Bulletin of the American Physical Society
APS March Meeting 2018
Volume 63, Number 1
Monday–Friday, March 5–9, 2018; Los Angeles, California
Session X50: Nanoscale Biophysics and Single Molecule Techniques |
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Sponsoring Units: DBIO Chair: Jing Xu, Univ of California - Merced Room: LACC 511B |
Friday, March 9, 2018 8:00AM - 8:12AM |
X50.00001: A Novel, High Throughput Assay for Characterizing Protein-Protein Interactions Indrani Chakraborty, Ram Avinery, Roy Beck, Yael Roichman It has long been recognized that specific protein-protein interactions can be harnessed to design targeted delivery for diagnostic imaging and treatment using synthetic nano-carriers. However, non-specific protein-protein interactions were found to interfere with such processes, for example by competing with the desired targets. These weak interactions are much harder to measure and characterize. Here we demonstrate a simple, high throughput, method of probing these complex interactions using single particle tracking. In our setup, the diffusion of nanoparticles coated with intrinsically disordered neurofilament proteins [1], near a surface coated with similar proteins, were recorded and analyzed using conventional dark-field microscopy. From the distribution of the diffusion constants, we observed that salt concentration is a very effective parameter in tuning the strength of these weak interactions. By truncating critical five amino-acids in the C-terminal domain [2], we arrested the short-range attraction, which led to a strikingly visible difference in the diffusion constants. |
Friday, March 9, 2018 8:12AM - 8:24AM |
X50.00002: Origin of icosahedral symmetry in large viruses. Siyu Li, Alex Travesset, Roya Zandi Most spherical viruses adopt structures with icosahedral symmetry. While small single stranded RNA viruses assemble spontaneously from a solution containing the protein subunits and genome molecules, the large icosahedral viruses, such as Bacteriophage P22, Infectious Bursal Disease viruses and Bluetongue viruses need scaffolding proteins or an inner core to form fully infectious particles. We model the inner core as a hard sphere and study the growth of viral shells built from identical protein subunits. We show that the attractive subunit-core interaction modifies the preferred curvature of the shell and has a key role in the formation of large icosahedral shells. Continuum elasticity theories of virial shells are used to rationalize the simulation results. |
Friday, March 9, 2018 8:24AM - 8:36AM |
X50.00003: The equilibrium structure of small self-assembled nano-shells SANAZ PANAHANDEH, Siyu Li, Roya Zandi Highly symmetric nano-shells are found in many biological systems, such as clathrin cages and viral shells and is a rapidly developing area of materials science. Using Monte Carlo simulation, we study the spontaneous assembly of protein shells composed of several identical subunits under equilibrium conditions. We construct a phase diagram to investigate the impact of the spontaneous curvature and mechanical properties of protein subunits on the size and geometry of the assembly products. |
Friday, March 9, 2018 8:36AM - 8:48AM |
X50.00004: Detection and manipulation of single nanoparticle (NP) dynamic assembly process by the integration of nanopore and nanoelectrode Popular Pandey, Jin He Nanopore and ultrasmall electrode are two promising electrochemical methods for single entity studies. However, sensitivity and the selectivity of these methods are still limited. In recent years, simultaneous multiparameter detection methods have received wide attention for improving the sensitivity and selectivity of individual methods. In this talk, I will show that the two methods (nanopore sensing and nanoelectrode sensing) can be incorporated together to study single nanoparticle (NP) in solution by using a multifunctional nanopipette that contain both nanopore and nanoelectrode at the nanopipette apex. Based on the complementary and correlated ionic current from the nanopore and potential signals from the nanoelectrode, we can unambiguously differentiate various single NP events. In addition to single NP events, the dynamic assembly of NPs can be manipulated and investigated in detail by both nanopore and nanoelectrode. |
Friday, March 9, 2018 8:48AM - 9:00AM |
