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Prajapati R, Mukherjee TK. Effect of surfactant assemblies on the resonance energy transfer from 4′,6-diamidino-2-phenylindole to silver nanoclusters. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.11.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Chovelon B, Fiore E, Faure P, Peyrin E, Ravelet C. A lifetime-sensitive fluorescence anisotropy probe for DNA-based bioassays: The case of SYBR Green. Biosens Bioelectron 2016; 90:140-145. [PMID: 27886600 DOI: 10.1016/j.bios.2016.11.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/01/2016] [Accepted: 11/20/2016] [Indexed: 12/12/2022]
Abstract
In standard steady-state fluorescence anisotropy (FA) DNA-based assays, the ligand binding to a given receptor is typically signalled by the rotational correlation time changes of the tracer. Herein, we report a radically different strategy that relies on the peculiar excited state lifetime features of the SYBR Green (SG) dye. This DNA-binding probe exhibits a drastically short lifetime in solution, leading to a high FA signal. Its complexation to oligonucleotides determines a singular and very large depolarization depending on the concerted effects of extreme lifetime enhancement and resonance energy homotransfer. On the basis of ligand-induced changes in the molar fractions of bound and free forms of SG, the approach provides an unprecedented means for the FA monitoring of the ligand binding to short DNA molecules, allowing the elaboration of a variety of intercalator displacement assays and label-free biosensors that involve diverse DNA structures (duplex, hairpin, G-quadruplex and single-stranded), ligand types (ion, small organic molecule and protein) and binding modes (intercalation, minor groove, allosteric switch). These findings open up promising avenues in the design of a new generation of FA assays.
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Affiliation(s)
- Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France; Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble site Nord - Institut de biologie et de pathologie, F-38041 Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France
| | - Patrice Faure
- Département de Biochimie, Toxicologie et Pharmacologie, CHU de Grenoble site Nord - Institut de biologie et de pathologie, F-38041 Grenoble, France; University Grenoble Alpes, Laboratory of Hypoxy Physiopathology Study Inserm U1042, 38700 La Tronche, France
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041 Grenoble, France; CNRS, DPM UMR 5063, F-38041 Grenoble, France.
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Prajapati R, Chatterjee S, Kannaujiya KK, Mukherjee TK. Effect of compartmentalization of donor and acceptor on the ultrafast resonance energy transfer from DAPI to silver nanoclusters. NANOSCALE 2016; 8:13006-13016. [PMID: 27304093 DOI: 10.1039/c6nr01792d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The mechanism and dynamics of excitation energy transfer (EET) from photo-excited 4',6-diamidino-2-phenylindole (DAPI) to silver nanoclusters (Ag NCs) and its subsequent modulation in the presence of cationic polymer poly(diallyldimethylammonium chloride) (PDADMAC) and Calf Thymus DNA (CT-DNA) have been demonstrated using steady-state fluorescence and femtosecond fluorescence upconversion techniques. The synthesized Ag NCs were characterized using FTIR, mass spectrometry, XPS, HRTEM, DLS, UV-Vis and PL spectroscopy. Mass spectrometric analysis reveals the formation of ultrasmall Ag4 NCs with a small amount of Ag5 NCs. UV-Vis and PL spectra reveal distinct molecular-like optoelectronic behaviour of these ultrasmall Ag NCs. The dihydrolipoic acid-capped Ag NCs strongly quench the fluorescence of DAPI with concomitant increase in its photoluminescence (PL) intensity at 675 nm. This steady-state fluorescence quenching proceeds with a significant shortening of the fluorescence lifetime of DAPI in the presence of Ag NCs, signifying the nonradiative Förster resonance energy transfer (FRET) from DAPI to Ag NCs. Various energy transfer parameters have been estimated from FRET theory. The present FRET pair shows a characteristic Förster distance of 2.45 nm and can be utilized as a reporter of short-range distances in various FRET based applications. Moreover, this nonradiative FRET is completely suppressed in the presence of both 0.2 wt% PDADMAC and CT-DNA. Our results reveal selective compartmentalization of Ag NCs and DAPI in the presence of 0.2 wt% PDADMAC and CT-DNA, respectively. This selective compartmentalization of donor and acceptor and the subsequent modification of the FRET process may find application in various sensing, photovoltaic, and light harvesting applications.
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Affiliation(s)
- Roopali Prajapati
- Discipline of Chemistry, Indian Institute of Technology Indore, Simrol Campus, Khandwa Road, Indore-453552, M.P., India.
