1
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Messenger H, Madrid D, Saini A, Kisley L. Native diffusion of fluorogenic turn-on dyes accurately report interfacial chemical reaction locations. Anal Bioanal Chem 2023:10.1007/s00216-023-04639-1. [PMID: 36907920 DOI: 10.1007/s00216-023-04639-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/14/2023]
Abstract
Single-molecule fluorescence microscopy with "turn-on" dyes that change fluorescent state after a reaction report on the chemistry of interfaces relevant to analytical and bioanalytical chemistry. Paramount to accurately understanding the phenomena at the ultimate detection limit of a single molecule is ensuring fluorophore properties such as diffusion do not obscure the chemical reaction of interest. Here, we develop Monte Carlo simulations of a dye that undergoes reduction to turn-on at the cathode of a corroded iron surface taking into account the diffusion of the dye molecules in a total internal reflection fluorescence (TIRF) excitation volume, location of the cathode, and chemical reactions. We find, somewhat counterintuitively, that a fast diffusion coefficient of D = 108 nm2/s, corresponding to the dye in aqueous solution, accurately reports the location of single reaction sites. The dyes turn on and are present for the acquisition of a single frame allowing for localization before diffusing out of the thin TIRF excitation volume axially. Previously turned-on (i.e., activated) dyes can also randomly hit the surface surrounding the reaction site leading to a uniform increase in the background. Using concentrations that lead to high turnover rates at the reaction site can achieve signal-to-background ratios of ~100 in our simulation. Therefore, the interplay between diffusion, turn-on reaction rate, and concentration of the dye must be strategically considered to produce accurate images of reaction locations. This work demonstrates that modeling can assist in the design of single-molecule microscopy experiments to understand interfaces related to analytical chemistry such as electrode, nanoparticle, and sensor surfaces.
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Affiliation(s)
- Hannah Messenger
- Department of Physics, Case Western Reserve University, 2076 Adelbert Road, Cleveland, OH, 44106, USA
| | - Daniel Madrid
- Department of Physics, Case Western Reserve University, 2076 Adelbert Road, Cleveland, OH, 44106, USA
| | - Anuj Saini
- Department of Physics, Case Western Reserve University, 2076 Adelbert Road, Cleveland, OH, 44106, USA
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, 2076 Adelbert Road, Cleveland, OH, 44106, USA. .,Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA.
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2
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Kisley L, Patil U, Dhamane S, Kourentzi K, Tauzin LJ, Willson RC, Landes CF. Competitive multicomponent anion exchange adsorption of proteins at the single molecule level. Analyst 2017; 142:3127-3131. [DOI: 10.1039/c7an00701a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Super-resolution imaging of multicomponent, competitive adsorption demonstrates that competitors block certain ligands from the analyte without changing analyte adsorption kinetics.
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Affiliation(s)
- Lydia Kisley
- Department of Chemistry
- Rice University
- Houston
- USA
| | - Ujwal Patil
- Department of Biology & Biochemistry
- University of Houston
- Houston
- USA
| | - Sagar Dhamane
- Department of Biology & Biochemistry
- University of Houston
- Houston
- USA
| | - Katerina Kourentzi
- Department of Chemical & Biomolecular Engineering
- University of Houston
- Houston
- USA
| | | | - Richard C. Willson
- Department of Chemical & Biomolecular Engineering
- University of Houston
- Houston
- USA
- Department of Biology & Biochemistry
| | - Christy F. Landes
- Department of Chemistry
- Rice University
- Houston
- USA
- Department of Electrical and Computer Engineering
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3
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Dominguez-Medina S, Kisley L, Tauzin LJ, Hoggard A, Shuang B, D. S. Indrasekara AS, Chen S, Wang LY, Derry PJ, Liopo A, Zubarev ER, Landes CF, Link S. Adsorption and Unfolding of a Single Protein Triggers Nanoparticle Aggregation. ACS NANO 2016; 10:2103-12. [PMID: 26751094 PMCID: PMC4768289 DOI: 10.1021/acsnano.5b06439] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The response of living systems to nanoparticles is thought to depend on the protein corona, which forms shortly after exposure to physiological fluids and which is linked to a wide array of pathophysiologies. A mechanistic understanding of the dynamic interaction between proteins and nanoparticles and thus the biological fate of nanoparticles and associated proteins is, however, often missing mainly due to the inadequacies in current ensemble experimental approaches. Through the application of a variety of single molecule and single particle spectroscopic techniques in combination with ensemble level characterization tools, we identified different interaction pathways between gold nanorods and bovine serum albumin depending on the protein concentration. Overall, we found that local changes in protein concentration influence everything from cancer cell uptake to nanoparticle stability and even protein secondary structure. We envision that our findings and methods will lead to strategies to control the associated pathophysiology of nanoparticle exposure in vivo.
