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Corradini MG, Demol M, Boeve J, Ludescher RD, Joye IJ. Fluorescence Spectroscopy as a Tool to Unravel the Dynamics of Protein Nanoparticle Formation by Liquid Antisolvent Precipitation. FOOD BIOPHYS 2017. [DOI: 10.1007/s11483-017-9477-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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UV-Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 2: selected applications. Biophys Rev 2016; 8:163-177. [PMID: 28510057 PMCID: PMC4884208 DOI: 10.1007/s12551-016-0197-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/14/2016] [Indexed: 11/07/2022] Open
Abstract
In Part 2 we discuss application of several different types of UV–Vis spectroscopy, such as normal, difference, and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, of the side-chain of tyrosine residues in different molecular environments. We review the ways these spectroscopies can be used to probe complex protein structures.
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Kierdaszuk B. Fluorescence anisotropy of tyrosinate anion using one-, two- and three-photon excitation: tyrosinate anion fluorescence. J Fluoresc 2013; 23:339-47. [PMID: 23233051 PMCID: PMC3590413 DOI: 10.1007/s10895-012-1152-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 12/02/2012] [Indexed: 11/04/2022]
Abstract
We examined the emission spectra and steady-state anisotropy of tyrosinate anion fluorescence with one-photon (250-310 nm), two-photon (570-620 nm) and three-photon (750-930 nm) excitation. Similar emission spectra of the neutral (pH 7.2) and anionic (pH 13) forms of N-acetyl-L-tyrosinamide (NATyrA) (pKa 10.6) were observed for all modes of excitation, with the maxima at 302 and 352 nm, respectively. Two-photon excitation (2PE) and three-photon excitation (3PE) spectra of the anionic form were the same as that for one-photon excitation (1PE). In contrast, 2PE spectrum from the neutral form showed ~30-nm shift to shorter wavelengths relative to 1PE spectrum (λmax 275 nm) at two-photon energy (550 nm), the latter being overlapped with 3PE spectrum, both at two-photon energy (550 nm). Two-photon cross-sections for NATyrA anion at 565-580 nm were 10 % of that for N-acetyl-L-tryptophanamide (NATrpA), and increased to 90 % at 610 nm, while for the neutral form of NATyrA decreased from 2 % of that for NATrpA at 570 nm to near zero at 585 nm. Surprisingly, the fundamental anisotropy of NATyrA anion in vitrified solution at -60 °C was ~0.05 for 2PE at 610 nm as compared to near 0.3 for 1PE at 305 nm, and wavelength-dependence appears to be a basic feature of its anisotropy. In contrast, the 3PE anisotropy at 900 nm was about 0.5, and 3PE and 1PE anisotropy values appear to be related by the cos(6) θ to cos(2) θ photoselection factor (approx. 10/6) independently of excitation wavelength. Attention is drawn to the possible effect of tyrosinate anions in proteins on their multi-photon induced fluorescence emission and excitation spectra as well as excitation anisotropy spectra.
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Affiliation(s)
- Borys Kierdaszuk
- Department of Biophysics, Stefan Pienkowski Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 93 Zwirki i Wigury St., 02-089 Warsaw, Poland.
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Durante-Rodríguez G, Valderrama JA, Mancheño JM, Rivas G, Alfonso C, Arias-Palomo E, Llorca O, García JL, Díaz E, Carmona M. Biochemical characterization of the transcriptional regulator BzdR from Azoarcus sp. CIB. J Biol Chem 2010; 285:35694-705. [PMID: 20826820 DOI: 10.1074/jbc.m110.143503] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The BzdR transcriptional regulator that controls the P(N) promoter responsible for the anaerobic catabolism of benzoate in Azoarcus sp. CIB constitutes the prototype of a new subfamily of transcriptional regulators. Here, we provide some insights about the functional-structural relationships of the BzdR protein. Analytical ultracentrifugation studies revealed that BzdR is homodimeric in solution. An electron microscopy three-dimensional reconstruction of the BzdR dimer has been obtained, and the predicted structures of the respective N- and C-terminal domains of each BzdR monomer could be fitted into such a reconstruction. Gel retardation and ultracentrifugation experiments have shown that the binding of BzdR to its cognate promoter is cooperative. Different biochemical approaches revealed that the effector molecule benzoyl-CoA induces conformational changes in BzdR without affecting its oligomeric state. The BzdR-dependent inhibition of the P(N) promoter and its activation in the presence of benzoyl-CoA have been established by in vitro transcription assays. The monomeric BzdR4 and BzdR5 mutant regulators revealed that dimerization of BzdR is essential for DNA binding. Remarkably, a BzdRΔL protein lacking the linker region connecting the N- and C-terminal domains of BzdR is also dimeric and behaves as a super-repressor of the P(N) promoter. These data suggest that the linker region of BzdR is not essential for protein dimerization, but rather it is required to transfer the conformational changes induced by the benzoyl-CoA to the DNA binding domain leading to the release of the repressor. A model of action of the BzdR regulator has been proposed.