X50.00005: Microfluidic Arrays Using Through-Holes in Printed-Wiring Board for High Throughput Nanopore Sensing Yusuke Goto, Mayu Aoki, Itaru Yanagi, Kunio Harada, Yoshimitsu Yanagawa, Ken-ichi Takeda Solid-state nanopore is expected as a long-read and low cost DNA sequencer. Integration and parallel sequencing of the nanopores are effective to enhance the analytical throughput. However, the integrated structure tends to be complicated, because each channel requires both fluidic access and electrical access individually. Also, the leakage current between adjacent channels must be sufficiently smaller than ionic current through a nanopore (target value is 10 pA at 0.1 V). In this study, to simplify the structure, we examined applying through-holes and interconnects of a printed-wiring board (PWD) to vertical fluidic access and electric access respectively. Also, we formed a polyimide pattern on the PWD by photolithography as an isolation layer between adjacent channels. As a result, a microfluidic device with a pitch of 0.7 mm and 400 arrays was successfully fabricated. |
Friday, March 9, 2018 9:00AM - 9:12AM |
X50.00006: Identification of Four-Nucleotide Single-Stranded DNA Homopolymers with a Solid-State Nanopore Using Alkaline CsCl Solution Yusuke Goto, Itaru Yanagi, Kazuma Matsui, Takahide Yokoi, Ken-ichi Takeda DNA sequencing with a solid-state nanopore is promising technology which has the potential to overcome the performance of conventional sequencers. However, identification of four nucleotides with a typical SiN nanopore has yet to be clearly demonstrated because a guanine homopolymer rapidly forms to G-quadruplex under a typical KCl aqueous solution. To overcome this issue, we introduced an alkaline CsCl aqueous solution which induces denaturation of G-quadruplex to single-stranded structure due to disruption of the hydrogen-bonding network between guanines. Using this alkaline CsCl solution, we demonstrated proof-of-principle that four nucleotide single-stranded DNA homopolymers were statistically identified according to the blockade currents with the same single nanopore. Additionally, we also confirmed that a triblock DNA copolymer including three nucleotides exhibited a trimodal gaussian distribution whose peaks correspond to those of DNA homopolymers. Our findings will open the door for actualizing solid-state nanopore sequencing. |
Friday, March 9, 2018 9:12AM - 9:24AM |
X50.00007: Numerical Studies of 3-mer Oligo Hybridization on an ssDNA Molecule Binquan Luan, Xinsheng Ling In the proposed nanopore DNA sequencing, the 4th generation polymerase-free DNA sequencing technology, a key question is whether one can discriminate DNA bases using short, 3-mer, oligonucleotides hybridization. In this numerical study, we employed the molecular dynamics (MD) method to investigate the stability of trimers hybridized on an ssDNA molecule. For a trimer with fully matched Watson-Crick base-pairing with the host ssDNA, we found that the hybridization was stable during the entire simulation time (hundreds of nanoseconds). Thus the actual residence time (or dwell time) for such pairs should be much longer. However, with a single mismatched base-pair, the tested trimer could diffuse away from the hybridization site on the ssDNA within one nano-second. To estimate the residence time of a fully matched trimer bound on the ssDNA, we applied pulling/biasing forces F on the trimer to facilitate its unbinding with the ssDNA. Using the Bell theory, we can numerically calculate the residence time (when F=0) for a trimer on its hybridization site. We expect that these results, providing temporal constraints on the nanopore-based DNA sequencing, will lead to a more optimized design for the nanopore sequencing platform. |
Friday, March 9, 2018 9:24AM - 9:36AM |
X50.00008: Design of Novel Magnetic Tweezers and its use for Studying DNA-Compacting Proteins Roberto Fabian, Christopher Tyson, Anneliese Striz, Pamela Tuma, Ian Pegg, Abhijit Sarkar We report the development of a horizontal magnetic tweezers capable of applying forces in the 0.1 - 100 piconewton (pN) range on single DNA molecules. The two ends of the DNA molecule are attached to 2.8 um paramagnetic beads with one bead immobilized on a rigid glass surface while the other bead is suspended near a small bar magnet. The magnet is moved towards the tethered DNA at a speed between 0.25 – 10 um/s and can generate forces greater than 70 pN on the DNA molecules. These forces are produced in the focal plane of the microscope objective, permitting direct DNA extension measurements with a precision of <10 nm. We calibrate the tweezers using the DNA overstretching transition, and study hysteretic effects in extension-compaction cycles. We describe the tweezers in detail and present data validating its performance. We conclude with a discussion of our ongoing single experiments on the binding mechanism of the protein mIHF, a protein that may play an important role in the infection pathway of tuberculosis. |
