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For: Elenko MP, Szostak JW, van Oijen AM. Single-molecule imaging of an in vitro-evolved RNA aptamer reveals homogeneous ligand binding kinetics. J Am Chem Soc 2009;131:9866-7. [PMID: 19572753 PMCID: PMC2716146 DOI: 10.1021/ja901880v] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Sathyan A, Archontakis E, Spiering AJH, Albertazzi L, Palmans ARA. Effect of Particle Heterogeneity in Catalytic Copper-Containing Single-Chain Polymeric Nanoparticles Revealed by Single-Particle Kinetics. Molecules 2024;29:1850. [PMID: 38675670 PMCID: PMC11054931 DOI: 10.3390/molecules29081850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]  Open
2
Scher Y, Lauber Bonomo O, Pal A, Reuveni S. Microscopic theory of adsorption kinetics. J Chem Phys 2023;158:094107. [PMID: 36889971 DOI: 10.1063/5.0121359] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]  Open
3
Qiao Y, Luo Y, Long N, Xing Y, Tu J. Single-Molecular Förster Resonance Energy Transfer Measurement on Structures and Interactions of Biomolecules. MICROMACHINES 2021;12:492. [PMID: 33925350 PMCID: PMC8145425 DOI: 10.3390/mi12050492] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
4
Scull CE, Dandpat SS, Romero RA, Walter NG. Transcriptional Riboswitches Integrate Timescales for Bacterial Gene Expression Control. Front Mol Biosci 2021;7:607158. [PMID: 33521053 PMCID: PMC7838592 DOI: 10.3389/fmolb.2020.607158] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022]  Open
5
Zhao Y, Zuo X, Li Q, Chen F, Chen YR, Deng J, Han D, Hao C, Huang F, Huang Y, Ke G, Kuang H, Li F, Li J, Li M, Li N, Lin Z, Liu D, Liu J, Liu L, Liu X, Lu C, Luo F, Mao X, Sun J, Tang B, Wang F, Wang J, Wang L, Wang S, Wu L, Wu ZS, Xia F, Xu C, Yang Y, Yuan BF, Yuan Q, Zhang C, Zhu Z, Yang C, Zhang XB, Yang H, Tan W, Fan C. Nucleic Acids Analysis. Sci China Chem 2020;64:171-203. [PMID: 33293939 PMCID: PMC7716629 DOI: 10.1007/s11426-020-9864-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
6
Lackey HH, Peterson EM, Harris JM, Heemstra JM. Probing the Mechanism of Structure-Switching Aptamer Assembly by Super-Resolution Localization of Individual DNA Molecules. Anal Chem 2020;92:6909-6917. [PMID: 32297506 DOI: 10.1021/acs.analchem.9b05563] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
7
Shen R, Tan J, Yuan Q. Chemically Modified Aptamers in Biological Analysis. ACS APPLIED BIO MATERIALS 2020;3:2816-2826. [DOI: 10.1021/acsabm.0c00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
8
Wang Y, Horáček M, Zijlstra P. Strong Plasmon Enhancement of the Saturation Photon Count Rate of Single Molecules. J Phys Chem Lett 2020;11:1962-1969. [PMID: 32073865 PMCID: PMC7061331 DOI: 10.1021/acs.jpclett.0c00155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/19/2020] [Indexed: 06/10/2023]
9
Peterson EM, Reece EJ, Li W, Harris JM. Super-Resolution Imaging of Competitive Unlabeled DNA Hybridization Reveals the Influence of Fluorescent Labels on Duplex Formation and Dissociation Kinetics. J Phys Chem B 2019;123:10746-10756. [PMID: 31731835 DOI: 10.1021/acs.jpcb.9b09736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
10
He D, Ho SL, Chan HN, Wang H, Hai L, He X, Wang K, Li HW. Molecular-Recognition-Based DNA Nanodevices for Enhancing the Direct Visualization and Quantification of Single Vesicles of Tumor Exosomes in Plasma Microsamples. Anal Chem 2019;91:2768-2775. [PMID: 30644724 DOI: 10.1021/acs.analchem.8b04509] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
11