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Affiliation(s)
- Gonzalo Durante-Rodríguez
- Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
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Georgakoudi I, Rice WL, Hronik-Tupaj M, Kaplan DL. Optical spectroscopy and imaging for the noninvasive evaluation of engineered tissues. TISSUE ENGINEERING PART B-REVIEWS 2009; 14:321-40. [PMID: 18844604 DOI: 10.1089/ten.teb.2008.0248] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Optical spectroscopy and imaging approaches offer the potential to noninvasively assess different aspects of the cellular, extracellular matrix, and scaffold components of engineered tissues. In addition, the combination of multiple imaging modalities within a single instrument is highly feasible, allowing acquisition of complementary information related to the structure, organization, biochemistry, and physiology of the sample. The ability to characterize and monitor the dynamic interactions that take place as engineered tissues develop promises to enhance our understanding of the interdependence of processes that ultimately leads to functional tissue outcomes. It is expected that this information will impact significantly upon our abilities to optimize the design of biomaterial scaffolds, bioreactors, and cell systems. Here, we review the principles and performance characteristics of the main methodologies that have been exploited thus far, and we present examples of corresponding tissue engineering studies.
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Affiliation(s)
- Irene Georgakoudi
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, USA.
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Manso I, Torres B, Andreu JM, Menéndez M, Rivas G, Alfonso C, Díaz E, García JL, Galán B. 3-Hydroxyphenylpropionate and phenylpropionate are synergistic activators of the MhpR transcriptional regulator from Escherichia coli. J Biol Chem 2009; 284:21218-28. [PMID: 19520845 DOI: 10.1074/jbc.m109.008243] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The degradation of the aromatic compound phenylpropionate (PP) in Escherichia coli K-12 requires the activation of two different catabolic pathways coded by the hca and the mhp gene clusters involved in the mineralization of PP and 3-hydroxyphenylpropionate (3HPP), respectively. The compound 3-(2,3-dihydroxyphenyl)propionate (DHPP) is a common intermediate of both pathways which must be cleaved by the MhpB dioxygenase before entering into the primary cell metabolism. Therefore, the degradation of PP has to be controlled by both its specific regulator (HcaR) but also by the MhpR regulator of the mhp cluster. We have demonstrated that 3HPP and DHPP are the true and best activators of MhpR, whereas PP only induces no response. However, in vivo and in vitro transcription experiments have demonstrated that PP activates the MhpR regulator synergistically with the true inducers, representing the first case of such a peculiar synergistic effect described for a bacterial regulator. The three compounds enhanced the interaction of MhpR with its DNA operator in electrophoretic mobility shift assays. Inducer binding to MhpR is detected by circular dichroism and fluorescence spectroscopies. Fluorescence quenching measurements have revealed that the true inducers (3HPP and DHPP) and PP bind with similar affinities and independently to MhpR. This type of dual-metabolite synergy provides great potential for a rapid modulation of gene expression and represents an important feature of transcriptional control. The mhp regulatory system is an example of the high complexity achievable in prokaryotes.
