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Matsumura Y, Saito S. Microscopic insights into dynamic disorder in the isomerization dynamics of the protein BPTI. J Chem Phys 2021; 154:224113. [PMID: 34241205 DOI: 10.1063/5.0055152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the dynamic disorder behind a process, i.e., the dynamic effect of fluctuations that occur on a timescale slower or comparable with the timescale of the process, is essential for elucidating the dynamics and kinetics of complicated molecular processes in biomolecules and liquids. Despite numerous theoretical studies of single-molecule kinetics, our microscopic understanding of dynamic disorder remains limited. In the present study, we investigate the microscopic aspects of dynamic disorder in the isomerization dynamics of the Cys14-Cys38 disulfide bond in the protein bovine pancreatic trypsin inhibitor, which has been observed by nuclear magnetic resonance. We use a theoretical model with a stochastic transition rate coefficient, which is calculated from the 1-ms-long time molecular dynamics trajectory obtained by Shaw et al. [Science 330, 341-346 (2010)]. The isomerization dynamics are expressed by the transitions between coarse-grained states consisting of internal states, i.e., conformational sub-states. In this description, the rate for the transition from the coarse-grained states is stochastically modulated due to fluctuations between internal states. We examine the survival probability for the conformational transitions from a coarse-grained state using a theoretical model, which is a good approximation to the directly calculated survival probability. The dynamic disorder changes from a slow modulation limit to a fast modulation limit depending on the aspects of the coarse-grained states. Our analysis of the rate modulations behind the survival probability, in relation to the fluctuations between internal states, reveals the microscopic origin of dynamic disorder.
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Affiliation(s)
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
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2
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Chatterjee T, Li Z, Khanna K, Montoya K, Tewari M, Walter NG, Johnson-Buck A. Ultraspecific analyte detection by direct kinetic fingerprinting of single molecules. Trends Analyt Chem 2020; 123:115764. [PMID: 32863484 PMCID: PMC7451408 DOI: 10.1016/j.trac.2019.115764] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The detection and quantification of biomarkers have numerous applications in biological research and medicine. The most widely used methods to detect nucleic acids require amplification via the polymerase chain reaction (PCR). However, errors arising from the imperfect copying fidelity of DNA polymerases, limited specificity of primers, and heat-induced damage reduce the specificity of PCR-based methods, particularly for single-nucleotide variants. Furthermore, not all analytes can be amplified efficiently. While amplification-free methods avoid these pitfalls, the specificity of most such methods is strictly constrained by probe binding thermodynamics, which for example hampers detection of rare somatic mutations. In contrast, single-molecule recognition through equilibrium Poisson sampling (SiMREPS) provides ultraspecific detection with single-molecule and single-nucleotide sensitivity by monitoring the repetitive interactions of a fluorescent probe with surface-immobilized targets. In this review, we discuss SiMREPS in comparison with other analytical approaches, and describe its utility in quantifying a range of nucleic acids and other analytes.
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Affiliation(s)
- Tanmay Chatterjee
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zi Li
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kunal Khanna
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Karen Montoya
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
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3
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Influence of triplet states on single donor-acceptor pair fluorescence. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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4
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Teng CY, Nguyen BS, Yeh TF, Lee YL, Chen SJ, Teng H. Roles of nitrogen functionalities in enhancing the excitation-independent green-color photoluminescence of graphene oxide dots. NANOSCALE 2017; 9:8256-8265. [PMID: 28585974 DOI: 10.1039/c7nr01037k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fluorescent graphene oxide dots (GODs) are environmentally friendly and biocompatible materials for photoluminescence (PL) applications. In this study, we employed annealing and hydrothermal ammonia treatments at 500 and 140 °C, respectively, to introduce nitrogen functionalities into GODs for enhancing their green-color PL emissions. The hydrothermal treatment preferentially produces pyridinic and amino groups, whereas the annealing treatment produces pyrrolic and amide groups. The hydrothermally treated GODs (A-GODs) present a high conjugation of the nonbonding electrons of nitrogen in pyridinic and amino groups with the aromatic π orbital. This conjugation introduces a nitrogen nonbonding (nN 2p) state 0.3 eV above the oxygen nonbonding state (nO 2p state; the valence band maximum of the GODs). The GODs exhibit excitation-independent green-PL emissions at 530 nm with a maximum quantum yield (QY) of 12% at 470 nm excitation, whereas the A-GODs exhibit a maximum QY of 63%. The transformation of the solvent relaxation-governed π* → nO 2p transition in the GODs to the direct π* → nN 2p transition in the A-GODs possibly accounts for the substantial QY enhancement in the PL emissions. This study elucidates the role of nitrogen functionalities in the PL emissions of graphitic materials and proposes a strategy for designing the electronic structure to promote the PL performance.
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Affiliation(s)
- Chiao-Yi Teng
- Department of Chemical Engineering and Research Center for Energy Technology and Strategy, National Cheng Kung University, Tainan 70101, Taiwan.
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5
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Chu JW, Yang H. Identifying the structural and kinetic elements in protein large-amplitude conformational motions. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1283885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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6
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Bajwa P, Gao F, Nguyen A, Omogo B, Heyes CD. Influence of the Inner-Shell Architecture on Quantum Yield and Blinking Dynamics in Core/Multishell Quantum Dots. Chemphyschem 2016; 17:731-40. [PMID: 26693950 PMCID: PMC5086001 DOI: 10.1002/cphc.201500868] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/16/2015] [Indexed: 11/11/2022]
Abstract
Choosing the composition of a shell for QDs is not trivial, as both the band-edge energy offset and interfacial lattice mismatch influence the final optical properties. One way to balance these competing effects is by forming multishells and/or gradient-alloy shells. However, this introduces multiple interfaces, and their relative effects on quantum yield and blinking are not yet fully understood. Here, we undertake a systematic, comparative study of the addition of inner shells of a single component versus gradient-alloy shells of cadmium/zinc chalogenides onto CdSe cores, and then capping with a thin ZnS outer shell to form various core/multishell configurations. We show that architecture of the inner shell between the CdSe core and the outer ZnS shell significantly influences both the quantum yield and blinking dynamics, but that these effects are not correlated-a high ensemble quantum yield doesn't necessarily equate to reduced blinking. Two mathematical models have been proposed to describe the blinking dynamics-the more common power-law model and a more recent multiexponential model. By binning the same data with 1 and 20 ms resolution, we show that the on times can be better described by the multiexponential model, whereas the off times can be better described by the power-law model. We discuss physical mechanisms that might explain this behavior and how it can be affected by the inner-shell architecture.