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Affiliation(s)
| | - Lydia Kisley
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
| | - Lawrence J. Tauzin
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
| | - Anneli Hoggard
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
| | - Bo Shuang
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
| | | | - Sishan Chen
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
| | - Lin-Yung Wang
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
| | - Paul J. Derry
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
| | - Anton Liopo
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
| | - Eugene R. Zubarev
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
- Department
of Materials Science and NanoEngineering, Rice University, Houston, Texas 77251, United States
| | - Christy F. Landes
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
- Department
of Electrical and Computer Engineering, Rice University, Houston, Texas 77251, United States
- E-mail:
| | - Stephan Link
- Department
of Chemistry, Rice University, Houston, Texas 77251, United States
- Department
of Electrical and Computer Engineering, Rice University, Houston, Texas 77251, United States
- E-mail:
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4
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Kisley L, Poongavanam MV, Kourentzi K, Willson RC, Landes CF. pH-dependence of single-protein adsorption and diffusion at a liquid chromatographic interface. J Sep Sci 2015; 39:682-8. [DOI: 10.1002/jssc.201500809] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/04/2015] [Accepted: 09/05/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Lydia Kisley
- Department of Chemistry; Rice University; Houston TX USA
| | | | - Katerina Kourentzi
- Department of Chemical & Biomolecular Engineering; University of Houston; Houston TX USA
| | - Richard C. Willson
- Department of Biology & Biochemistry; University of Houston; Houston TX USA
- Department of Chemical & Biomolecular Engineering; University of Houston; Houston TX USA
- Houston Methodist Research Institute; Houston TX USA
- Centro de Biotecnología FEMSA, Departamento de Biotecnología e Ingeniería de Alimentos; Tecnológico de Monterrey; Monterrey NL Mexico
| | - Christy F. Landes
- Department of Chemistry; Rice University; Houston TX USA
- Department of Electrical and Computer Engineering; Rice University; Houston TX USA
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Kisley L, Brunetti R, Tauzin LJ, Shuang B, Yi X, Kirkeminde AW, Higgins DA, Weiss S, Landes CF. Characterization of Porous Materials by Fluorescence Correlation Spectroscopy Super-resolution Optical Fluctuation Imaging. ACS NANO 2015; 9:9158-66. [PMID: 26235127 PMCID: PMC10706734 DOI: 10.1021/acsnano.5b03430] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Porous materials such as cellular cytosol, hydrogels, and block copolymers have nanoscale features that determine macroscale properties. Characterizing the structure of nanopores is difficult with current techniques due to imaging, sample preparation, and computational challenges. We produce a super-resolution optical image that simultaneously characterizes the nanometer dimensions of and diffusion dynamics within porous structures by correlating stochastic fluctuations from diffusing fluorescent probes in the pores of the sample, dubbed here as "fluorescence correlation spectroscopy super-resolution optical fluctuation imaging" or "fcsSOFI". Simulations demonstrate that structural features and diffusion properties can be accurately obtained at sub-diffraction-limited resolution. We apply our technique to image agarose hydrogels and aqueous lyotropic liquid crystal gels. The heterogeneous pore resolution is improved by up to a factor of 2, and diffusion coefficients are accurately obtained through our method compared to diffraction-limited fluorescence imaging and single-particle tracking. Moreover, fcsSOFI allows for rapid and high-throughput characterization of porous materials. fcsSOFI could be applied to soft porous environments such hydrogels, polymers, and membranes in addition to hard materials such as zeolites and mesoporous silica.