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Guler MO, Hsu L, Soukasene S, Harrington DA, Hulvat JF, Stupp SI. Presentation of RGDS epitopes on self-assembled nanofibers of branched peptide amphiphiles. Biomacromolecules 2006; 7:1855-63. [PMID: 16768407 PMCID: PMC2547993 DOI: 10.1021/bm060161g] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Branched peptide amphiphile (PA) molecules bearing biological epitopes were designed and synthesized using orthogonal protecting group chemistry on amine groups at lysine residues. These molecules self-assemble into high-aspect-ratio cylindrical nanofibers, and their branched architecture enhances accessibility of epitopes for protein binding and also allows the presentation of more than one epitope in a single molecule. The RGDS cell adhesion epitope was used as a model bioactive signal on PA molecules for potential biomedical applications. Aggregation of the branched PA molecules into nanofibers was demonstrated by TEM and through shifts in the protonation profiles of peripheral amines. These systems also formed self-supporting gels in the presence of physiological fluids and other biologically relevant macromolecules such as synovial fluid and DNA, an important property for their potential use in medicine. Fluorescence anisotropy measurements on the PAs with tryptophan residues were performed to examine the effect of branching on packing and mobility of the peptides in the self-assembled nanofibers. The mobility of tryptophan residues was observed to be restricted upon packing of PA molecules into nanofibers. However, relative to linear analogues, branched molecules retain more mobility in the supramolecular aggregates.
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Affiliation(s)
| | | | | | - Daniel A. Harrington
- Department of Materials Science and Engineering
- Institute for BioNanotechnology in Medicine
| | - James F. Hulvat
- Department of Chemistry
- Institute for BioNanotechnology in Medicine
| | - Samuel I. Stupp
- E-mail address:
- Department of Chemistry
- Department of Materials Science and Engineering
- Institute for BioNanotechnology in Medicine
- Feinberg School of Medicine
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Tirri ME, Huttunen RJ, Toivonen J, Härkönen PL, Soini JT, Hänninen PE. Two-photon excitation in fluorescence polarization receptor-ligand binding assay. ACTA ACUST UNITED AC 2005; 10:314-9. [PMID: 15964932 DOI: 10.1177/1087057104273334] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fluorescence polarization is one of the most commonly used homogeneous assay principles in drug discovery for screening of potential lead compounds. In this article, the fluorescence polarization technique is combined with 2-photon excitation of fluorescence. Theoretically, the use of 2-photon excitation of fluorescence increases the volumetric sensitivity and polarization contrast of fluorescence polarization assays. The work in this report demonstrates these predictions for an estrogen receptor ligand binding assay.
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Affiliation(s)
- Marko E Tirri
- Laboratory of Biophysics, Institute of Biomedicine, University of Turku, Finland.
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Belfield KD, Bondar MV, Hales JM, Morales AR, Przhonska OV, Schafer KJ. One- and two-photon fluorescence anisotropy of selected fluorene derivatives. J Fluoresc 2005; 15:3-11. [PMID: 15711871 DOI: 10.1007/s10895-005-0207-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2004] [Accepted: 09/15/2004] [Indexed: 10/25/2022]
Abstract
The steady-state excitation anisotropy spectra of fluorene derivatives were measured in viscous solvents, under the one- and two-photon excitation, over a broad spectral range (UV-Visible). The orientation of their absorption transition moments for the first, S0 --> S1, and second, S0 --> S2, excited states were determined. It was shown experimentally that a decrease in the angle between S0 --> S1 and S0 --> S2 transitions corresponded to an increased value of two-photon absorption (2PA) cross section for these molecules. Two-photon excitation anisotropy was nearly constant over the spectral region investigated (in contrast to one-photon excitation anisotropy spectra) and can be roughly explained by a simple model of 2PA based on the single intermediate state approximation. For comparison, the same trend in two-photon excitation anisotropy was observed for Rhodamine B in glycerol.
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Affiliation(s)
- K D Belfield
- Department of Chemistry, University of Central Florida, Orlando, Florida, USA.
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Abstract
Two-photon fluorescence microscopy is one of the most important recent inventions in biological imaging. This technology enables noninvasive study of biological specimens in three dimensions with submicrometer resolution. Two-photon excitation of fluorophores results from the simultaneous absorption of two photons. This excitation process has a number of unique advantages, such as reduced specimen photodamage and enhanced penetration depth. It also produces higher-contrast images and is a novel method to trigger localized photochemical reactions. Two-photon microscopy continues to find an increasing number of applications in biology and medicine.
