1
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Clayborn AL, Rebstock JA, Camardella LJ, Comeau EP, Dabhi SK, Graber EG, Joyce TH, Maricar IN, Pinckney BN, Puri D, Shekleton TB, Tran QBT, Harbron EJ. Self-Reporting Conjugated Polymer Nanoparticles for Superoxide Generation and Detection. ACS APPLIED MATERIALS & INTERFACES 2024; 16:38478-38489. [PMID: 39007528 DOI: 10.1021/acsami.4c06749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Conjugated polymer nanoparticles (CPNs or Pdots) have become increasingly popular fluorophores for multimodal applications that combine imaging with phototherapeutic effects. Reports of CPNs in photodynamic therapy applications typically focus on their ability to generate singlet oxygen. Alternatively, CPN excited states can interact with oxygen to form superoxide radical anion and a CPN-based hole polaron, both of which can have deleterious effects on fluorescence properties. Here, we demonstrate that CPNs prepared from the common conjugated polymer poly[(9,9-dioctylfluorenyl-2,7-diyl)-alt-co-(1,4-benzo-{2,1',3}-thiadiazole)] (PFBT, also known as F8BT) generate superoxide upon irradiation. We use the same CPNs to detect superoxide by doping them with a superoxide-responsive hydrocyanine dye developed by Murthy and co-workers. Superoxide induces off-to-on fluorescence switching by converting quenching hydrocyanine dyes to fluorescent cyanine dyes that act as fluorescence resonance energy transfer (FRET) acceptors for PFBT chromophores. Amplified FRET from the multichromophoric CPNs yields fluorescence signal intensities that are nearly 50 times greater than when the dye is excited directly or over 100 times greater when signal readout is from the CPN channel. The dye loading level governs the maximum amount of superoxide that induces a change in fluorescence properties and also influences the rate of superoxide generation by furnishing competitive excited state deactivation pathways. These results suggest that CPNs can be used to deliver superoxide in applications in which it is desirable and provide a caution for fluorescence-based CPN applications in which superoxide can damage fluorophores.
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Affiliation(s)
- Anna L Clayborn
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Jaclyn A Rebstock
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Lauren J Camardella
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Elizabeth P Comeau
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Sonali K Dabhi
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Eleanor G Graber
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Thomas H Joyce
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Isabelle N Maricar
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Brianna N Pinckney
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Devika Puri
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Tayli B Shekleton
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Quyen Beatrice T Tran
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
| | - Elizabeth J Harbron
- Department of Chemistry, William & Mary, Williamsburg, Virginia 23187-8795, United States
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2
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Direct experimental observation of blue-light-induced conformational change and intermolecular interactions of cryptochrome. Commun Biol 2022; 5:1103. [PMID: 36257983 PMCID: PMC9579160 DOI: 10.1038/s42003-022-04054-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 09/30/2022] [Indexed: 11/30/2022] Open
Abstract
Cryptochromes are blue light receptors that mediate circadian rhythm and magnetic sensing in various organisms. A typical cryptochrome consists of a conserved photolyase homology region domain and a varying carboxyl-terminal extension across species. The structure of the flexible carboxyl-terminal extension and how carboxyl-terminal extension participates in cryptochrome’s signaling function remain mostly unknown. In this study, we uncover the potential missing link between carboxyl-terminal extension conformational changes and downstream signaling functions. Specifically, we discover that the blue-light induced opening of carboxyl-terminal extension in C. reinhardtii animal-like cryptochrome can structurally facilitate its interaction with Rhythm Of Chloroplast 15, a circadian-clock-related protein. Our finding is made possible by two technical advances. Using single-molecule Förster resonance energy transfer technique, we directly observe the displacement of carboxyl-terminal extension by about 15 Å upon blue light excitation. Combining structure prediction and solution X-ray scattering methods, we propose plausible structures of full-length cryptochrome under dark and lit conditions. The structures provide molecular basis for light active conformational changes of cryptochrome and downstream regulatory functions. Refined structures, protein-docking analysis and single molecule assays provides insights into light-induced conformational changes in the cryptochrome CraCRY.