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Affiliation(s)
- Pooja Bajwa
- Department of Chemistry and Biochemistry, University of Arkansas, 345 N. Campus Drive, Fayetteville, AR, 72701, USA
| | - Feng Gao
- Department of Chemistry and Biochemistry, University of Arkansas, 345 N. Campus Drive, Fayetteville, AR, 72701, USA
| | - Anh Nguyen
- Department of Chemistry and Biochemistry, University of Arkansas, 345 N. Campus Drive, Fayetteville, AR, 72701, USA
| | - Benard Omogo
- Department of Chemistry and Biochemistry, University of Arkansas, 345 N. Campus Drive, Fayetteville, AR, 72701, USA
| | - Colin D Heyes
- Department of Chemistry and Biochemistry, University of Arkansas, 345 N. Campus Drive, Fayetteville, AR, 72701, USA
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7
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Osad'ko IS. Dependence of FRET efficiency on distance in single donor-acceptor pairs. J Chem Phys 2015; 142:125102. [PMID: 25833609 DOI: 10.1063/1.4915279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Possibility to create single donor-acceptor (D-A) pairs by attaching dye molecules to various sites of DNA strands with control of the inter-dye distance R enables one to measure average Förster resonance energy transfer (FRET) efficiency E as a function of R. Triplet states of the dyes influence the dependence E(R) considerably. Two types of FRET efficiency are considered: E = EA and E = ED. The efficiency EA(R) = JA(R)/[JA(R) + JD(R)] depends on the donor and the acceptor average intensities JD(R) and JA(R) measured in D- and A-fluorescence, whereas the efficiency ED(R) = 1 - JD(R)/JD(∞) depends only on the intensity of D-fluorescence, so-called the donor quenching method. The shape of the functions ED (R) and EA (R) depends strongly on whether the dyes have blinking fluorescence. FRET efficiencies ED (R) and EA (R) undergo the influence of many experimental factors and therefore, differ considerably from pure FRET efficiencies ED (s) (R) and EA (s) (R). Pure FRET efficiencies ED,A (s) (R) are calculated with the help of rate equations for D-A pairs, whose molecules have triplet states. It is shown how the calculated efficiencies ED,A (s) (R) can be compared to FRET efficiencies measured with the help of the intensities ID,A(R) corrected by cross talk and background light.
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Affiliation(s)
- I S Osad'ko
- Institute for Spectroscopy, RAS, 142190 Moscow, Russia
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8
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Stennett EMS, Ciuba MA, Levitus M. Photophysical processes in single molecule organic fluorescent probes. Chem Soc Rev 2014; 43:1057-75. [DOI: 10.1039/c3cs60211g] [Citation(s) in RCA: 214] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Osad'ko IS. Conformational changes in complex macromolecules studied by single donor-acceptor pair fluorescence. Phys Chem Chem Phys 2013; 15:16190-7. [PMID: 23996051 DOI: 10.1039/c3cp51464a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A single donor-acceptor (D-A) pair with a fluctuating FRET rate F is studied theoretically in the frame of a "two-state model" in which the FRET rate F fluctuates taking two values, F1 and F2, with average rates B for the forward and b for the backward transitions. Theoretical expressions are derived for the autocorrelation function g((2))(DA)(τ) and for the Mandel parameter Q(D,A)(τ) allowing for background emission. Fluctuating intensities ID,A(t) and FRET efficiency E(t) = IA(t)/[IA(t) + ID(t)] are calculated with the help of the Monte Carlo technique. The probability w(D,A)(N)(T) of finding N photons in a time interval T, and the distribution of the FRET efficiency P(E) are found by statistical treating of the fluctuating intensities ID,A(t). The shape of the distribution w(D,A)(N)(T) enables one to find the values of the parameters: F1, F2, and b/B. The influence of the background light on g((2))(DA)(τ), Q(D,A)(τ) and w(D,A)(N)(T) is studied. It is shown how the background light influences the ratio b/B found from the analysis of w(D,A)(N)(T) and P(E).
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Affiliation(s)
- Igor S Osad'ko
- Molecular Spectroscopy Department, Institute for Spectroscopy, Russian Academy of Sciences, Moscow, Troitsk 142190, Russia.
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10
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Affiliation(s)
- Jens Michaelis
- Biophysics
Institute, Faculty of Natural Sciences, Ulm University, Albert-Einstein-Allee
11, 89081 Ulm, Germany
- Center
for Integrated Protein Science Munich (CIPSM), Department
of Chemistry and Biochemistry, Munich University, Butenandtstrasse 5-13, 81377 München, Germany
| | - Barbara Treutlein
- Department
of Bioengineering, Stanford University, James H. Clark Center, E-300, 318
Campus Drive, Stanford, California 94305-5432, United States
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11
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Lew MD, Backlund MP, Moerner WE. Rotational mobility of single molecules affects localization accuracy in super-resolution fluorescence microscopy. NANO LETTERS 2013; 13:3967-72. [PMID: 23360306 PMCID: PMC3696529 DOI: 10.1021/nl304359p] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The asymmetric nature of single-molecule (SM) dipole emission patterns limits the accuracy of position determination in localization-based super-resolution fluorescence microscopy. The degree of mislocalization depends highly on the rotational mobility of SMs; only for SMs rotating within a cone half angle α > 60° can mislocalization errors be bounded to ≤10 nm. Simulations demonstrate how low or high rotational mobility can cause resolution degradation or distortion in super-resolution reconstructions.
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Affiliation(s)
- Matthew D. Lew
- Department of Chemistry, Stanford University, Stanford, California 94305
- Department of Electrical Engineering, Stanford University, Stanford, California 94305
| | - Mikael P. Backlund
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305
- Corresponding Author. To whom correspondence should be addressed.
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12
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Cooper D, Uhm H, Tauzin LJ, Poddar N, Landes CF. Photobleaching lifetimes of cyanine fluorophores used for single-molecule Förster resonance energy transfer in the presence of various photoprotection systems. Chembiochem 2013; 14:1075-80. [PMID: 23733413 DOI: 10.1002/cbic.201300030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Indexed: 12/19/2022]
Abstract
Lengthening smFRET lifetimes: We investigated various photoprotection system combinations to find the combination that optimally extended the photobleach lifetime of a Cy3/Cy5 smFRET pair attached to a DNA hairpin in a single-molecule environment. We found that the glucose/glucose oxygen-scavenging solution in combination with redox-based photostabilization solutions yielded the longest average photobleaching lifetimes.