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Affiliation(s)
- P T So
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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Abstract
We observed emission from the tyrosine derivative N-acetyl-L-tyrosinamide (NATyrA) when excited with the fundamental output of a femtosecond Ti:Sapphire laser from 780 to 855 nm. The dependence on incident laser power indicates a three-photon process. The emission spectra and intensity decay in glycerol-water (30:70) at 5 degrees C were found to be identical for one- and three-photon excitation. Also the excitation spectrum of three-photon-induced fluorescence of NATyrA corresponds to the one-photon excitation spectrum. The time-zero or fundamental anisotropy spectrum was reconstructed from the frequency-domain anisotropy decays. The three-photon anisotropies are similar or larger than the one-photon anisotropies. These three-photon anisotropies are surprising given the near zero values known for tyrosine with two-photon excitation. The observations indicate that one- and three-photon excitation directly populates the same singlet excited states(s). However, the origin of the anisotropies with multi-photon excitation of tyrosine remain unclear and unpredictable.
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Affiliation(s)
- I Gryczynski
- Department of Biochemistry and Molecular Biology, University of Maryland at Baltimore 21201, USA
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Zhang ZX, Sonek GJ, Wei XB, Sun C, Berns MW, Tromberg BJ. Cell Viability and DNA Denaturation Measurements by Two-Photon Fluorescence Excitation in CW Al:GaAs Diode Laser Optical Traps. JOURNAL OF BIOMEDICAL OPTICS 1999; 4:256-9. [PMID: 23015212 DOI: 10.1117/1.429948] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Cell viability and DNA denaturation are measured through two-photon fluorescence excitation using a single diode laser beam as the trapping and exciting source simultaneously. Two-photon fluorescence emission spectra are presented for CHO cells and T lymphocytes loaded with various fluorescent probes. This single beam method is demonstrated to be a safe tool to monitor the viability of optically trapped cells, even under intense 809 nm diode laser illumination (∼106 W/cm2). The dynamics of cellular necrosis is monitored by adding ethanol to the cell suspension during trapping. Thermal damage to heat-treated samples is assessed by recording shifts in the emission spectra from trapped cells loaded with the nucleic acid probe, acridine orange. © 1999 Society of Photo-Optical Instrumentation Engineers.
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Samuels AC, Jensen JO, Hameka HF. Theoretical studies of the fluorescence and phosphorescence of tyrosine. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(98)00195-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gryczynski I, Gryczynski Z, Lakowicz JR. Fluorescence Anisotropy Controlled by Light Quenching. Photochem Photobiol 1998. [DOI: 10.1111/j.1751-1097.1998.tb09106.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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15
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Gryczynski I, Gryczynski Z, Lakowicz JR. Fluorescence Anisotropy Controlled by Light Quenching. Photochem Photobiol 1998. [DOI: 10.1111/j.1751-1097.1998.tb09467.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Nonresonant two-photon electronic spectroscopy of polyatomic molecules is reviewed for the period since 1979. Emphasis is placed on studies that expose patterns in the two-photon fluorescence (also ionization, optoacoustic) excitation spectra of aromatic hydrocarbons and the effect of vibrations and substitution, particularly within the framework of pseudoparity rules. A section is devoted to biological molecules and the emerging use of two-photon-induced fluorescence anisotropy. Relevant theoretical results are discussed, with emphasis on quantum chemical predictions of vibronic coupling and substituent effects on two-photon absorptivity and tensor properties of individual molecules. This chapter includes higher-order spectroscopy, and a limited number of three- and four-photon studies are discussed.
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Affiliation(s)
- P R Callis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.
