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Fazel M, Vallmitjana A, Scipioni L, Gratton E, Digman MA, Pressé S. Fluorescence lifetime: Beating the IRF and interpulse window. Biophys J 2023; 122:672-683. [PMID: 36659850 PMCID: PMC9989884 DOI: 10.1016/j.bpj.2023.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
Fluorescence lifetime imaging captures the spatial distribution of chemical species across cellular environments employing pulsed illumination confocal setups. However, quantitative interpretation of lifetime data continues to face critical challenges. For instance, fluorescent species with known in vitro excited-state lifetimes may split into multiple species with unique lifetimes when introduced into complex living environments. What is more, mixtures of species, which may be both endogenous and introduced into the sample, may exhibit 1) very similar lifetimes as well as 2) wide ranges of lifetimes including lifetimes shorter than the instrumental response function or whose duration may be long enough to be comparable to the interpulse window. By contrast, existing methods of analysis are optimized for well-separated and intermediate lifetimes. Here, we broaden the applicability of fluorescence lifetime analysis by simultaneously treating unknown mixtures of arbitrary lifetimes-outside the intermediate, Goldilocks, zone-for data drawn from a single confocal spot leveraging the tools of Bayesian nonparametrics (BNP). We benchmark our algorithm, termed BNP lifetime analysis, using a range of synthetic and experimental data. Moreover, we show that the BNP lifetime analysis method can distinguish and deduce lifetimes using photon counts as small as 500.
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Affiliation(s)
- Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona
| | - Alexander Vallmitjana
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Lorenzo Scipioni
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Michelle A Digman
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona; School of Molecular Science, Arizona State University, Tempe, Arizona.
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2
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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Thienoguanosine, a unique non-perturbing reporter for investigating rotational dynamics of DNA duplexes and their complexes with proteins. Int J Biol Macromol 2022; 213:210-225. [DOI: 10.1016/j.ijbiomac.2022.05.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/23/2022] [Indexed: 11/05/2022]
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4
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Jonely M, Singh RK, Donelick HM, Bass BL, Noriega R. Loquacious-PD regulates the terminus-dependent molecular recognition of Dicer-2 toward double-stranded RNA. Chem Commun (Camb) 2021; 57:10879-10882. [PMID: 34590626 DOI: 10.1039/d1cc03843e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dicer-2 cleaves double-stranded RNA into siRNAs in a terminus-dependent manner as part of D. melanogaster's RNA interference pathway. Using ultrafast fluorescence, we probe the local environment of chromophores at the dsRNA terminus upon binding by Dicer-2 and interrogate the effects of Loquacious-PD, an accessory protein. We find substrate-selective modes of molecular recognition that distinguish between blunt and 3'overhang termini, but whose differences are greatly reduced by Loquacious-PD. These results connect the molecular recognition properties of Dicer-2 to its selective processing of dsRNAs with different termini and to its need for Loquacious-PD to efficiently produce endogenous siRNAs.
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Affiliation(s)
- McKenzie Jonely
- University of Utah, Department of Chemistry, Salt Lake City, UT 84112, USA.
| | - Raushan K Singh
- University of Utah, Department of Biochemistry, Salt Lake City, UT 84112, USA
| | - Helen M Donelick
- University of Utah, Department of Biochemistry, Salt Lake City, UT 84112, USA
| | - Brenda L Bass
- University of Utah, Department of Biochemistry, Salt Lake City, UT 84112, USA
| | - Rodrigo Noriega
- University of Utah, Department of Chemistry, Salt Lake City, UT 84112, USA.