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Affiliation(s)
- David Cooper
- Department of Chemistry, Rice University, 6100 Main St. Houston, TX 77005, USA
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13
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Osad'ko IS, Shchukina AL. Blinking fluorescence of single donor-acceptor pairs: important role of "dark'' states in resonance energy transfer via singlet levels. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:061907. [PMID: 23005127 DOI: 10.1103/physreve.85.061907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 03/23/2012] [Indexed: 06/01/2023]
Abstract
The influence of triplet levels on Förster resonance energy transfer via singlet levels in donor-acceptor (D-A) pairs is studied. Four types of D-A pair are considered: (i) two-level donor and two-level acceptor, (ii) three-level donor and two-level acceptor, (iii) two-level donor and three-level acceptor, and (iv) three-level donor and three-level acceptor. If singlet-triplet transitions in a three-level acceptor molecule are ineffective, the energy transfer efficiency E=I_{A}/(I_{A}+I_{D}), where I_{D} and I_{A} are the average intensities of donor and acceptor fluorescence, can be described by the simple theoretical equation E(F)=FT_{D}/(1+FT_{D}). Here F is the rate of energy transfer, and T_{D} is the donor fluorescence lifetime. In accordance with the last equation, 100% of the donor electronic energy can be transferred to an acceptor molecule at FT_{D}≫1. However, if singlet-triplet transitions in a three-level acceptor molecule are effective, the energy transfer efficiency is described by another theoretical equation, E(F)=F[over ¯](F)T_{D}/[1+F[over ¯](F)T_{D}]. Here F[over ¯](F) is a function of F depending on singlet-triplet transitions in both donor and acceptor molecules. Expressions for the functions F[over ¯](F) are derived. In this case the energy transfer efficiency will be far from 100% even at FT_{D}≫1. The character of the intensity fluctuations of donor and acceptor fluorescence indicates which of the two equations for E(F) should be used to find the value of the rate F. Therefore, random time instants of photon emission in both donor and acceptor fluorescence are calculated by the Monte Carlo method for all four types of D-A pair. Theoretical expressions for start-stop correlators (waiting time distributions) in donor and acceptor fluorescence are derived. The probabilities w_{N}^{D}(t) and w_{N}^{A}(t) of finding N photons of donor and acceptor fluorescence in the time interval t are calculated for various values of the energy transfer rate F and for all four types of D-A pair. Comparison of the calculated D and A fluorescence trajectories with those measured by Weiss and co-workers proves the important role of triplet levels in energy transfer via singlet levels.
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Affiliation(s)
- I S Osad'ko
- Institute for Spectroscopy, RAS, Troitsk, Russia
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14
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Yim SW, Kim T, Laurence TA, Partono S, Kim D, Kim Y, Weiss S, Reitmair A. Four-color alternating-laser excitation single-molecule fluorescence spectroscopy for next-generation biodetection assays. Clin Chem 2012; 58:707-16. [PMID: 22266381 DOI: 10.1373/clinchem.2011.176958] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Single-molecule detection (SMD) technologies are well suited for clinical diagnostic applications by offering the prospect of minimizing precious patient sample requirements while maximizing clinical information content. Not yet available, however, is a universal SMD-based platform technology that permits multiplexed detection of both nucleic acid and protein targets and that is suitable for automation and integration into the clinical laboratory work flow. METHODS We have used a sensitive, specific, quantitative, and cost-effective homogeneous SMD method that has high single-well multiplexing potential and uses alternating-laser excitation (ALEX) fluorescence-aided molecule sorting extended to 4 colors (4c-ALEX). Recognition molecules are tagged with different-color fluorescence dyes, and coincident confocal detection of ≥2 colors constitutes a positive target-detection event. The virtual exclusion of the majority of sources of background noise eliminates washing steps. Sorting molecules with multidimensional probe stoichiometries (S) and single-molecule fluorescence resonance energy transfer efficiencies (E) allows differentiation of numerous targets simultaneously. RESULTS We show detection, differentiation, and quantification-in a single well-of (a) 25 different fluorescently labeled DNAs; (b) 8 bacterial genetic markers, including 3 antibiotic drug-resistance determinants found in 11 septicemia-causing Staphylococcus and Enterococcus strains; and (c) 6 tumor markers present in blood. CONCLUSIONS The results demonstrate assay utility for clinical molecular diagnostic applications by means of multiplexed detection of nucleic acids and proteins and suggest potential uses for early diagnosis of cancer and infectious and other diseases, as well as for personalized medicine. Future integration of additional technology components to minimize preanalytical sample manipulation while maximizing throughput should allow development of a user-friendly ("sample in, answer out") point-of-care platform for next-generation medical diagnostic tests that offer considerable savings in costs and patient sample.
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Affiliation(s)
- Seok W Yim
- Nesher Technologies, Inc., Los Angeles, CA 90057, USA
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15
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Observation of protein folding/unfolding dynamics of ubiquitin trapped in agarose gel by single-molecule FRET. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:189-98. [DOI: 10.1007/s00249-011-0772-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/13/2011] [Accepted: 10/24/2011] [Indexed: 11/27/2022]
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16
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Codon-dependent tRNA fluctuations monitored with fluorescence polarization. Biophys J 2011; 99:3849-58. [PMID: 21112310 DOI: 10.1016/j.bpj.2010.10.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 10/14/2010] [Accepted: 10/18/2010] [Indexed: 11/21/2022] Open
Abstract
During protein synthesis dictated by the codon sequence of messenger RNA, the ribosome selects aminoacyl-tRNA (aa-tRNA) with high accuracy, the exact mechanism of which remains elusive. By using a single-molecule fluorescence resonance energy transfer method coupled with fluorescence emission anisotropy, we provide evidence of random thermal motion of tRNAs within the ribosome in nanosecond timescale that we refer to as fluctuations. Our results indicate that cognate aa-tRNA fluctuates less frequently than near-cognate. This is counterintuitive because cognate aa-tRNA is expected to fluctuate more frequently to reach the ribosomal A-site faster than near-cognate. In addition, cognate aa-tRNA occupies the same position in the ribosome as near-cognate. These results argue for a mechanism which guides cognate aa-tRNA more accurately toward the A-site as compared to near-cognate. We suggest that a basis for this mechanism is the induced fit of the 30S subunit upon cognate aa-tRNA binding. Our single-molecule fluorescence resonance energy transfer time traces also point to a mechanistic model for GTP hydrolysis on elongation factor Tu mediated by aa-tRNA.