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Wang SC, Morris MD. Electrophoresis with Polarized Fluorescence Detection. Application to Capillary Fluorescence Rejection. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200500106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Zhu Z, Xu L, Zhou X, Qin J, Yang C. Designing label-free DNA sequences to achieve controllable turn-off/on fluorescence response for Hg2+ detection. Chem Commun (Camb) 2011; 47:8010-2. [DOI: 10.1039/c1cc12384j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Noothi SK, Kombrabail M, Kundu TK, Krishnamoorthy G, Rao BJ. Enhanced DNA dynamics due to cationic reagents, topological states of dsDNA and high mobility group box 1 as probed by PicoGreen. FEBS J 2008; 276:541-51. [DOI: 10.1111/j.1742-4658.2008.06802.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Barcellona ML, Gammon S, Hazlett T, Digman MA, Gratton E. Polarized fluorescence correlation spectroscopy of DNA-DAPI complexes. Microsc Res Tech 2005; 65:205-17. [PMID: 15630690 DOI: 10.1002/jemt.20121] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We discuss the use of fluorescence correlation spectroscopy for the measurement of relatively slow rotations of large macromolecules in solution or attached to other macromolecular structures. We present simulations and experimental results to illustrate the range of rotational correlation times and diffusion times that the technique can analyze. In particular, we examine various methods to analyze the polarization fluctuation data. We have found that by first constructing the polarization function and then calculating the autocorrelation function, we can obtain the rotational motion of the molecule with very little interference from the lateral diffusion of the macromolecule, as long as the rotational diffusion is significantly faster than the lateral diffusion. Surprisingly, for common fluorophores the autocorrelation of the polarization function is relatively unaffected by the photon statistics. In our instrument, two-photon excitation is used to define a small volume of illumination where a few molecules are present at any instant of time. The measurements of long DNA molecules labeled with the fluorescent probe DAPI show local rotational motions of the polymers in addition to translation motions of the entire polymer. For smaller molecules such as EGFP, the viscosity of the solution must be increased to bring the relaxation due to rotational motion into the measurable range. Overall, our results show that polarized fluorescence correlation spectroscopy can be used to detect fast and slow rotational motion in the time scale from microsecond to second, a range that cannot be easily reached by conventional fluorescence anisotropy decay methods.
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Affiliation(s)
- Maria Luisa Barcellona
- Department of Biological Chemistry and Molecular Biology, University of Catania, Catania, Italy
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Kalinin S, Johansson LBA. Utility and considerations of donor-donor energy migration as a fluorescence method for exploring protein structure-function. J Fluoresc 2005; 14:681-91. [PMID: 15649020 DOI: 10.1023/b:jofl.0000047218.51768.59] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This review aims at surveying the use of electronic energy transport between chemically identical fluorophores (i.e. donors) in studies of various protein systems. Applications of intra- and interprotein energy migration are presented that make use of polarised steady-state and time-resolved fluorescence spectroscopic techniques. The donor-donor energy migration (DDEM) and the partial donor-donor energy migration (PDDEM) models for calculating distances between donor groups are exposed together with the most recent development of an extended Forster theory (EFT). Synthetic fluorescence depolarisation data that mimic time-correlated single photon counting experiments were generated using the EFT, and then further re-analysed by the different models. The results obtained were compared with the known parameters used to generate EFT data. Aspects on how to adopt the EFT in the analyses of time-correlated single photon counting experiments are also presented, as well as future aspects on using energy migration for examining protein structure.
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Affiliation(s)
- Stanislav Kalinin
- Department of Chemistry, Biophysical Chemistry, University of Umeå, S-901 87 Umeå, Sweden
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Alba FJ, Daban JR. Inhibition of Peroxyoxalate Chemiluminescence by Intercalation of Fluorescent Acceptors between DMA Bases. Photochem Photobiol 1999. [DOI: 10.1111/j.1751-1097.1999.tb03305.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lakowicz JR, Gryczynski I, Gryczynski Z. High Throughput Screening with Multiphoton Excitation. JOURNAL OF BIOMOLECULAR SCREENING 1999; 4:355-362. [PMID: 10838432 PMCID: PMC6986387 DOI: 10.1177/108705719900400610] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fluorescence detection is extensively used in high throughput screening. In HTS there is a continuous migration toward higher density plates and smaller sample volumes. In the present report we describe the advantages of two-photon or multiphoton excitation for HTS. Multiphoton excitation (MPE) is the simultaneous absorption of two long-wavelength photons to excite the lowest singlet state of the fluorophore. MPE is typically accomplished with short but high-intensity laser pulses, which allows simultaneous absorption of two or more photons. The intensity of the multiphoton-induced fluorescence is proportional to the square, cube, or higher power of the instantneous photon flux. Consequently, two-photon or multiphoton excitation only occurs at the focal point of the incident beam. This property of two-photon excitation allows the excited volume to be very small and to be localized in the center of each well in the HTS plate. We show that two-photon-induced fluorescence of fluorescein can be reliably measured in microwell plates. We also show the use of 6-carboxy fluorescein as a pH probe with two-photon excitation, and measure 4'-6-diamidino-2-phenylindole (DAPI) binding and two-photon-induced fluorescence. In further studies we measure the time-dependent intensity decays of DAPI bound to DNA and of calcium-dependent fluorophores. Finally, we demonstrate the possibility of three-photon excitation of several fluorophores, including indole, in the HTS plate. These results suggest that MPE can be used in high-density multiwell plates.
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Affiliation(s)
- JR Lakowicz
- University of Maryland, School of Medicine, Baltimore, MD
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Carlsson C, Larsson A, Björkman M, Jonsson M, Albinsson B. Experimental and simulated fluorescence depolarization due to energy transfer as tools to study DNA-dye interactions. Biopolymers 1997. [DOI: 10.1002/(sici)1097-0282(19970415)41:5<481::aid-bip1>3.0.co;2-i] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
Time-resolved fluorescence spectroscopy is used to monitor molecular interactions and motions that occur in the picosecond-nanosecond time range, and is especially useful in the analysis of biomolecular structure and dynamics. Recent advances in the application of time-resolved fluorescence spectroscopy to biological systems have led to a better understanding of the origin of nonexponential fluorescence decay in proteins, the use of tryptophan analogs as unique spectroscopic probes of protein-protein interactions, the detailed characterization of protein-folding processes and intermediates, and the development of new approaches to the study of DNA-protein interactions.
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Affiliation(s)
- D P Millar
- Scripps Research Institute, Department of Molecular Biology, La Jolla, CA 92037, USA.
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