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3
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Bartels K, Lasitza‐Male T, Hofmann H, Löw C. Single-Molecule FRET of Membrane Transport Proteins. Chembiochem 2021; 22:2657-2671. [PMID: 33945656 PMCID: PMC8453700 DOI: 10.1002/cbic.202100106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/03/2021] [Indexed: 12/31/2022]
Abstract
Uncovering the structure and function of biomolecules is a fundamental goal in structural biology. Membrane-embedded transport proteins are ubiquitous in all kingdoms of life. Despite structural flexibility, their mechanisms are typically studied by ensemble biochemical methods or by static high-resolution structures, which complicate a detailed understanding of their dynamics. Here, we review the recent progress of single molecule Förster Resonance Energy Transfer (smFRET) in determining mechanisms and timescales of substrate transport across membranes. These studies do not only demonstrate the versatility and suitability of state-of-the-art smFRET tools for studying membrane transport proteins but they also highlight the importance of membrane mimicking environments in preserving the function of these proteins. The current achievements advance our understanding of transport mechanisms and have the potential to facilitate future progress in drug design.
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Affiliation(s)
- Kim Bartels
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Tanya Lasitza‐Male
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Hagen Hofmann
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
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4
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Use of molecular homology model to identify inhibitors of Staphylococcus pseudintermedius sortase A. RESULTS IN CHEMISTRY 2021. [DOI: 10.1016/j.rechem.2021.100185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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5
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Quantifying Intramolecular Protein Conformational Dynamics Under Lipid Interaction Using smFRET and FCCS. Methods Mol Biol 2018. [PMID: 30317517 DOI: 10.1007/978-1-4939-8760-3_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fӧrster-type resonance energy transfer (FRET) with fluorescence cross-correlation spectroscopy (FCCS) is a powerful combination for observing intramolecular conformational dynamics on the micro- to millisecond timescale. Owing to its sensitivity to various physical parameters, FRET-FCCS has also been used to detect the reagent effects on proteins dynamics. However, FRET-FCCS alone cannot acquire the exact measurements of rate constants. Moreover, this technique is highly model dependent and can be unreliable when determining too many parameters at once. On the contrary, single-molecular FRET (smFRET) can measure the conformational states and their populations directly, although it is extremely challenging for probing fast dynamics under 1 ms. In this chapter, we describe how to realize sub-millisecond conformational dynamics measurements of a SNARE protein Ykt6 under lipid environments by smFRET and FRET-FCCS. This protocol includes sample preparation, microscope designs, data acquisition, and analysis methodology.
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6
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Optimal Background Estimators in Single-Molecule FRET Microscopy. Biophys J 2017; 111:1278-1286. [PMID: 27653486 DOI: 10.1016/j.bpj.2016.07.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 06/21/2016] [Accepted: 07/26/2016] [Indexed: 11/23/2022] Open
Abstract
Single-molecule total internal reflection fluorescence (TIRF) microscopy constitutes an umbrella of powerful tools that facilitate direct observation of the biophysical properties, population heterogeneities, and interactions of single biomolecules without the need for ensemble synchronization. Due to the low signal/noise ratio in single-molecule TIRF microscopy experiments, it is important to determine the local background intensity, especially when the fluorescence intensity of the molecule is used quantitatively. Here we compare and evaluate the performance of different aperture-based background estimators used particularly in single-molecule Förster resonance energy transfer. We introduce the general concept of multiaperture signatures and use this technique to demonstrate how the choice of background can affect the measured fluorescence signal considerably. A new, to our knowledge, and simple background estimator is proposed, called the local statistical percentile (LSP). We show that the LSP background estimator performs as well as current background estimators at low molecular densities and significantly better in regions of high molecular densities. The LSP background estimator is thus suited for single-particle TIRF microscopy of dense biological samples in which the intensity itself is an observable of the technique.