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17
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McCann JJ, Choi UB, Zheng L, Weninger K, Bowen ME. Optimizing methods to recover absolute FRET efficiency from immobilized single molecules. Biophys J 2010; 99:961-70. [PMID: 20682275 PMCID: PMC2913196 DOI: 10.1016/j.bpj.2010.04.063] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 04/22/2010] [Accepted: 04/26/2010] [Indexed: 10/19/2022] Open
Abstract
Microscopy-based fluorescence resonance energy transfer (FRET) experiments measure donor and acceptor intensities by isolating these signals with a series of optical elements. Because this filtering discards portions of the spectrum, the observed FRET efficiency is dependent on the set of filters in use. Similarly, observed FRET efficiency is also affected by differences in fluorophore quantum yield. Recovering the absolute FRET efficiency requires normalization for these effects to account for differences between the donor and acceptor fluorophores in their quantum yield and detection efficiency. Without this correction, FRET is consistent across multiple experiments only if the photophysical and instrument properties remain unchanged. Here we present what is, to our knowledge, the first systematic study of methods to recover the true FRET efficiency using DNA rulers with known fluorophore separations. We varied optical elements to purposefully alter observed FRET and examined protein samples to achieve quantum yields distinct from those in the DNA samples. Correction for calculated instrument transmission reduced FRET deviations, which can facilitate comparison of results from different instruments. Empirical normalization was more effective but required significant effort. Normalization based on single-molecule photobleaching was the most effective depending on how it is applied. Surprisingly, per-molecule gamma-normalization reduced the peak width in the DNA FRET distribution because anomalous gamma-values correspond to FRET outliers. Thus, molecule-to-molecule variation in gamma has an unrecognized effect on the FRET distribution that must be considered to extract information on sample dynamics from the distribution width.
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Affiliation(s)
- James J. McCann
- Department of Pharmacology, Stony Brook University, Stony Brook, New York
| | - Ucheor B. Choi
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Liqiang Zheng
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina
| | - Mark E. Bowen
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York
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18
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Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging. Biophys J 2009; 96:2371-81. [PMID: 19289062 DOI: 10.1016/j.bpj.2008.11.061] [Citation(s) in RCA: 167] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 11/12/2008] [Accepted: 11/17/2008] [Indexed: 01/12/2023] Open
Abstract
Organic fluorophores common to fluorescence-based investigations suffer from unwanted photophysical properties, including blinking and photobleaching, which limit their overall experimental performance. Methods to control such processes are particularly important for single-molecule fluorescence and fluorescence resonance energy transfer imaging where uninterrupted, stable fluorescence is paramount. Fluorescence and FRET-based assays have been carried out on dye-labeled DNA and RNA-based systems to quantify the effect of including small-molecule solution additives on the fluorescence and FRET behaviors of both cyanine and Alexa fluorophores. A detailed dwell time analysis of the fluorescence and FRET trajectories of more than 200,000 individual molecules showed that two compounds identified previously as triplet state quenchers, cyclooctatetraene, and Trolox, as well as 4-nitrobenzyl alcohol, act to favorably attenuate blinking, photobleaching, and influence the rate of photoresurrection in a concentration-dependent and context-dependent manner. In both biochemical systems examined, a unique cocktail of compounds was shown to be optimal for imaging performance. By simultaneously providing the most rapid and direct access to multiple photophysical kinetic parameters, smFRET imaging provides a powerful avenue for future investigations aimed at discovering new compounds, and effective combinations thereof. These efforts may ultimately facilitate tuning organic dye molecule performance according to each specific experimental demand.
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Abstract
Interactions between the synaptic protein alpha-Synuclein and cellular membranes may be relevant both to its native function as well as its role in Parkinson's disease. We use single molecule Forster resonance energy transfer to probe the structure of alpha-Synuclein bound to detergent micelles and lipid vesicles. We find evidence that it forms a bent-helix when bound to highly curved detergent micelles, whereas it binds more physiological 100 nm diameter lipid vesicles as an elongated helix. Our results highlight the influence of membrane curvature in determining alpha-Synuclein conformation, which may be important for both its normal and disease-associated functions.
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Affiliation(s)
- Adam J. Trexler
- Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208114, New Haven, CT 06520
| | - Elizabeth Rhoades
- Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208114, New Haven, CT 06520
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Vogelsang J, Cordes T, Tinnefeld P. Single-molecule photophysics of oxazines on DNA and its application in a FRET switch. Photochem Photobiol Sci 2009; 8:486-96. [PMID: 19337662 DOI: 10.1039/b822318c] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role and interplay of triplet states and radical ion states in single-molecule fluorescence spectroscopy has recently been elaborated providing us with new insights into the photophysics and photobleaching pathways of fluorescent dyes. Adjustment of fluorophore redox properties in combination with specific redox properties of the environment, i.e. addition of reducing and oxidizing agents, allows control of the emission properties: it has become possible to suppress blinking and to also induce blinking in single-molecule fluorescence transient by selectively opening and closing specific excited state pathways. Induced blinking is, for example, of interest for super-resolution fluorescence microscopy based on the subsequent localization of single fluorophores. For oxazines this control even allowed the separation of the influence of reducing and oxidizing agents, enabling switching the fluorescence of single fluorophores. Here, we study the factors that contribute to the kinetics of the photophysical pathways more closely with a focus on the photophysics of the oxazine ATTO655 labeled to DNA. Our data show that the oxazine ATTO655 interacts with DNA, shielding it efficiently from reagents in solution. Besides redox reactions, the pH also influences the blinking kinetics and especially the off-times. Moreover, we present the extension of ATTO655 as a single-molecule redox sensor to a ratiometric fluorescence-resonance-energy-transfer based sensor. Therefore, we designed FRET probes that showed the highest possible contrast of FRET changes and demonstrate reversible FRET-switching of Cy3B-ATTO655 DNA constructs.
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Affiliation(s)
- Jan Vogelsang
- Angewandte Physik-Biophysik and Center for NanoScience CeNS, Ludwig-Maximilians-Universität München, Amalienstr. 54, 80799, München, Germany.
