Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session N21: Focus Session: Single Molecule Nanobiology |
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Sponsoring Units: DBP Chair: Saw-Wai Hla, Ohio University Room: LACC 409A |
Wednesday, March 23, 2005 8:00AM - 8:36AM |
N21.00001: Single molecule studies in spatially restricted fluid systems Invited Speaker: We have used simple nanofluidic devices to isolate individual active biomolecules in solution in order to observe there identity and activity. We have 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 for the observation of single molecule binding activity at meaningful rates and concentrations. Small fluid channels have also been used to isolate individual optically detected molecules. Temporal observation of either the driven or diffusive motion of molecules through the restricted observation volume provides information about the identity of the molecule and can also be used to detect specific chemical binding events. Single specific molecular binding events can be observed by optically observing the spectral characteristics of labeled molecules. In this talk we will describe several approaches and applications of the single molecule studies in microfabricated fluidic systems. [Preview Abstract] |
Wednesday, March 23, 2005 8:36AM - 8:48AM |
N21.00002: The Physics of Nanoconfined DNA Walter Reisner, Keith Morton, Robert Riehn, Yan Mei Wang, Zhaoning Yu, Erwin Frey, Stephen Chou, Robert Austin Nanotechnology has the potential to revolutionize biology by making possible the construction of chip-based devices with nanoscale features that can not only detect and separate single DNA molecules by size but also--it is hoped in the future--actually sequence at the single molecule level. Understanding the physics of nanoconfined DNA is important for the future design of such devices. Here we present measurements of the static properties and Brownian dynamics of single DNA molecules confined in nanochannels using fluorescence microscopy techniques (end labeling and staining of the entire molecule using intercalating dyes). We study the effect of varying the degree of nanoconfinement, using nanochannels with widths ranging from 10 to 500nm. The nanochannels are fabricated using interference lithography and imprinting techniques. We also present scaling arguments and Monte Carlo simulations on the problem of confined semiflexible polymers and discuss how these results can be interpreted in the context of our experimental work. [Preview Abstract] |
Wednesday, March 23, 2005 8:48AM - 9:00AM |
N21.00003: Real-time restriction mapping of DNA stretched in nanofluidic devices Robert Riehn, Walter Reisner, Shuang Fang Lim, Yan Mei Wang, Robert H. Austin, Manchun Lu, Edward C. Cox We present real-time sequence-specific restriction mapping of single DNA molecules stretched in nanofabricated channels. In these channels, DNA is linearized and extended to up to 3/4 of its contour length, permitting attribution of the cutting sites to specific regions in the genetic code. We will present real-time restriction of genomic viral DNA with the enzymes Sma I, Sac I, Kpn I. We are able to determine cutting sites and can quantify the cutting rates at different genomic locations. Complete digestion can be achieved within less than 10 seconds. Our device operates in a quasi-continous mode, which we achieved by controlling the concetration of the necessary co-factor Mg$^{2+}$ throughout the mixed micro- and nanofluidic device. DNA was observed using fluorescence micrcoscopy and intercalating DNA stains. [Preview Abstract] |
Wednesday, March 23, 2005 9:00AM - 9:12AM |
N21.00004: A DNA catalyst for speeding up a single-molecule DNA nanomotor Yufang Wang, Y. Zhang, N. P. Ong A drawback of single-molecule DNA-based nanomotors is the slow cycling speed. Previously, a motor based on the cyclic folding and unfolding of a DNA single strand was described by Tan et al. The DNA motor strand M is a 17-base sequence that folds into a chair-type quadruplex structure in the presence of potassium ions. A fuel strand A complementary to M is added. Hybridization of M with A unfolds the chair structure. Next, addition of a restoration fuel strand B de-hybridizes the double strand and restores M to its chair configuration, completing the cycle. We have found that the bottleneck for this cycle is the tendency for B to also fold into the chair structure. By introducing a short catalyst strand C which inhibits this premature folding, we have achieved a doubling of the speed of the motor. The catalyst shows robust behavior over several cycles. [Preview Abstract] |
Wednesday, March 23, 2005 9:12AM - 9:48AM |