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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6
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Snyder JA, Charnay AP, Kohl FR, Zhang Y, Kohler B. DNA-like Photophysics in Self-Assembled Silver(I)–Nucleobase Nanofibers. J Phys Chem B 2019; 123:5985-5994. [PMID: 31283245 DOI: 10.1021/acs.jpcb.9b00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Joshua A. Snyder
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Aaron P. Charnay
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Forrest R. Kohl
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yuyuan Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Remington JM, McCullagh M, Kohler B. Molecular Dynamics Simulations of 2-Aminopurine-Labeled Dinucleoside Monophosphates Reveal Multiscale Stacking Kinetics. J Phys Chem B 2019; 123:2291-2304. [PMID: 30767498 DOI: 10.1021/acs.jpcb.8b12172] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulations of 2-aminopurine (2Ap)-labeled DNA dinucleoside monophosphates (DNMPs) were performed to investigate the hypothesis that base stacking dynamics occur on timescales sufficiently rapid to influence the emission signals measured in time-resolved fluorescence experiments. Analysis of multiple microsecond-length trajectories shows that the DNMPs sample all four coplanar stacking motifs. In addition, three metastable unstacked conformations are detected. A hidden Markov-state model (HMSM) was applied to the simulations to estimate transition rates between the stacked and unstacked states. Transitions between different stacked states generally occur at higher rates when the number of nucleobase faces requiring desolvation is minimized. Time constants for structural relaxation range between 1.6 and 25 ns, suggesting that emission from photoexcited 2Ap, which has an excited-state lifetime of 10 ns, is sensitive to base stacking kinetics. A master equation model for the excited-state population of 2Ap predicts multiexponential emission decays that reproduce the sub-10 ns emission decay lifetimes and amplitudes seen in experiments. Combining MD simulations with HMSM analysis is a powerful way to understand the dynamics that influence 2Ap excited-state relaxation and represents an important step toward using observed emission signals to validate MD simulations.
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Affiliation(s)
- Jacob M Remington
- Department of Chemistry and Biochemistry , Montana State University , Bozeman , Montana 59717 , United States
| | - Martin McCullagh
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States
| | - Bern Kohler
- Department of Chemistry and Biochemistry , The Ohio State University , 100 West 18th Avenue , Columbus , Ohio 43210 , United States
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Böhnke H, Röttger K, Ingle RA, Marroux HJB, Bohnsack M, Orr-Ewing AJ, Temps F. Efficient intersystem crossing in 2-aminopurine riboside probed by femtosecond time-resolved transient vibrational absorption spectroscopy. Phys Chem Chem Phys 2018; 20:20033-20042. [DOI: 10.1039/c8cp02664e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The photophysical dynamics of 2-aminopurine, a fluorescent analogue of the canonical nucleobase adenine, has been studied by femtosecond transient vibrational absorption spectroscopy.
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Affiliation(s)
- Hendrik Böhnke
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | - Katharina Röttger
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
- School of Chemistry
| | | | | | - Mats Bohnsack
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
| | | | - Friedrich Temps
- Institute of Physical Chemistry
- Christian-Albrechts-University Kiel
- 24098 Kiel
- Germany
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9
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Tolbert M, Morgan CE, Pollum M, Crespo-Hernández CE, Li ML, Brewer G, Tolbert BS. HnRNP A1 Alters the Structure of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation. J Mol Biol 2017; 429:2841-2858. [PMID: 28625847 PMCID: PMC5610934 DOI: 10.1016/j.jmb.2017.06.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/08/2017] [Accepted: 06/08/2017] [Indexed: 01/25/2023]
Abstract
Enteroviruses use a type I Internal Ribosome Entry Site (IRES) structure to facilitate protein synthesis and promote genome replication. Type I IRES elements require auxiliary host proteins to organize RNA structure for 40S ribosomal subunit assembly. Heterogeneous nuclear ribonucleoprotein A1 stimulates enterovirus 71 (EV71) translation in part through specific interactions with its stem loop II (SLII) IRES domain. Here, we determined a conjoined NMR-small angle x-ray scattering structure of the EV71 SLII domain and a mutant that significantly attenuates viral replication by abrogating hnRNP A1 interactions. Native SLII adopts a locally compact structure wherein stacking interactions in a conserved 5'-AUAGC-3' bulge preorganize the adjacent helices at nearly orthogonal orientations. Mutating the bulge sequence to 5'-ACCCC-3' ablates base stacking in the loop and globally reorients the SLII structure. Biophysical titrations reveal that the 5'-AUAGC-3' bulge undergoes a conformational change to assemble a functional hnRNP A1-RNA complex. Importantly, IRES mutations that delete the bulge impair viral translation and completely inhibit replication. Thus, this work provides key details into how an EV71 IRES structure adapts to hijack a cellular protein, and it suggests that the SLII domain is a potential target for antiviral therapy.
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Affiliation(s)
- Michele Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106-7078 USA
| | - Christopher E Morgan
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106-7078 USA
| | - Marvin Pollum
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106-7078 USA
| | | | - Mei-Ling Li
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, 08854 USA
| | - Gary Brewer
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, 08854 USA
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106-7078 USA.
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