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21
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Wang X, Lu HP. 2D regional correlation analysis of single-molecule time trajectories. J Phys Chem B 2009; 112:14920-6. [PMID: 18950223 DOI: 10.1021/jp804453j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a new approach of 2D regional correlation analysis capable of analyzing fluctuation dynamics of complex multiple correlated and anticorrelated fluctuations under a noncorrelated noise background. Using this new method, by changing and scanning the start time and end time along a pair of fluctuation trajectories, we are able to map out any defined segments along the fluctuation trajectories and determine whether they are correlated, anticorrelated, or noncorrelated; after which, a cross-correlation analysis can be applied for each specific segment to obtain a detailed fluctuation dynamics analysis. We specifically discuss an application of this approach to analyze single-molecule fluorescence resonance energy transfer (FRET) fluctuation dynamics where the fluctuations are often complex, although this approach can be useful for analyzing other types of fluctuation dynamics of various physical variables as well.
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Affiliation(s)
- Xuefei Wang
- Bowling Green State University, Center for Photochemical Sciences, Department of Chemistry, Bowling Green, Ohio 43403, USA
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22
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Walter MJ, Borys NJ, van Schooten KJ, Lupton JM. Light-harvesting action spectroscopy of single conjugated polymer nanowires. NANO LETTERS 2008; 8:3330-3335. [PMID: 18783280 DOI: 10.1021/nl801757p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We study exciton migration in single molecular nanowires, dye-endcapped multichromophoric conjugated polymers, as a function of excitation energy. This approach reveals the actual molecular absorption properties, uncovering the molecules within an ensemble and the chromophores within a molecule which contribute to absorption at a given wavelength. As the excitation energy is raised, an increasing number of polymers exhibit energy transfer suggesting that, in contrast to the emission spectrum, the absorption of a single chain under energy transfer conditions can be very broad even at 5 K. At the same time, the polarization anisotropy in excitation decreases due to an increase in the number of noncolinear chromophores involved in absorption. Power and wavelength-dependent measurements clearly discern the exciton blockade effect that gives rise to strong fluctuations of energy transfer. Although the polymer and endcap constitute nominally discrete spectroscopic entities, we are able to identify a subtle influence of the primary backbone exciton energy on the ultimate endcap emission. This demonstration of interchromophoric cooperativity provides a direct realization of how nonradiative energy dissipation in one nanoscale unit influences the spectroscopy of another.
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Affiliation(s)
- Manfred J Walter
- Department of Physics, University of Utah, Salt Lake City, Utah 84112, USA
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23
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Abstract
Decades of studies have established translation as a multistep, multicomponent process that requires intricate communication to achieve high levels of speed, accuracy, and regulation. A crucial next step in understanding translation is to reveal the functional significance of the large-scale motions implied by static ribosome structures. This requires determining the trajectories, timescales, forces, and biochemical signals that underlie these dynamic conformational changes. Single-molecule methods have emerged as important tools for the characterization of motion in complex systems, including translation. In this review, we chronicle the key discoveries in this nascent field, which have demonstrated the power and promise of single-molecule techniques in the study of translation.
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Affiliation(s)
- R Andrew Marshall
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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24
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Correction for Tomschik
et al.
, Fast, long-range, reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer. Proc Natl Acad Sci U S A 2008. [DOI: 10.1073/pnas.0804959105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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25
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Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) is one of the most general and adaptable single-molecule techniques. Despite the explosive growth in the application of smFRET to answer biological questions in the last decade, the technique has been practiced mostly by biophysicists. We provide a practical guide to using smFRET, focusing on the study of immobilized molecules that allow measurements of single-molecule reaction trajectories from 1 ms to many minutes. We discuss issues a biologist must consider to conduct successful smFRET experiments, including experimental design, sample preparation, single-molecule detection and data analysis. We also describe how a smFRET-capable instrument can be built at a reasonable cost with off-the-shelf components and operated reliably using well-established protocols and freely available software.
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26
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An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys J 2007; 94:1826-35. [PMID: 17921203 DOI: 10.1529/biophysj.107.117689] [Citation(s) in RCA: 607] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The application of single-molecule fluorescence techniques to complex biological systems places demands on the performance of single fluorophores. We present an enzymatic oxygen scavenging system for improved dye stability in single-molecule experiments. We compared the previously described protocatechuic acid/protocatechuate-3,4-dioxygenase system to the currently employed glucose oxidase/catalase system. Under standardized conditions, we observed lower dissolved oxygen concentrations with the protocatechuic acid/protocatechuate-3,4-dioxygenase system. Furthermore, we observed increased initial lifetimes of single Cy3, Cy5, and Alexa488 fluorophores. We further tested the effects of chemical additives in this system. We found that biological reducing agents increase both the frequency and duration of blinking events of Cy5, an effect that scales with reducing potential. We observed increased stability of Cy3 and Alexa488 in the presence of the antioxidants ascorbic acid and n-propyl gallate. This new O(2)-scavenging system should have wide application for single-molecule fluorescence experiments.
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27
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Shang J, Geva E. Computational Study of a Single Surface-Immobilized Two-Stranded Coiled-Coil Polypeptide. J Phys Chem B 2007; 111:4178-88. [PMID: 17397215 DOI: 10.1021/jp067138+] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The equilibrium structure and dynamics of a two-stranded coiled-coil polypeptide are investigated via Langevin dynamics simulations. An off-lattice model of the polypeptide chain is employed, which gives rise to a well-defined helical dimer native state and two-state folding kinetics. The behavior of the freely diffusing and surface-immobilized polypeptide is studied under different surface and denaturation conditions. The effect of surface immobilization on the distributions of structural and dynamical properties is considered in detail. The relationship between the simulation results and recent single-molecule fluorescence resonance energy transfer experiments performed on the two-stranded coiled-coil from the yeast transcription factor GCN4 (Jia et al. Chem. Phys. 1999, 247, 69; Talaga et al. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 13021) is discussed.
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Affiliation(s)
- Jianyuan Shang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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28
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Shang J, Geva E. Extracting the Time Scales of Conformational Dynamics from Single-Molecule Single-Photon Fluorescence Statistics. J Phys Chem B 2007; 111:4220-6. [PMID: 17391019 DOI: 10.1021/jp067657c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The quenching rate of a fluorophore attached to a macromolecule can be rather sensitive to its conformational state. The decay of the corresponding fluorescence lifetime autocorrelation function can therefore provide unique information on the time scales of conformational dynamics. The conventional way of measuring the fluorescence lifetime autocorrelation function involves evaluating it from the distribution of delay times between photoexcitation and photon emission. However, the time resolution of this procedure is limited by the time window required for collecting enough photons in order to establish this distribution with sufficient signal-to-noise ratio. Yang and Xie have recently proposed an approach for improving the time resolution, which is based on the argument that the autocorrelation function of the delay time between photoexcitation and photon emission is proportional to the autocorrelation function of the square of the fluorescence lifetime [Yang, H.; Xie, X. S. J. Chem. Phys. 2002, 117, 10965]. In this paper, we show that the delay-time autocorrelation function is equal to the autocorrelation function of the square of the fluorescence lifetime divided by the autocorrelation function of the fluorescence lifetime. We examine the conditions under which the delay-time autocorrelation function is approximately proportional to the autocorrelation function of the square of the fluorescence lifetime. We also investigate the correlation between the decay of the delay-time autocorrelation function and the time scales of conformational dynamics. The results are demonstrated via applications to a two-state model and an off-lattice model of a polypeptide.