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7
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Maleki P, Budhathoki JB, Roy WA, Balci H. A practical guide to studying G-quadruplex structures using single-molecule FRET. Mol Genet Genomics 2017; 292:483-498. [PMID: 28150040 DOI: 10.1007/s00438-017-1288-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/05/2017] [Indexed: 11/26/2022]
Abstract
In this article, we summarize the knowledge and best practices learned from bulk and single-molecule measurements to address some of the frequently experienced difficulties in single-molecule Förster resonance energy transfer (smFRET) measurements on G-quadruplex (GQ) structures. The number of studies that use smFRET to investigate the structure, function, dynamics, and interactions of GQ structures has grown significantly in the last few years, with new applications already in sight. However, a number of challenges need to be overcome before reliable and reproducible smFRET data can be obtained in measurements that include GQ. The annealing and storage conditions, the location of fluorophores on the DNA construct, and the ionic conditions of the experiment are some of the factors that are of critical importance for the outcome of measurements, and many of these manifest themselves in unique ways in smFRET assays. By reviewing these aspects and providing a summary of best practices, we aim to provide a practical guide that will help in successfully designing and performing smFRET studies on GQ structures.
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Affiliation(s)
- Parastoo Maleki
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | | | - William A Roy
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH, 44242, USA.
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8
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Liu Y, Yu P, Dyba M, Sousa R, Stagno JR, Wang YX. Applications of PLOR in labeling large RNAs at specific sites. Methods 2016; 103:4-10. [PMID: 27033177 PMCID: PMC10802919 DOI: 10.1016/j.ymeth.2016.03.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/15/2016] [Accepted: 03/22/2016] [Indexed: 12/18/2022] Open
Abstract
Incorporation of modified or labeled nucleotides at specific sites in RNAs is critical for gaining insights into the structure and function of RNAs. Preparation of site-specifically labeled large RNAs in amounts suitable for structural or functional studies is extremely difficult using current methodologies. The position-selective labeling of RNA, PLOR, is a recently developed method that makes such syntheses possible. PLOR allows incorporation of various probes, including (2)D/(13)C/(15)N-isotopic labels, Cy3/Cy5/Alexa488/Alexa555 fluorescent dyes, biotin and other chemical groups, into specific positions in long RNAs. Here, we describe in detail the use of PLOR to label RNAs at specific segment(s) or discrete sites.
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Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
| | - Ping Yu
- Structural Biophysics Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marzena Dyba
- Structural Biophysics Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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9
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Liu Y, Sousa R, Wang YX. Specific labeling: An effective tool to explore the RNA world. Bioessays 2015; 38:192-200. [DOI: 10.1002/bies.201500119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
| | - Rui Sousa
- Department of Biochemistry; University of Texas Health Science Center; San Antonio TX USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
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10
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Siraj N, El-Zahab B, Hamdan S, Karam TE, Haber LH, Li M, Fakayode SO, Das S, Valle B, Strongin RM, Patonay G, Sintim HO, Baker GA, Powe A, Lowry M, Karolin JO, Geddes CD, Warner IM. Fluorescence, Phosphorescence, and Chemiluminescence. Anal Chem 2015; 88:170-202. [PMID: 26575092 DOI: 10.1021/acs.analchem.5b04109] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Noureen Siraj
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Bilal El-Zahab
- Department of Mechanical and Materials Engineering, Florida International University , Miami, Florida 33174, United States
| | - Suzana Hamdan
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Tony E Karam
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Louis H Haber
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Min Li
- Process Development Center, Albemarle Corporation , Baton Rouge, Louisiana 70805, United States
| | - Sayo O Fakayode
- Department of Chemistry, Winston-Salem State University , Winston-Salem, North Carolina 27110, United States
| | - Susmita Das
- Department of Civil Engineering, Adamas Institute of Technology , Barasat, Kolkata 700126, West Bengal India
| | - Bertha Valle
- Department of Chemistry, Texas Southern University , Houston, Texas 77004, United States
| | - Robert M Strongin
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Gabor Patonay
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-4098, United States
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gary A Baker
- Department of Chemistry, University of Missouri Columbia , Columbia, Missouri 65211-7600, United States
| | - Aleeta Powe
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40208, United States
| | - Mark Lowry