Friday, March 9, 2018 9:36AM - 9:48AM |
X50.00009: High-Force Freely-Orbiting and Torque-Wrench Magnetic Tweezers Qingnan Tang, Ricksen Winardhi, Yinan Wang, Clarence Chong, xiangjun zeng, Jie Yan Magnetic tweezers have been extensively applied to study the stability and interactions of nucleic acids and protein structures under versatile mechanical constraints. Most current high-resolution magnetic tweezers have a vertical design, with the sample stage between a pair of permanent magnets that generates force to the molecule of interest and an objective lens that records the bead image. This design requires a small opening in the middle of the magnets to allow light to pass through, compromising the flexibility of magnets arrangement and the force range it can generate. Previously we developed magnetic tweezers based on objective illumination, which provides high flexibility on the arrangement of magnets above the sample channel. In this study, we further show that this design enables developing high-force torque-wrench and free-orbiting magnetic tweezers, which is not easy to achieve in traditionally designed transmission-illumination. We also show that by using a reflective coverslip on the top of sample chamber, high-quality imaging of bead can be obtained using air objective lens, making it possible to directly control the sample temperature. The capabilities of the high-force torque-wrench/freely-orbiting magnetic tweezers are demonstrated with several examples. |
Friday, March 9, 2018 9:48AM - 10:00AM |
X50.00010: Optoelectronic Tuning of Quantum Dots by Biological Cells Bong Han Lee, Sindhuja Suresh, Andrew Ekpenyong Quantum dots (QDs) have applications and promising myriad applications in photovoltaic cells, biomedical imaging, targeted drug delivery, and quantum information processing. These have led to much research on their interactions with other systems. For biological systems, research has focused on the biocompatibility and cytotoxicity of QDs in the context of imaging/therapy. However, there is a paucity of work on how biological systems might be used to alter the optoelectronic properties of QDs. Here, we show that these properties can be altered by biological macromolecules following controlled changes in cellular activities. Using CdSe/ZnS core-shell QDs, spectroscopic analysis of optically excited colloidal QDs with HL60, K562, and HCN2 cell lines are performed. Our results show statistically significant (p < 0.0001) quenching of the emission spectra of the colloidal dispersions due to the reactive oxygen species (ROS) produced by these cells following chemotherapy and radiotherapy. This optical modulation constitutes what we describe as cyto-molecular tuning. This type of tuning will possibly enhance applications of QDs in green energy and biomedical imaging. |
Friday, March 9, 2018 10:00AM - 10:12AM |
X50.00011: Role of quantum decoherence in FRET Phil Nelson Resonance energy transfer has become an indispensable experimental tool. Its physical underpinnings, however, are subtle: It involves a discrete jump of excitation from one molecule to another, and so we regard it as a strongly quantum-mechanical process. And yet, its kinetics differ strongly from what many of us were taught about two-state quantum systems: Quantum superpositions of the states do not seem to arise; and so on. Although J. R. Oppenheimer and Th. Förster navigated these subtleties successfully, it remains hard to find a simple derivation in modern language, outside of specialized quantum optics treatises. The key step involves acknowledging quantum decoherence. Appreciating that aspect can be helpful when we attempt to extend our understanding to situations where the original analysis is not applicable. |
Friday, March 9, 2018 10:12AM - 10:24AM |
X50.00012: Abstract Withdrawn |
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