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Affiliation(s)
- Lydia Kisley
- Department of Chemistry and Rice University, Houston, Texas 77251, United States
| | - Rachel Brunetti
- Department of Physics, Scripps College, Claremont, California 91711, United States
| | - Lawrence J. Tauzin
- Department of Chemistry and Rice University, Houston, Texas 77251, United States
| | - Bo Shuang
- Department of Chemistry and Rice University, Houston, Texas 77251, United States
| | - Xiyu Yi
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Alec W. Kirkeminde
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506-0401, United States
| | - Daniel A. Higgins
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506-0401, United States
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Physiology, and University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Christy F. Landes
- Department of Chemistry and Rice University, Houston, Texas 77251, United States
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77251, United States
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Poongavanam MV, Kisley L, Kourentzi K, Landes CF, Willson RC. Ensemble and single-molecule biophysical characterization of D17.4 DNA aptamer-IgE interactions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:154-64. [PMID: 26307469 DOI: 10.1016/j.bbapap.2015.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 08/09/2015] [Accepted: 08/18/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND The IgE-binding DNA aptamer 17.4 is known to inhibit the interaction of IgE with the high-affinity IgE Fc receptor FcεRI. While this and other aptamers have been widely used and studied, there has been relatively little investigation of the kinetics and energetics of their interactions with their targets, by either single-molecule or ensemble methods. METHODS The dissociation kinetics of the D17.4/IgE complex and the effects of temperature and ionic strength were studied using fluorescence anisotropy and single-molecule spectroscopy, and activation parameters calculated. RESULTS The dissociation of D17.4/IgE complex showed a strong dependence on temperature and salt concentration. The koff of D17.4/IgE complex was calculated to be (2.92±0.18)×10(-3) s(-1) at 50 mM NaCl, and (1.44±0.02)×10(-2) s(-1) at 300 mM NaCl, both in 1 mM MgCl2 and 25°C. The dissociation activation energy for the D17.4/IgE complex, Ea, was 16.0±1.9 kcal mol(-1) at 50 mM NaCl and 1 mM MgCl2. Interestingly, we found that the C19A mutant of D17.4 with stabilized stem structure showed slower dissociation kinetics compared to D17.4. Single-molecule observations of surface-immobilized D17.4/IgE showed much faster dissociation kinetics, and heterogeneity not observable by ensemble techniques. CONCLUSIONS The increasing koff value with increasing salt concentration is attributed to the electrostatic interactions between D17.4/IgE. We found that both the changes in activation enthalpy and activation entropy are insignificant with increasing NaCl concentration. The slower dissociation of the mutant C19A/IgE complex is likely due to the enhanced stability of the aptamer. GENERAL SIGNIFICANCE The activation parameters obtained by applying transition state analysis to kinetic data can provide details on mechanisms of molecular recognition and have applications in drug design. Single-molecule dissociation kinetics showed greater kinetic complexity than was observed in the ensemble in-solution systems, potentially reflecting conformational heterogeneity of the aptamer. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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Affiliation(s)
| | - Lydia Kisley
- Department of Chemistry, Rice University, Houston, TX77005-1827, USA
| | - Katerina Kourentzi
- Department of Chemical and Biomolecular Engineering, University of Houston, TX 77204-4004, USA
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, TX77005-1827, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005-1827, USA.
| | - Richard C Willson
- Department of Biology and Biochemistry, University of Houston, TX 77204-5001, USA; Department of Chemical and Biomolecular Engineering, University of Houston, TX 77204-4004, USA; Houston Methodist Research Institute, Houston, TX 77030, USA; Centro de Biotecnología FEMSA, Departamento de Biotecnología e Ingeniería de Alimentos, Tecnológico de Monterrey, Monterrey 64849, Mexico.
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7
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Affiliation(s)
- Lydia Kisley
- Department of Chemistry and Department of Electrical and Computer
Engineering,
Rice Quantum Institute, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Christy F. Landes
- Department of Chemistry and Department of Electrical and Computer
Engineering,
Rice Quantum Institute, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
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8
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Pal R, Beeby A. Simple and versatile modifications allowing time gated spectral acquisition, imaging and lifetime profiling on conventional wide-field microscopes. Methods Appl Fluoresc 2014; 2:037001. [DOI: 10.1088/2050-6120/2/3/037001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Tauzin L, Shuang B, Kisley L, Mansur AP, Chen J, de Leon A, Advincula RC, Landes CF. Charge-dependent transport switching of single molecular ions in a weak polyelectrolyte multilayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8391-9. [PMID: 24960617 PMCID: PMC4216201 DOI: 10.1021/la5012007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The tunable nature of weak polyelectrolyte multilayers makes them ideal candidates for drug loading and delivery, water filtration, and separations, yet the lateral transport of charged molecules in these systems remains largely unexplored at the single molecule level. We report the direct measurement of the charge-dependent, pH-tunable, multimodal interaction of single charged molecules with a weak polyelectrolyte multilayer thin film, a 10 bilayer film of poly(acrylic acid) and poly(allylamine hydrochloride) PAA/PAH. Using fluorescence microscopy and single-molecule tracking, two modes of interaction were detected: (1) adsorption, characterized by the molecule remaining immobilized in a subresolution region and (2) diffusion trajectories characteristic of hopping (D ∼ 10(-9) cm(2)/s). Radius of gyration evolution analysis and comparison with simulated trajectories confirmed the coexistence of the two transport modes in the same single molecule trajectories. A mechanistic explanation for the probe and condition mediated dynamics is proposed based on a combination of electrostatics and a reversible, pH-induced alteration of the nanoscopic structure of the film. Our results are in good agreement with ensemble studies conducted on similar films, confirm a previously-unobserved hopping mechanism for charged molecules in polyelectrolyte multilayers, and demonstrate that single molecule spectroscopy can offer mechanistic insight into the role of electrostatics and nanoscale tunability of transport in weak polyelectrolyte multilayers.