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Affiliation(s)
- Jianyuan Shang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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29
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Rasnik I, McKinney SA, Ha T. Nonblinking and long-lasting single-molecule fluorescence imaging. Nat Methods 2006; 3:891-3. [PMID: 17013382 DOI: 10.1038/nmeth934] [Citation(s) in RCA: 532] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Accepted: 08/11/2006] [Indexed: 11/09/2022]
Abstract
Photobleaching and blinking of fluorophores pose fundamental limitations on the information content of single-molecule fluorescence measurements. Photoinduced blinking of Cy5 has hampered many previous investigations using this popular fluorophore. Here we show that Trolox in combination with the enzymatic oxygen-scavenging system eliminates Cy5 blinking, dramatically reduces photobleaching and improves the signal linearity at high excitation rates, significantly extending the applicability of single-molecule fluorescence techniques.
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Affiliation(s)
- Ivan Rasnik
- Department of Physics, Emory University, Atlanta, Georgia 30322, USA.
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30
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Joo C, McKinney SA, Nakamura M, Rasnik I, Myong S, Ha T. Real-time observation of RecA filament dynamics with single monomer resolution. Cell 2006; 126:515-27. [PMID: 16901785 DOI: 10.1016/j.cell.2006.06.042] [Citation(s) in RCA: 235] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 05/16/2006] [Accepted: 06/20/2006] [Indexed: 11/27/2022]
Abstract
RecA and its homologs help maintain genomic integrity through recombination. Using single-molecule fluorescence assays and hidden Markov modeling, we show the most direct evidence that a RecA filament grows and shrinks primarily one monomer at a time and only at the extremities. Both ends grow and shrink, contrary to expectation, but a higher binding rate at one end is responsible for directional filament growth. Quantitative rate determination also provides insights into how RecA might control DNA accessibility in vivo. We find that about five monomers are sufficient for filament nucleation. Although ordinarily single-stranded DNA binding protein (SSB) prevents filament nucleation, single RecA monomers can easily be added to an existing filament and displace SSB from DNA at the rate of filament extension. This supports the proposal for a passive role of RecA-loading machineries in SSB removal.
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Affiliation(s)
- Chirlmin Joo
- Howard Hughes Medical Institute and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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31
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Michalet X, Weiss S, Jäger M. Single-molecule fluorescence studies of protein folding and conformational dynamics. Chem Rev 2006; 106:1785-813. [PMID: 16683755 PMCID: PMC2569857 DOI: 10.1021/cr0404343] [Citation(s) in RCA: 388] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xavier Michalet
- Department of Chemistry & Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095
| | - Marcus Jäger
- Department of Chemistry & Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095
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32
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Margeat E, Kapanidis AN, Tinnefeld P, Wang Y, Mukhopadhyay J, Ebright RH, Weiss S. Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes. Biophys J 2005; 90:1419-31. [PMID: 16299085 PMCID: PMC1367292 DOI: 10.1529/biophysj.105.069252] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using total-internal-reflection fluorescence microscopy equipped with alternating-laser excitation, we were able to detect abortive initiation and promoter escape within single immobilized transcription complexes. Our approach uses fluorescence resonance energy transfer to monitor distances between a fluorescent probe incorporated in RNA polymerase (RNAP) and a fluorescent probe incorporated in DNA. We observe small, but reproducible and abortive-product-length-dependent, decreases in distance between the RNAP leading edge and DNA downstream of RNAP upon abortive initiation, and we observe large decreases in distance upon promoter escape. Inspection of population distributions and single-molecule time traces for abortive initiation indicates that, at a consensus promoter, at saturating ribonucleoside triphosphate concentrations, abortive-product release is rate-limiting (i.e., abortive-product synthesis and RNAP-active-center forward translocation are fast, whereas abortive-product dissociation and RNAP-active-center reverse translocation are slow). The results obtained using this new methodology confirm and extend those obtained from diffusing single molecules, and pave the way for real-time, single-molecule observations of the transitions between various states of the transcription complex throughout transcription.
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Affiliation(s)
- Emmanuel Margeat
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
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33
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Shang J, Geva E. A Computational Study of the Correlations between Structure and Dynamics in Free and Surface-Immobilized Single Polymer Chains. J Phys Chem B 2005; 109:16340-9. [PMID: 16853077 DOI: 10.1021/jp052275c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The correlations between structure and dynamics in free and surface-immobilized polymers were investigated via Langevin dynamics simulations of a free-jointed homopolymer. A detailed analysis was performed for a polymer in free solution and a polymer attached to a surface. The cases of repulsive and attractive surfaces, as well as poor and good solvents, were considered. The analysis focuses on properties that are particularly relevant to single molecule measurements, namely: (1) the distribution of end-to-end distance, (2) the correlations between the conformational structure and the time scale of its motion, (3) the correlations, at equilibrium, between the end-to-end distance and its displacement, and (4) the correlation between the initial coil conformation and the collapse pathway into the globular state. The differences and similarities between this model and a previously considered model of a protein, with two-state folding kinetics and a well-defined native state, are also discussed.
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Affiliation(s)
- Jianyuan Shang
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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34
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Luong AK, Gradinaru CC, Chandler DW, Hayden CC. Simultaneous Time- and Wavelength-Resolved Fluorescence Microscopy of Single Molecules. J Phys Chem B 2005; 109:15691-8. [PMID: 16852991 DOI: 10.1021/jp050465h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single fluorophores and single-pair fluorescence resonance energy transfer were studied with a new confocal fluorescence microscope that allows, for the first time, the wavelength and emission time of each detected photon to be simultaneously measured with single molecule sensitivity. In this apparatus, the photons collected from the sample are imaged through a dispersive optical system onto a time and position sensitive photon detector. For each detected photon the detection system records its wavelength, its emission time relative to the excitation pulse, and its absolute emission time. A histogram over many photons can generate a full fluorescence spectrum and correlated decay plot for a single molecule for any time interval. At the single molecule level, this approach makes possible entirely new types of temporal and spectral correlation spectroscopies. This paper presents our initial results on simultaneous time- and wavelength-resolved fluorescence measurements of single rhodamine 6G (R6G), tetramethylrhodamine (TMR), and Cy3 molecules embedded in thin films of poly(methyl methacrylate) (PMMA), and of single-pair fluorescence resonance energy transfer between two Alexa fluorophores spaced apart by a short polyproline peptide.