N21.00005: Single-molecule studies of biological molecules Invited Speaker: Structural heterogeniety, i.e., the existence of multiple nearly-degenerate conformational substates of molecules, plays a key role in biological machinery. Therefore, in order to understand many biological processes, it is necessary to examine processes at the single molecule level. This talk will describe AFM imaging of processes involved in turning on genes (1), methods for chemically-identifying single proteins (2) and methods for wiring single molecules into electrical circuits (3). .1. H. Wang\textit{ et al.}, \textit{Biophys. J.} \textbf{87}, 1964--1971 (2004). 2. C. Stroh\textit{ et al.}, \textit{Proc. Natl. Acad. Sci. (USA)} \textbf{101}, 12503--12507 (2004). 3. X. D. Cui\textit{ et al.}, \textit{Science} \textbf{294}, 571 (2001). [Preview Abstract] |
Wednesday, March 23, 2005 9:48AM - 10:00AM |
N21.00006: Single molecule studies of the mechanical stability of packed DNA Michelle Wang, Alla Shundrovsky Biological organisms must compactly store and yet efficiently read the huge amounts of genetic information contained in their DNA. In the cell nucleus, DNA is highly compact as compared to naked DNA. The primary packing unit, the nucleosome, consists of roughly two turns of DNA wrapped around a core histone octamer. The mechanical stability of nucleosomes determines the accessibility of DNA to the cellular machinery that must decode it. We will discuss our recent progress towards understanding the mechanical stability of nucleosomes using single-molecule studies. [Preview Abstract] |
Wednesday, March 23, 2005 10:00AM - 10:12AM |
N21.00007: Single Molecule Manipulation and Spectroscopy of Chlorophyll-a from Spinach Jessica-Jones Benson, Violeta Iancu, Saw-Wai Hla Chlorophyll-a, a molecule produced from `Spinach', adsorbed on a Au(111) surface has been investigated by using an ultra-high-vacuum low-temperature scanning-tunneling-microscope (UHV-LT-STM) at liquid helium temperatures. Studies are carried out both on isolated single molecules and on self-assembled molecular layers. The tunneling I-V and dI-dV spectroscopy of chlorophyll-a elucidate electronic properties of single molecule, such as the HOMO-LOMO gap and molecular orbital states. Mechanical stability of the chlorophyll-a is examined by using STM lateral manipulation (1,2). Here, the STM tip is placed just a few angstrom separation from the molecule to increase the tip-molecule interaction. Then the tip is laterally scanned across the surface resulting in pulling of the molecule. The detailed molecule movement is directly monitored through the corresponding STM-tip height signals. Our results reveal that the spinach molecule is a promising candidate for environmental friendly nano-device applications. (1). S.-W. Hla, K.-H. Rieder, Ann. Rev. Phys. Chem. \textbf{54} (2003) 307-330. (2). S.-W. Hla, et al. Phys. Rev. Lett. \textbf{93} (2004), 208302. This work is financially supported by the US-DOE grant DE-FG02-02ER46012. [Preview Abstract] |
Wednesday, March 23, 2005 10:12AM - 10:24AM |
N21.00008: Twirling DNA Rings - Swimming Nanomotors Ready for a Kickstart Igor Kulic, Rochish Thaokar, Helmut Schiessel We propose a rotary DNA nanomachine that shows a continuous rotation with a frequency of 10$^{2}$ -10$^{4}$Hz. The device consists of a minicircle with the DNA sequence chosen appropriately to achieve anisotropic elastic features generating a ratchet potential. The motor can be externally driven via the ratchet effect through periodic temperature oscillations. As a result the ring self-propels through the fluid like a molecular ``ring of smoke" with a speed up to microns per second. Hydrodynamic interactions open the possibility of self-organized collective ratchet behavior in semi-dilute solutions of twirling DNA rings. [Preview Abstract] |
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N21.00009: Biomotor-based single molecular biosensor Chia-Fu Chou, Yingjie Liu, Takeyoshi Nishio, Mrinalini Prasad, Frederic Zenhausern We present our development of novel engineering devices based on biomolecular motors. Adenosine triphosphate synthase (ATPase) is the only rotary motor in nature. The ATPase motor molecules have been genetically engineered to facilitate the immobilization of the motor to Ni surface and to attach additional nanofabricated rods or biomolecules to the $\gamma $ subunit of the biomotor. These properties enable the possibility of utilizating ATPase in the fabrication of novel engineeting devices and systems. This approach may enable the creation of a new class of sensors, mechanical force transducers, and actuators. Here we report our work on constructing an ATPase--nanobar based hybrid system for nanoscale molecular biosensing. We demonstrated avidin-coated Au nanobar can be attached to biotinylated $\gamma $ unit of the ATPase motor through biotin-avidin interaction and we observed single rotational assay by bright-field imaging. [Preview Abstract] |
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