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Jan O Karolin
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Chris D Geddes
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Isiah M Warner
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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11
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Hildebrandt LL, Preus S, Birkedal V. Quantitative single molecule FRET efficiencies using TIRF microscopy. Faraday Discuss 2015; 184:131-42. [PMID: 26416760 DOI: 10.1039/c5fd00100e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Förster resonance energy transfer (FRET) microscopy at the single molecule level has the potential to yield information on intra and intermolecular distances within the 2-10 nm range of molecules or molecular complexes that undergo frequent conformation changes. A pre-requirement for obtaining accurate distance information is to determine quantitative instrument independent FRET efficiency values. Here, we applied and evaluated a procedure to determine quantitative FRET efficiencies directly from individual fluorescence time traces of surface immobilized DNA molecules without the need for external calibrants. To probe the robustness of the approach over a wide range of FRET efficiencies we used a set of doubly labelled double stranded DNA samples, where the acceptor position was varied systematically. Interestingly, we found that fluorescence contributions arising from direct acceptor excitation following donor excitation are intrinsically taken into account in these conditions as other correction factors can compensate for inaccurate values of these parameters. We give here guidelines, that can be used through tools within the iSMS software (), for determining quantitative FRET and assess uncertainties linked with the procedure. Our results provide insights into the experimental parameters governing quantitative FRET determination, which is essential for obtaining accurate structural information from a wide range of biomolecules.
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Affiliation(s)
- Lasse L Hildebrandt
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
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12
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Søndergaard S, Aznauryan M, Haustrup EK, Schiøtt B, Birkedal V, Corry B. Dynamics of fluorescent dyes attached to G-quadruplex DNA and their effect on FRET experiments. Chemphyschem 2015; 16:2562-70. [PMID: 26174803 DOI: 10.1002/cphc.201500271] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/05/2015] [Indexed: 11/08/2022]
Abstract
FRET spectroscopy is a promising approach for investigating the dynamics of G-quadruplex DNA folds and improving the targeting of G-quadruplexes by potential anticancer compounds. To better interpret such experiments, classical and replica-exchange molecular dynamics simulations and fluorescence-lifetime measurements are used to understand the behavior of a range of Cy3-based dyes attached to the 3' end of G-quadruplex DNA. The simulations revealed that the dyes interact extensively with the G-quadruplex. Identification of preferred dye positions relative to the G-quadruplex in the simulations allows the impact of dye-DNA interactions on FRET results to be determined. All the dyes show significant deviations from the common approximation of being freely rotating and not interacting with the host, but one of the Cy3 dye analogues is slightly closer to this case.
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Affiliation(s)
- Siri Søndergaard
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C (Denmark).,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C (Denmark)
| | - Mikayel Aznauryan
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C (Denmark)
| | - Emil K Haustrup
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C (Denmark)
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C (Denmark).,Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C (Denmark)
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds vej 14, 8000 Aarhus C (Denmark).
| | - Ben Corry
- Research School of Biology, Australian National University, Linnaeus Way, Canberra ACT 2601 (Australia).
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13
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Shing Ho P, Mergny JL. Nucleic acid structure: a continuing tradition. Methods 2013; 64:1-2. [PMID: 24160748 DOI: 10.1016/j.ymeth.2013.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, CO 80523-1870, USA.
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14
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Mergny JL. Meeting report: Fourth international meeting on G-quadruplex Nucleic Acids (Singapore, July 1-4, 2013). Biochimie 2013; 95:2320-5. [PMID: 24120569 DOI: 10.1016/j.biochi.2013.08.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 08/27/2013] [Indexed: 11/19/2022]
Abstract
The fourth international meeting on G-quadruplex Nucleic Acids was held in the Nanyang Technological University (NTU) of Singapore. Over 150 participants gathered from more than 25 countries. Over 40 talks and 100 posters summarized our current knowledge of these unusual DNA and RNA structures.
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Affiliation(s)
- Jean-Louis Mergny
- Inserm U869, ARNA Laboratory, IECB, F-33600 Pessac, France; Univ. Bordeaux, ARNA Laboratory, F-33000 Bordeaux, France.
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