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Affiliation(s)
- A Khai Luong
- Sandia National Laboratories, 7011 East Avenue, MS 9055, Livermore, California 94550, USA.
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35
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Heilemann M, Margeat E, Kasper R, Sauer M, Tinnefeld P. Carbocyanine dyes as efficient reversible single-molecule optical switch. J Am Chem Soc 2005; 127:3801-6. [PMID: 15771514 DOI: 10.1021/ja044686x] [Citation(s) in RCA: 289] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We demonstrate that commercially available unmodified carbocyanine dyes such as Cy5 (usually excited at 633 nm) can be used as efficient reversible single-molecule optical switch, whose fluorescent state after apparent photobleaching can be restored at room temperature upon irradiation at shorter wavelengths. Ensemble photobleaching and recovery experiments of Cy5 in aqueous solution irradiating first at 633 nm, then at 337, 488, or 532 nm, demonstrate that restoration of absorption and fluorescence strongly depends on efficient oxygen removal and the addition of the triplet quencher beta-mercaptoethylamine. Single-molecule fluorescence experiments show that individual immobilized Cy5 molecules can be switched optically in milliseconds by applying alternating excitation at 633 and 488 nm between a fluorescent and nonfluorescent state up to 100 times with a reliability of >90% at room temperature. Because of their intriguing performance, carbocyanine dyes volunteer as a simple alternative for ultrahigh-density optical data storage. Measurements on single donor/acceptor (tetramethylrhodamine/Cy5) labeled oligonucleotides point out that the described light-driven switching behavior imposes fundamental limitations on the use of carbocyanine dyes as energy transfer acceptors for the study of biological processes.
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Affiliation(s)
- Mike Heilemann
- Applied Laserphysics & Laserspectroscopy, Physics Faculty, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
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36
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Sabanayagam CR, Eid JS, Meller A. Using fluorescence resonance energy transfer to measure distances along individual DNA molecules: Corrections due to nonideal transfer. J Chem Phys 2005; 122:061103. [PMID: 15740360 DOI: 10.1063/1.1854120] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single molecule fluorescence resonance energy transfer has been extensively used to measure distance changes and kinetics in various biomolecular systems. However, due to complications involving multiple de-excitation pathways of the dyes, the absolute inter-dye distance information has seldom been recovered. To circumvent this we directly probe the relative variations in the quantum yield of individual fluorophores. B-DNA was used as a scaffold to position the donor (Cy3 or TMR) at precise distances from the acceptor (Cy5) within the Forster radius. We found that the variation in the Cy3 quantum yield is approximately 5 times larger than that of TMR. By taking into account the molecule-to-molecule variability in the acceptor/donor quantum yield ratio, the apparent fluorescence resonance energy transfer efficiencies were scaled to yield the theoretical values. We obtained very good agreement with a physical model that predicts distances along B-DNA.
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37
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Wang D, Geva E. Protein Structure and Dynamics from Single-Molecule Fluorescence Resonance Energy Transfer. J Phys Chem B 2005; 109:1626-34. [PMID: 16851134 DOI: 10.1021/jp0478864] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The pros and cons of single-molecule vs ensemble-averaged fluorescence resonance energy transfer (FRET) experiments, performed on proteins, are explored with the help of Langevin dynamics simulations. An off-lattice model of the polypeptide chain is employed, which gives rise to a well-defined native state and two-state folding kinetics. A detailed analysis of the distribution of the donor-acceptor distance is presented at different points along the denaturation curve, along with its dependence on the averaging time window. We show that unique information on the correlation between structure and dynamics, which can only be obtained from single-molecule experiments, is contained in the correlation between the donor-acceptor distance and its displacement. The latter is shown to provide useful information on the free energy landscape of the protein, which is complementary to that obtained from the distribution of donor-acceptor distances.
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Affiliation(s)
- Dong Wang
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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38
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Kapanidis AN, Lee NK, Laurence TA, Doose S, Margeat E, Weiss S. Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules. Proc Natl Acad Sci U S A 2004; 101:8936-41. [PMID: 15175430 PMCID: PMC428450 DOI: 10.1073/pnas.0401690101] [Citation(s) in RCA: 465] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We use alternating-laser excitation to achieve fluorescence-aided molecule sorting (FAMS) and enable simultaneous analysis of biomolecular structure and interactions at the level of single molecules. This was performed by labeling biomolecules with fluorophores that serve as donor-acceptor pairs for Förster resonance energy transfer, and by using alternating-laser excitation to excite directly both donors and acceptors present in single diffusing molecules. Emissions were reduced to the distance-dependent ratio E, and a distance-independent, stoichiometry-based ratio S. Histograms of E and S sorted species based on the conformation and association status of each species. S was sensitive to the stoichiometry and relative brightness of fluorophores in single molecules, observables that can monitor oligomerization and local-environment changes, respectively. FAMS permits equilibrium and kinetic analysis of macromolecule-ligand interactions; this was validated by measuring equilibrium and kinetic dissociation constants for the interaction of Escherichia coli catabolite activator protein with DNA. FAMS is a general platform for ratiometric measurements that report on structure, dynamics, stoichiometries, environment, and interactions of diffusing or immobilized molecules, thus enabling detailed mechanistic studies and ultrasensitive diagnostics.
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Affiliation(s)
- Achillefs N Kapanidis
- Department of Chemistry and Biochemistry, University of California, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA.
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39
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Kis-Petikova K, Gratton E. Distance measurement by circular scanning of the excitation beam in the two-photon microscope. Microsc Res Tech 2004; 63:34-49. [PMID: 14677132 DOI: 10.1002/jemt.10417] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We developed a method to measure relative distances with nanometer accuracy of fluorescent particles of different color in a two-photon scanning fluorescence microscope, with two-channel photon counting detection. The method can be used in the 10-500 nm range, for distances below the resolution limit of standard far field microscopy. The proposed technique is more efficient than the methods using raster scanning. To achieve maximum sensitivity in the radial direction, the excitation beam is moved periodically in a circular orbit with a radius of the size of the point spread function. The phase and the modulation of the periodic fluorescence signal, calculated by fast Fourier transform, gives the phase and the radial distance of the particle from the center of scanning. The coordinates of particles are recovered simultaneously in the two channels and the relative distance is calculated in real time. Particles can be tracked by moving the center of scanning to the recovered position, while measuring the distance from the second particle. Intensity data are saved and fitted later by a model accounting for light leakage between the channels. The total number of detected photons limited the accuracy of the position and distance measurement. Experiments demonstrating the advantages of the method were performed on fluorescent spheres and single dye molecules immobilized on quartz surface.