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Affiliation(s)
- Lawrence
J. Tauzin
- Department
of Chemistry and Department of Electrical and Chemical Engineering, Rice University, Houston, Texas 77251, United States
| | - Bo Shuang
- Department
of Chemistry and Department of Electrical and Chemical Engineering, Rice University, Houston, Texas 77251, United States
| | - Lydia Kisley
- Department
of Chemistry and Department of Electrical and Chemical Engineering, Rice University, Houston, Texas 77251, United States
| | - Andrea P. Mansur
- Department
of Chemistry and Department of Electrical and Chemical Engineering, Rice University, Houston, Texas 77251, United States
| | - Jixin Chen
- Department
of Chemistry and Department of Electrical and Chemical Engineering, Rice University, Houston, Texas 77251, United States
| | - Al de Leon
- Department
of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Rigoberto C. Advincula
- Department
of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Christy F. Landes
- Department
of Chemistry and Department of Electrical and Chemical Engineering, Rice University, Houston, Texas 77251, United States
- E-mail:
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10
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Kisley L, Chen J, Mansur AP, Dominguez-Medina S, Kulla E, Kang MK, Shuang B, Kourentzi K, Poongavanam MV, Dhamane S, Willson RC, Landes CF. High ionic strength narrows the population of sites participating in protein ion-exchange adsorption: a single-molecule study. J Chromatogr A 2014; 1343:135-42. [PMID: 24751557 DOI: 10.1016/j.chroma.2014.03.075] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/27/2014] [Indexed: 11/19/2022]
Abstract
The retention and elution of proteins in ion-exchange chromatography is routinely controlled by adjusting the mobile phase salt concentration. It has repeatedly been observed, as judged from adsorption isotherms, that the apparent heterogeneity of adsorption is lower at more-eluting, higher ionic strength. Here, we present an investigation into the mechanism of this phenomenon using a single-molecule, super-resolution imaging technique called motion-blur Points Accumulation for Imaging in Nanoscale Topography (mbPAINT). We observed that the number of functional adsorption sites was smaller at high ionic strength and that these sites had reduced desorption kinetic heterogeneity, and thus narrower predicted elution profiles, for the anion-exchange adsorption of α-lactalbumin on an agarose-supported, clustered-charge ligand stationary phase. Explanations for the narrowing of the functional population such as inter-protein interactions and protein or support structural changes were investigated through kinetic analysis, circular dichroism spectroscopy, and microscopy of agarose microbeads, respectively. The results suggest the reduction of heterogeneity is due to both electrostatic screening between the protein and ligand and tuning the steric availability within the agarose support. Overall, we have shown that single molecule spectroscopy can aid in understanding the influence of ionic strength on the population of functional adsorbent sites participating in the ion-exchange chromatographic separation of proteins.
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Affiliation(s)
- Lydia Kisley
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | - Jixin Chen
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | - Andrea P Mansur
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | | | - Eliona Kulla
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | - Marci K Kang
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | - Bo Shuang
- Department of Chemistry, Rice University, Houston, TX 77251, USA.
| | - Katerina Kourentzi
- Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77004, USA.
| | | | - Sagar Dhamane
- Department of Biology & Biochemistry, University of Houston, Houston, TX 77004, USA.
| | - Richard C Willson
- Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77004, USA; Department of Biology & Biochemistry, University of Houston, Houston, TX 77004, USA; Houston Methodist Research Institute, Houston, TX 77030, USA; Centro de Biotecnología FEMSA, Departamento de Biotecnología e Ingeniería de Alimentos, Tecnológico de Monterrey, Monterrey NL 64849, Mexico.
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, TX 77251, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA.
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11
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Shuang B, Chen J, Kisley L, Landes CF. Troika of single particle tracking programing: SNR enhancement, particle identification, and mapping. Phys Chem Chem Phys 2014; 16:624-34. [PMID: 24263676 PMCID: PMC4041580 DOI: 10.1039/c3cp53968g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single particle tracking (SPT) techniques provide a microscopic approach to probe in vivo and in vitro structure and reactions. Automatic analysis of SPT data with high efficiency and accuracy spurs the development of SPT algorithms. In this perspective, we review a range of available techniques used in SPT analysis programs. In addition, we present an example SPT program step-by-step to provide a guide so that researchers can use, modify, and/or write a SPT program for their own purposes.
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Affiliation(s)
- Bo Shuang
- Department of Chemistry, Rice University, Houston, Texas, United States. Tel: (1)713 348 4437
| | - Jixin Chen
- Department of Chemistry, Rice University, Houston, Texas, United States. Tel: (1)713 348 4437
| | - Lydia Kisley
- Department of Chemistry, Rice University, Houston, Texas, United States. Tel: (1)713 348 4437
| | - Christy F. Landes
- Department of Chemistry, Rice University, Houston, Texas, United States. Tel: (1)713 348 4437
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas, United States. Tel: (1)713 348 4232
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