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Three-photon-induced fluorescence of diphenylhexatriene in solvents and lipid bilayers. J Fluoresc 1997. [DOI: 10.1007/bf02760500] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Song OK, Woodford JN, Wang CH. Effects of Two-Photon Fluorescence and Polymerization on the First Hyperpolarizability of an Azobenzene Dye. J Phys Chem A 1997. [DOI: 10.1021/jp962735p] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- O. K. Song
- Department of Chemistry, University of NebraskaLincoln, Lincoln, Nebraska 68588-0304
| | - J. N. Woodford
- Department of Chemistry, University of NebraskaLincoln, Lincoln, Nebraska 68588-0304
| | - C. H. Wang
- Department of Chemistry, University of NebraskaLincoln, Lincoln, Nebraska 68588-0304
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Lakowicz JR, Gryczynski I, Malak H, Schrader M, Engelhardt P, Kano H, Hell SW. Time-resolved fluorescence spectroscopy and imaging of DNA labeled with DAPI and Hoechst 33342 using three-photon excitation. Biophys J 1997; 72:567-78. [PMID: 9017187 PMCID: PMC1185585 DOI: 10.1016/s0006-3495(97)78696-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We examined the fluorescence spectral properties of the DNA stains DAPI (4',6-diamidino-2-phenylindole, hydrochloride) and Hoechst 33342 (bis-benzimide, or 2,5'-bi'1H-benzimidazole2'-(4-ethoxyphenyl)-5-(4-methyl-1-piperazi nyl)) with two-photon (2h nu) and three-photon (3h nu) excitation using femtosecond pulses from a Ti:sapphire laser from 830 to 885 nm. The mode of excitation of DAPI bound to DNA changed from two-photon at 830 nm to three-photon at 885 nm. In contrast, Hoechst 33342 displayed only two-photon excitation from 830 to 885 nm. DAPI-DNA displayed the same emission spectra and decay times for 2h nu and 3h nu excitation. Hoechst 33342-DNA displayed the same intensity decay for excitation at 830 and 885 nm. Both probes displayed higher anisotropies for multiphoton excitation as compared to one-photon excitation with ultraviolet wavelengths, and DAPI-DNA displays a higher anisotropy for 3h nu at 885 nm than for 2h nu at 830 nm. We used 970-nm excitation of DAPI-stained chromosomes to obtain the first three-dimensional images with three-photon excitation. Three-photon excitation of DAPI-stained chromosomes at 970 nm was demonstrated by the power dependence in the fluorescence microscope.
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Affiliation(s)
- J R Lakowicz
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore 21201, USA.
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Kierdaszuk B, Malak H, Gryczynski I, Callis P, Lakowicz JR. Fluorescence of reduced nicotinamides using one- and two-photon excitation. Biophys Chem 1996; 62:1-13. [PMID: 8962467 DOI: 10.1016/s0301-4622(96)02182-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We examined the steady-state and time-resolved emission of NADH and NAMH resulting from one-photon and two-photon excitation. Similar emission spectra were observed for both modes of excitation. The fundamental anisotropy of NADH is near 0.54 for two-photon excitation from 690 to 740 nm, which is 46% higher than the value of 0.37 observed for one-photon excitation. This observation of a higher anisotropy with two-photon excitation was consistent with INDO/SDCI calculations of the one- and two-photon transitions. Minor differences in the multi-exponential decays of NADH were observed for one- and two-photon excitation, but presently available resolution does not allow us to conclude the decays are distinct. NADH-LADH-IBA complex formation led to an order of magnitude larger of the average lifetimes of NADH fluorescence resulting from one- and two-photon excitation. Fluorescence intensity and fluorescence anisotropy decays of NADH was double-exponential for both modes of excitation and show that the observed heterogeneity of the fluorescence decay kinetics of reduced nicotinamides arises from the inherent photoprocess of the dihydronicotinamide chromophore and not due to any intramolecular interactions with adenine part of NADH. Such interactions are responsible for the depolarization of NADH fluorescence observed for excitation wavelength below 300 nm for OPE and 600 nm for TPE, respectively. NADH displays a low cross-section for two-photon excitation which suggests that fluorescence from NADH will be moderately difficult to observe with two-photon fluorescence microscopy, and may not interfere with observations of TPIF of other extrinsic probes used to label cells.
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Affiliation(s)
- B Kierdaszuk
- Department of Biological Chemistry, University of Maryland School of Medicine, Baltimore 21201, USA
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