Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session W26: Interrogating Biomolecules with Synthetic NanostructuresFocus
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Sponsoring Units: DBIO DSOFT DCP DFD Chair: Binquan Luan, IBM TJ Watson Research Center Room: 403 |
Friday, March 6, 2020 8:00AM - 8:12AM |
W26.00001: Optimal Signal Transduction with Silicon Transistors Enable Therapeutic Enzyme Regulation Arvind Balijepalli, Son Le, Michelle A Morris, Harish C Pant, Curt Richter We used commercially sourced n-channel silicon field-effect transistors (nFETs) operating under PID control to demonstrate pH measurements with a resolution of (7.2±0.3)x10-3 at 10 Hz. The results represent a 3-fold improvement over open loop operation of the nFETs and over ion sensitive field-effective transistors (ISFETs). The improved performance was realized when the pH sensing membrane was separated from the nFETs and connected electrically to the transistor gate. The technique leverages key operating procedures from our previous work with dual-gate 2D field-effect transistors (dg2DFET) fabricated with 2D semi-conducting MoS2 channels [1]. The devices were used to measure the function of the enzyme Cdk5, which facilitates signaling within cells by modifying proteins via the hydrolysis of adenosine triphosphate (ATP), and thereby changing the pH of the surrounding solution by a very small amount. By measuring this subtle change in pH, we quantified the activity of Cdk5, which has been previously implicated in Alzheimer’s disease, under physiological conditions. Finally, we demonstrated the effectiveness of a custom polypeptide, p5, as a therapeutic agent in restoring the function of the pathological form of Cdk5. |
Friday, March 6, 2020 8:12AM - 8:24AM |
W26.00002: Protein-Corona-by-Design in 2D: A Molecular Dynamics study to Decode Bio-Nano Interactions for Quality-by-Design Nanomedicines Mohamed Ali Al-Badri, Khuloud al-Jamal, Christian Lorenz Nanoparticles and nanomaterials are increasingly studied for use in biomedical applications including drug delivery, imaging and hyperthermic therapies. However, upon their introduction to a biological medium, the nanomaterial's size, shape, surface charge, surface functional groups, and hydrophilicity/hydrophobicity all play a role in the formation of a hard protein corona. The components of which affect the biological fate of nanomedicine carried by the material, these have consequences on the cellular uptake and toxicity of the corona-nanomaterial complex. |
Friday, March 6, 2020 8:24AM - 8:36AM |
W26.00003: Single-Molecule Characterization of Nanoparticle Bioconjugates using Microwell Array Analysis Mohammad Abdul-Moqueet, Leeana Tovias, Kathryn Mayer Nanoparticles functionalized with biomolecules have been studied extensively for their applications in nanomedicine. A need for characterizing these nanoparticle bioconjugates at the single-particle level using optical methods is needed. Microwell array analysis is a useful tool for single-molecule studies in which enzyme molecules are isolated in femtoliter wells; the enzymes convert non-fluorescent substrates into fluorescent products which can be measured using optical microscopy. Gold bipyramids were synthesized and functionalized with a self-assembled-monolayer (SAM). These particles were then bioconjugated using carbodiimide crosslinking with mouse anti-human epidermal growth factor receptor (EGFR)[KM1] antibodies, followed by human EGFR labeled with horseradish peroxidase (HRP). Microwell arrays were loaded with the nanoparticle bioconjugates such only that a small number of wells were occupied according to Poisson statistics. The fluorescence intensity of the microwells was then used to determine the number of antibodies that were conjugated to the gold bipyramids. |
Friday, March 6, 2020 8:36AM - 8:48AM |
W26.00004: Single-Molecule Kinetics of Taq Polymerase up to 94 °C Mackenzie Walker Turvey, Wonbae Lee, Jeffrey J Taulbee, Calvin J Lau, Kristin Gabriel, Rebecca Vargas, Gregory Weiss, Philip G Collins Single-molecule enzymology is a useful tool for understanding protein kinetics, function, and inhibition, but common techniques work in a limited temperature range. Here, we extend single-molecule science up to 94 °C with MHz resolution using solid-state, carbon nanotube biosensors. Their operation, which is essentially independent of temperature, provides unprecedented access to commercially important enzymes such as Taq, the DNA polymerase I from Thermus aquaticus. Taq is the linchpin protein for the polymerase chain reaction (PCR) amplification of DNA [1]. Our electronic biosensor approach provides direct access to single-nucleotide incorporation activity [2] from room temperature up to 94 °C. For example, the incorporation rate of a single Taq molecule was monitored from 1 bp/s at 22 °C to greater than 100 bp/s at 72 °C, the typical PCR operating temperature. In addition, the biosensor transduces the distinct motions of Taq subdomains, such as brief, 20-µsec flutters as the fingers domain tests nucleotides for complementarity. |
Friday, March 6, 2020 8:48AM - 9:00AM |