Morris FD, Peterson EM, Heemstra JM, Harris JM. Single-Molecule Kinetic Investigation of Cocaine-Dependent Split-Aptamer Assembly. Anal Chem 2018;90:12964-12970. [PMID: 30280568 DOI: 10.1021/acs.analchem.8b03637] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
12
Peterson EM, Harris JM. Identification of Individual Immobilized DNA Molecules by Their Hybridization Kinetics Using Single-Molecule Fluorescence Imaging. Anal Chem 2018;90:5007-5014. [DOI: 10.1021/acs.analchem.7b04512] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
13
Hua B, Wang Y, Park S, Han KY, Singh D, Kim JH, Cheng W, Ha T. The Single-Molecule Centroid Localization Algorithm Improves the Accuracy of Fluorescence Binding Assays. Biochemistry 2018;57:1572-1576. [PMID: 29457977 PMCID: PMC6149537 DOI: 10.1021/acs.biochem.7b01293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
14
Svobodová M, Skouridou V, Botero ML, Jauset-Rubio M, Schubert T, Bashammakh AS, El-Shahawi MS, Alyoubi AO, O'Sullivan CK. The characterization and validation of 17β-estradiol binding aptamers. J Steroid Biochem Mol Biol 2017;167:14-22. [PMID: 27669644 DOI: 10.1016/j.jsbmb.2016.09.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 01/26/2023]
15
Entzian C, Schubert T. Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis. J Vis Exp 2017. [PMID: 28117825 DOI: 10.3791/55070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]  Open
16
Nasiri AH, Wurm JP, Immer C, Weickhmann AK, Wöhnert J. An intermolecular G-quadruplex as the basis for GTP recognition in the class V-GTP aptamer. RNA (NEW YORK, N.Y.) 2016;22:1750-1759. [PMID: 27659052 PMCID: PMC5066627 DOI: 10.1261/rna.058909.116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
17
Börner R, Kowerko D, Miserachs HG, Schaffer MF, Sigel RK. Metal ion induced heterogeneity in RNA folding studied by smFRET. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
18
Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy. Methods Enzymol 2016;581:105-145. [PMID: 27793278 PMCID: PMC5403009 DOI: 10.1016/bs.mie.2016.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
19
Entzian C, Schubert T. Studying small molecule-aptamer interactions using MicroScale Thermophoresis (MST). Methods 2015;97:27-34. [PMID: 26334574 DOI: 10.1016/j.ymeth.2015.08.023] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/27/2015] [Accepted: 08/31/2015] [Indexed: 11/18/2022]  Open
20
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]
21
Chang AL, McKeague M, Liang JC, Smolke CD. Kinetic and equilibrium binding characterization of aptamers to small molecules using a label-free, sensitive, and scalable platform. Anal Chem 2014;86:3273-8. [PMID: 24548121 PMCID: PMC3983011 DOI: 10.1021/ac5001527] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
22
Role of substrate unbinding in Michaelis-Menten enzymatic reactions. Proc Natl Acad Sci U S A 2014;111:4391-6. [PMID: 24616494 DOI: 10.1073/pnas.1318122111] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
23
Bruno WJ, Ullah G, Mak DOD, Pearson JE. Automated maximum likelihood separation of signal from baseline in noisy quantal data. Biophys J 2014;105:68-79. [PMID: 23823225 DOI: 10.1016/j.bpj.2013.02.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 01/03/2013] [Accepted: 02/25/2013] [Indexed: 10/26/2022]  Open
24
Peterson EM, Harris JM. Single-molecule fluorescence imaging of DNA at a potential-controlled interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013;29:8292-8301. [PMID: 23741971 DOI: 10.1021/la400884t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
25
Haghighat Jahromi A, Honda M, Zimmerman SC, Spies M. Single-molecule study of the CUG repeat-MBNL1 interaction and its inhibition by small molecules. Nucleic Acids Res 2013;41:6687-97. [PMID: 23661680 PMCID: PMC3711446 DOI: 10.1093/nar/gkt330] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
