA fragments using fluorescent markers, and how to perform enzymatic reactions, such as restriction mapping using endonucleases, in nanochannels. We will also present our recent progress in the development of ``nanoplumbing'', that is devices that contain junctions of nanochannels. We will show how device dimensions influence the transport of DNA at those nanochannel junctions, and how those properties can be utilized in the design of devices and exotic materials. [Preview Abstract] |
Wednesday, March 15, 2006 9:12AM - 9:24AM |
N26.00005: Nanoscale electrical detection of DNA Chih-kuan Tung, Robert Reihn, Lukas Urban, Ali Yazdani, Robert Austin We try to detect DNA electrically by different nano-devices, including single-walled carbon nanotubes and platinum nano- wires. We will demonstrate the responses of carbon nanotubes conductance to the exposure to DNA, and ac lock-in measurements across metal nano-wires based on the biochemical properties of the DNA bases. The effects of different bases are also studied, which may provide us a real opportunity to sequence DNA electrically. [Preview Abstract] |
Wednesday, March 15, 2006 9:24AM - 9:36AM |
N26.00006: DNA Translocation Dependence on Ionic Solution Concentration in a Solid-State Nanopore Device Brian Thomas, Daniel Fologea, Jiali Li Our work describes dsDNA translocations through a silicon nitride nanopore subjected to an applied electric field in solutions of different ionic strengths. We demonstrate how the ion concentration affects DNA shielding and, consequently, its effective negative charge. These modifications alter key parameters of the translocation process, such as the dwell time and current drop of the event. In this way, the DNA/salt interaction process can be explored by translocation experiments. [Preview Abstract] |
Wednesday, March 15, 2006 9:36AM - 9:48AM |
N26.00007: DNA size and conformations analysis using a synthetic nanopore Daniel Fologea, James Uplinger, Brian Thomas, Bradley Ledden, Eric Brandin, Daniel Branton, Jiali Li Our work reveals the ability of a synthetic nanopore made in a silicon nitride membrane to discriminate between different conformations and lengths of DNA molecules and presents a comparative analysis with the electrophoretic behavior of the same DNA. Double stranded linear, supercoiled and relaxed form of the same DNA, linear restriction fragments, as well as single stranded DNA, are passed through a synthetic nanopore filled with a buffered ionic solution, and a subsequent analysis in terms of current blockage, translocation time and integrated events area shows the analytical ability of such a device. Also, we prove that an intercalating agent increases the temporal resolution by increasing the translocation time up to a factor of two. [Preview Abstract] |
Wednesday, March 15, 2006 9:48AM - 10:24AM |
N26.00008: Microfluidic Protein Crystallography Invited Speaker: Due to their impressive economies of scale and unique mass transport properties microfluidic devices have become viable technologies for nano-volume protein crystallization screening and growth. In particular, soft microfluidic devices based on multilayer soft lithography (MSL) have been successfully applied to systematic protein solubility studies and efficient nanoliter volume screening by free interface diffusion. While these systems have proven highly effective in identifying crystallization conditions for a large number challenging crystallization targets, realizing the full potential of microscale crystallization requires complementary technologies for crystal optimization and harvesting. In this talk I will briefly review previous studies of protein phase space mapping and crystallization screening, and will present recent work on a microfluidic device which provides a link between chip-based nanoliter volume crystallization screening and structure analysis through ``kinetic optimization'' of crystallization reactions and direct in situ structure determination. Using this device we demonstrate control over crystal quality, reliable scale-up from nanoliter volume reactions, facile harvesting and cryo-protectant screening, and protein structure determination at atomic resolution from data collected in-chip. [Preview Abstract] |
Wednesday, March 15, 2006 10:24AM - 10:36AM |
N26.00009: Statics and Dynamics of Single DNA Molecules Confined in Nanoslits Po-Keng Lin, Chi-Cheng Fu, Y.R. Chen, Wunshain Fann, C.H. Kuan de Gennes provided the scaling predictions for the linear polymer chain trapped in slit with dimension close to the Kuhn length decades ago; however, it has yet to be compared with experiments. We have fabricated nano-slits with vertical dimension similar to the Kuhn length of ds-DNA, $\sim $ 100nm, using standard photolithography. Single DNA molecules with length range from 2 to75 micrometers were successfully inject into the slits and the Brownian motions were imaged by fluorescence microscopy. The distributions of the radius of gyration and the two-dimensional asphericity were measured and it is found that the DNA exhibit highly anisotropic shape distribution. The scaling exponents for the chain extension and the center-of-mass diffusion coefficient will also be discussed. [Preview Abstract] |
Wednesday, March 15, 2006 10:36AM - 10:48AM |
N26.00010: Slowing down DNA translocation using magnetic and optical tweezers Hongbo Peng, Shanshan Wu, Sang Ryul Park, Andrew Potter, X. S. Ling Electric-field driven DNA translocation through nanopores can be exploited for DNA sequencing and other applications. However, the DNA translocation under normal patch-clamp-type measurement is too fast to allow detailed measurements of individual or few nucleotides. We propose a concept to slow down the DNA translocation through the nanopore by using magnetic (or optical) tweezers. The 3' end of a single-strand DNA can be attached to a streptavidin-coated magnetic bead through a single biotin molecule. During DNA translocation, the 5' end of DNA will be electrophoretically drawn through the nanopore to the \textit{trans} side while the 3' end of DNA stays in the \textit{cis }side with the magnetic bead. A set of permanent magnets or electric coils can be used to generate a magnetic field gradient large enough to pull the bead, hence the DNA out of the nanopore. The net force on the magnetic bead will determine this back-translocation speed. By carefully tuning the magnetic field gradient and the voltage bias on the nanopore, one can make the back-translocation much slower than the conventional forward-translocation in which case the DNA is driven only by the electric force. We will report our experimental design as well as the preliminary results. [Preview Abstract] |
Wednesday, March 15, 2006 10:48AM - 11:00AM |
N26.00011: Patterned Periodic Nanofilter Array for Continuous-Flow Bimolecular Separation Jianping Fu, Jongyoon Han We present an experimental study on sieving process of small biomolecules (i.e., proteins and small DNAs) in one- and two-dimensional periodic arrays of nanofilter. The nanofilters served as artificial sieves with precise pore size characterization and showed exceptional size selectivity and separation efficiency from the periodicity of the environment. A kinetic model is developed to explain the electrophoretic drift of charged molecules across periodically modulated free energy landscapes. Further experimental evidence shows the crossover from Ogston-like sieving to entropic trapping mechanism depending on nanofilter thickness and on electric field strength. We also demonstrate continuous-flow biomolecule separation with a device containing of two-dimensional periodic nanofilter arrays. The interaction between migrating molecules and the two-dimensional physical landscapes cause molecules of different sizes to follow radically different paths leading to separation. Continuous-flow fractionations of small DNA molecules (50bp-766bp) as well as SDS-protein complexes (11kDa-200kDa) were achieved in about 5 minutes with a resolution of 10{\%}. By virtue of its gel-free and continuous-flow operation, this device suggests himself a key component to an integrated biomolecule sample preparation and analysis microsystem. [Preview Abstract] |
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