W26.00005: Monitoring Antipsychotic Drug Effects on Stimulated Dopamine Release Using Carbon Nanotube Transistors with Nafion-Radical Hybrid Films Inkyoung Park, Viet Anh Pham Ba, Dong-guk Cho, Seunghun Hong We developed floating electrode-based carbon nanotube biosensors for the monitoring of antipsychotic drug effects on the dopamine release from nerve cells (PC12) under potassium stimulation. In this work, carbon nanotube field-effect transistors with floating electrodes were functionalized with nafion films containing 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS●) radicals to build selective biosensors for the dopamine detection. The selective interaction between ABTS● radicals and dopamine allowed us to discriminate dopamine from the simultaneous presence of other neurotransmitters such as glutamate and acetylcholine with a detection limit down to 10 nM. Furthermore, we demonstrated the real-time monitoring of dopamine release from PC12 cells under the stimulation of potassium solutions at various concentrations. Significantly, we could also evaluate the effects of antipsychotic drug (pimozide) on the dopamine release from potassium-stimulated PC12 cells. Since our method enables the quantitative and real-time evaluation of drug effects on living cells, it should be a versatile tool for both biomedical researches and applications. |
Friday, March 6, 2020 9:00AM - 9:12AM |
W26.00006: Synthesis and toxicity of bio-templated fluorescent metal nanoclusters in human Neuro-2a cells Shashi P Karna, Karima Jeneh Perry, Raj Kumar, Raj K. Gupta Bio-templated fluorescent metal nanoclusters (fMNC) have attracted a great deal of attention recently for their potential applications in sensing, cellular imaging, and as photonic probes. More recently, there have been reports of in situ synthesis of fluorescent MNC by tumorigenic (cancerous) as well as healthy animal cell cultures. Here we present the synthesis of Au and Fe nanoclusters synthesized in vitro using human neuro-2a cells. Additionally, protein (BSA and Chicken Egg-White) synthesized fMNCs were also incubated in neuro-2a cells. The cells exhibit significant uptake of protein-templated fMNCs. In both cases the cells exhibited significant viability at relatively elevated metal concentration, up to tens of micrograms. |
Friday, March 6, 2020 9:12AM - 9:48AM |
W26.00007: Protein Aggregation Characterization by Nanopore technology Invited Speaker: Jiali Li Protein aggregation is one of the leading causes of many neurodegenerative diseases such as Alzheimer’s and Parkinson’s. In this talk, we report our study on characterizing protein aggregation with a solid-state nanopore device, together with AFM and DLS techniques. Our model proteins used in these studies are ß-lactoglobulin variant A (bLGa) and neuronal Tau and tubulin proteins. The main component of a nanopore device is a nanometer size pore fabricated in free-standing silicon nitride membrane supported by a silicon substrate which separates two PDMA chambers containing salt solution. A stable ionic current is established by applying a biased voltage on a pair of silver chloride (AgCl) electrodes across the nanopore membrane. When charged protein molecules are added to the grounded chamber, applying a correct biase potential to the other chamber drives a protein molecule into the nanopore which partially blocks ionic flow that can be measured as a transient current drop signal. A protein aggregate which has larger volume than a single protein molecule would block larger amount of current or generate a greater current drop amplitude, therefore a nanopore device can be used to characterize protein aggregation at single molecule level. The volume of translocating protein aggregates are estimated using a calibrated nanopore by a standard that has known geometry such as a dsDNA molecule. We show that solid state nanopore method is capable of measuring protein aggregation number and the aggregation number distribution in the conditions close to their native aqueous environment. The nanopore experiments were performed under applied voltages from 60-210 mV at different pH, temperature, and salt concentrations. We present data of bLga, and Tau and tubulin aggregations measured by nanopore method, and compare them with the results from AFM and DLS. |
Friday, March 6, 2020 9:48AM - 10:00AM |
W26.00008: Active and stable palladium nano-thin-film structure development for rapid and direct biomolecules conjugation and sensing Chia-Ching Chang, Chia-Yu Chang, Yun-Tzu Huang, Wei Chen Metal atoms on surface edges or with specific coordinates possess high surface potentials and serve as core atoms for organic molecule bonding. Unlike self-organized or surface modified nanoparticles, these active metal nanostructures may lose their activity by surface self-diffusion process. It is challenging to create a metal surface structure which possesses both active and stable properties. However, a surface template with native nano-roughness may solve this dilemma. In this study, a PET substrate has been selected for metal atoms absorption and a stable and active Pd nano-thin-film (NTF) surface has been developed. Further studies indicated that the surface contains an (1,1,1) like structure and Pd-NTF growth followed a Stranski-Krastanov-like growth model. This nanostructure thin-film (Pd NTF-PET) electrode has been developed for electrochemical impedance spectroscopy (EIS) usage. Both DNA and protein can be immobilized on the Pd NTF-PET electrodes directly, within 15 min and its biosensing sensitivity was as low as 0.1 ng per-test in 1 µl. In summary, we have developed an active and stable Pd NTF-PET electrode for biosensing applications. |