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Affiliation(s)
- Katarina Kis-Petikova
- Laboratory of Fluorescence Dynamics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3080, USA.
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40
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Schröder GF, Grubmüller H. Maximum likelihood trajectories from single molecule fluorescence resonance energy transfer experiments. J Chem Phys 2003. [DOI: 10.1063/1.1616511] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Böhmer M, Enderlein J. Fluorescence spectroscopy of single molecules under ambient conditions: methodology and technology. Chemphyschem 2003; 4:793-808. [PMID: 12961976 DOI: 10.1002/cphc.200200565] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This review presents an overview of the fluorescence detection and spectroscopy of single molecules (SMS) in liquids and on surfaces under ambient conditions. The various techniques of SMS, such as confocal epifluorescence detection and wide-field imaging are presented and discussed, together with the different methods of data analysis such as fluorescence correlation spectroscopy and burst-by-burst analysis. Selected applications of the various techniques in physics, chemistry, and biology are described.
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Affiliation(s)
- Martin Böhmer
- IBI-1, Forschungszentrum Jülich 52425 Jülich, Germany
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42
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Tinnefeld P, Buschmann V, Weston KD, Sauer M. Direct Observation of Collective Blinking and Energy Transfer in a Bichromophoric System. J Phys Chem A 2003. [DOI: 10.1021/jp026565u] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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43
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Kapanidis AN, Weiss S. Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules. J Chem Phys 2002. [DOI: 10.1063/1.1521158] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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44
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Yang S, Cao J. Direct measurements of memory effects in single-molecule kinetics. J Chem Phys 2002. [DOI: 10.1063/1.1521155] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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45
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Daniel DC, Thompson M, Woodbury NW. DNA-binding interactions and conformational fluctuations of Tc3 transposase DNA binding domain examined with single molecule fluorescence spectroscopy. Biophys J 2002; 82:1654-66. [PMID: 11867477 PMCID: PMC1301963 DOI: 10.1016/s0006-3495(02)75516-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The fluorescent dye tetramethylrhodamine (TMR) was conjugated to a synthetic peptide containing the sequence-specific DNA binding domain of Tc3 transposase. Steady-state and single molecule fluorescence spectroscopy was used to investigate protein conformational fluctuations and the thermodynamics of binding interactions. Evidence is presented to show that the TMR-Tc3 conjugate exists in at least two conformational states. The most stable conformation is one in which the TMR fluorescence is quenched. Upon binding to DNA, the total fluorescence from TMR-Tc3 increases by three- to fourfold. Single molecule measurements of TMR-Tc3 bound to DNA shows that this complex also fluctuates between a fluorescent and quenched form. The fluorescent form of the conjugate is stabilized when bound to DNA, and this accounts for part of the increase in total fluorescence. In addition, the inherent photodynamics of the dye itself is also altered (e.g., fluorescent lifetime or triplet yield) in such a way that the total fluorescence from the conjugate bound to DNA is enhanced relative to the unbound form.
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Affiliation(s)
- Douglas C Daniel
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA
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Abstract
Fluorescent resonance energy transfer (FRET) is a powerful technique for studying conformational distribution and dynamics of biological molecules. Some conformational changes are difficult to synchronize or too rare to detect using ensemble FRET. FRET, detected at the single-molecule level, opens up new opportunities to probe the detailed kinetics of structural changes without the need for synchronization. Here, we discuss practical considerations for its implementation including experimental apparatus, fluorescent probe selection, surface immobilization, single-molecule FRET analysis schemes, and interpretation.
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Affiliation(s)
- T Ha
- Department of Physics, Center for Biophysics and Computational Biology, Urbana 61801, USA.
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Abstract
Studies on single protein molecules have advanced from mere proofs of principle to insightful investigations of otherwise inaccessible biological phenomena. Recent studies predict a tremendous number of possible future applications. The long-term vision of biologists to watch single molecular processes in real time by peering into a cell with three-dimensional resolution might finally be realized. Another fascinating perspective is the identification and selection of single favorable variants from complex libraries of diverse biomolecules.
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Affiliation(s)
- P Schwille
- Experimental Biophysics Group, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
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Widengren J, Schweinberger E, Berger S, Seidel CAM. Two New Concepts to Measure Fluorescence Resonance Energy Transfer via Fluorescence Correlation Spectroscopy: Theory and Experimental Realizations. J Phys Chem A 2001. [DOI: 10.1021/jp010301a] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jerker Widengren
- Department of Spectroscopy and Photochemical Kinetics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Enno Schweinberger
- Department of Spectroscopy and Photochemical Kinetics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sylvia Berger
- Department of Spectroscopy and Photochemical Kinetics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Claus A. M. Seidel
- Department of Spectroscopy and Photochemical Kinetics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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Yang S, Cao J. Two-Event Echos in Single-Molecule Kinetics: A Signature of Conformational Fluctuations. J Phys Chem B 2001. [DOI: 10.1021/jp004349k] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shilong Yang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jianshu Cao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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50
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Cao J. Single molecule tracking of heterogeneous diffusion. PHYSICAL REVIEW E 2001; 63:041101. [PMID: 11308813 DOI: 10.1103/physreve.63.041101] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2000] [Indexed: 11/07/2022]
Abstract
The mean square displacement of heterogeneous diffusion obeys the Einstein relation, thereby showing no sign of heterogeneities in the ensemble measurement of the diffusion constant. The signature of spatial heterogeneities appears in the time evolution of the non-Gaussian distribution and in the cross correlation between the square displacements at different times, both available from single molecule diffusional trajectories. As a quantitative measure, the non-Gaussian indicator g(t) decays asymptotically to zero according to 1/t for finite time correlation, but saturates at a plateau value for power-law correlation. In addition, the joint moment correlation function f(t,tau) provides a direct probe of the memory effect of the fluctuating rate constant. A two-state diffusion model and a stochastic Gaussian model are constructed to evaluate these quantities and are shown to yield the same result within the second cumulant expansion.
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Affiliation(s)
- J Cao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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