26
Liu S, Zhao B, Zhang D, Li C, Wang H. Imaging of Nonuniform Motion of Single DNA Molecules Reveals the Kinetics of Varying-Field Isotachophoresis. J Am Chem Soc 2013;135:4644-7. [DOI: 10.1021/ja400126b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
27
Wang P, Querard J, Maurin S, Nath SS, Le Saux T, Gautier A, Jullien L. Photochemical properties of Spinach and its use in selective imaging. Chem Sci 2013. [DOI: 10.1039/c3sc50729g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]  Open
28
Yang J, Pearson JE. Origins of concentration dependence of waiting times for single-molecule fluorescence binding. J Chem Phys 2012;136:244506. [PMID: 22755586 DOI: 10.1063/1.4729947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
29
Hong H, Goel S, Zhang Y, Cai W. Molecular imaging with nucleic acid aptamers. Curr Med Chem 2012;18:4195-205. [PMID: 21838686 DOI: 10.2174/092986711797189691] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 06/22/2011] [Accepted: 06/22/2011] [Indexed: 01/16/2023]
30
Single Molecule Analysis Research Tool (SMART): an integrated approach for analyzing single molecule data. PLoS One 2012;7:e30024. [PMID: 22363412 PMCID: PMC3282690 DOI: 10.1371/journal.pone.0030024] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 12/12/2011] [Indexed: 11/19/2022]  Open
31
Zhu TF, Szostak JW. Exploding vesicles. ACTA ACUST UNITED AC 2011. [DOI: 10.1186/1759-2208-2-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
32
Bao J, Krylova SM, Reinstein O, Johnson PE, Krylov SN. Label-free solution-based kinetic study of aptamer-small molecule interactions by kinetic capillary electrophoresis with UV detection revealing how kinetics control equilibrium. Anal Chem 2011;83:8387-90. [PMID: 21995945 DOI: 10.1021/ac2026699] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
33
Greenfeld M, Solomatin SV, Herschlag D. Removal of covalent heterogeneity reveals simple folding behavior for P4-P6 RNA. J Biol Chem 2011;286:19872-9. [PMID: 21478155 DOI: 10.1074/jbc.m111.235465] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
34
van Oijen AM. Single-molecule approaches to characterizing kinetics of biomolecular interactions. Curr Opin Biotechnol 2011;22:75-80. [DOI: 10.1016/j.copbio.2010.10.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/06/2010] [Accepted: 10/06/2010] [Indexed: 12/01/2022]
35
Elenko MP, Szostak JW, van Oijen AM. Single-molecule binding experiments on long time scales. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010;81:083705. [PMID: 20815611 DOI: 10.1063/1.3473936] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 07/11/2010] [Indexed: 05/29/2023]
36
Greenfeld M, Herschlag D. Measuring the Energetic Coupling of Tertiary Contacts in RNA Folding using Single Molecule Fluorescence Resonance Energy Transfer. Methods Enzymol 2010;472:205-20. [DOI: 10.1016/s0076-6879(10)72009-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
37
Peterson EM, Harris JM. Quantitative Detection of Single Molecules in Fluorescence Microscopy Images. Anal Chem 2009;82:189-96. [PMID: 19957961 DOI: 10.1021/ac901710t] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
38
Helm M, Kobitski AY, Nienhaus GU. Single-molecule Förster resonance energy transfer studies of RNA structure, dynamics and function. Biophys Rev 2009;1:161. [PMID: 28510027 PMCID: PMC5418384 DOI: 10.1007/s12551-009-0018-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 10/09/2009] [Indexed: 11/24/2022]  Open
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