Friday, March 6, 2020 10:00AM - 10:12AM |
W26.00009: Spontaneous ssDNA Stretching on Graphene and Hexagonal Boron Nitride In-plane Heterostructures Binquan Luan
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Friday, March 6, 2020 10:12AM - 10:24AM |
W26.00010: Block Optical DNA Sequencing with Plasmonic Substrates for Rapid Biomarker Diagnostics Lee Korshoj, Ameya Gajanan Prabhune, Prashant Nagpal Precision medicine requires high-throughput point-of-care diagnostics with multiomics capability for sensing biomolecules and their molecular variants. In a push for improved precision diagnostics, we describe an optical sequencing platform that uses surface-enhanced Raman spectroscopy (SERS) measurements from plasmonic nanostructured surfaces and nanoparticles for label-free determination of nucleobase content in DNA k-mer blocks. With SERS on cationic silver nanoparticles, we achieved >93% accuracy for predicting A-G-C-T content in 10-mer DNA blocks. The high-accuracy measurements were used with a content-scoring bioinformatics algorithm to correctly identify a β-lactamase antibiotic resistance gene and confirm the Pseudomonas aeruginosa pathogen from merely <12 measurements (<15% coverage of the gene) [1,2]. We further proved applicability on RNA and chemically modified nucleobases for extensions to transcriptomics and epigenomics. With the versatility of plasmonic substrates for simple data acquisition, resolution to single-molecules, and multiplexing, optical sequencing can provide rapid biomarker diagnostics in the clinical setting [3]. |
Friday, March 6, 2020 10:24AM - 10:36AM |
W26.00011: Dynamics of DNA in periodic temperature gradient field created by plasmonic heating Ryoko Shimada, Hiroshi Watanabe Different molecules in a solution can be separated from each other along a temperature gradient. This phenomenon, so-called Soret effect, offers an interesting method of molecular manipulation in various research fields. Plasmonic heating from periodic metal domains is one of the effective ways to create a periodic temperature gradient. In this work, we utilized the plasmonic heating from periodic silver (Ag) domains under emission of blue light (400 – 440 nm) to create the periodic temperature gradient (with a large amplitude of ~ 0.5 K/um), thereby attempting to observe the Soret effect on DNA molecules mixed in polyethylene glycol (PEG) solutions. The DNA molecules, labeled with fluorescent dyes, were concentrated in high temperature zones, confirming the positive Soret effect. In addition, for large DNA molecules (~ 166 Kbp), stretched conformations bridging two hot zones were occasionally observed and their diffusion appeared to deviate from the simple Fickian behavior, possibly because of the microscopic Soret effect within the molecule. Details of this observation will be discussed on site. |
Friday, March 6, 2020 10:36AM - 10:48AM |
W26.00012: Tunneling Spectroscopy on Engineered Surfaces for RNA Nucleotide and Structural Label Identification Lee Korshoj, Gary R Abel Jr., Anushree Chatterjee, Prashant Nagpal Although several advances have been made in RNA sequencing and structural characterization, the lack of a method for directly determining the sequence and structure of single RNA molecules has limited our ability to probe heterogeneity in gene expression at the level of single cells. We present a method for identification of RNA nucleotides and structural labels for mapping of single RNA molecules. With non-perturbative tunneling spectroscopy, we probed the molecular orbitals of distinct nucleobases within RNA macromolecules immobilized with restricted conformational freedom on a chemically modified surface. From the measurements, models for tunneling were combined to obtain twelve biophysical parameters unique to the ribonucleotides within the electronic junction [1]. The twelve parameters serve as a comprehensive molecular fingerprint, enabling ribonucleotide discrimination and identification of structure-dependent chemical labels with machine learning. We show high accuracy for both ribonucleotide discrimination (>99%) and chemical label identification (>98%) with a modest 35 repeat measurements [2]. This technique facilitates probing the transcriptome with a previously unattainable level of detail. |
Friday, March 6, 2020 10:48AM - 11:00AM |
W26.00013: Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox Guang Shi, Dave Thirumalai Hi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between two loci increases. However, studies comparing Hi-C and FISH data show that in some cases the distance between one pair of loci, with larger Hi-C readout, is paradoxically larger compared to another pair with a smaller value of the contact probability. Here, we show that the FISH-Hi-C paradox can be resolved using a theory based on a Generalized Rouse Model for Chromosomes (GRMC). The FISH-Hi-C paradox arises because the cell population is highly heterogeneous, which means that a given contact is present in only a fraction of cells. Insights from the GRMC is used to construct a theory, without any adjustable parameters, to extract the distribution of subpopulations from the FISH data, which quantitatively reproduces the Hi-C data. Our results show that heterogeneity is pervasive in genome organization at all length scales, reflecting large cell-to-cell variations. |
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