1
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Tse YWE, Yun HY, Wyatt HDM. Annealing and purification of fluorescently labeled DNA substrates for in vitro assays. STAR Protoc 2023; 4:102128. [PMID: 36853679 PMCID: PMC9958487 DOI: 10.1016/j.xpro.2023.102128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/09/2023] [Accepted: 02/03/2023] [Indexed: 02/22/2023] Open
Abstract
We present a protocol to generate high-quality fluorescently labeled DNA substrates that can be used for biochemical assays, including DNA-binding and nuclease activity assays. We describe polyacrylamide-gel-electrophoresis-based purification of DNA oligonucleotides, followed by annealing the oligonucleotides and purifying the annealed substrates using anion-exchange chromatography. This protocol circumvents the use of radioisotopes, which require training and dedicated equipment for safe handling and necessitate specialized waste disposal. This protocol is amenable to varying lengths of oligonucleotides and DNA substrates. For complete details on the use and execution of this protocol, please refer to Payliss and Tse et al. (2022).1.
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Affiliation(s)
| | - Hwa Young Yun
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Haley Doris Myskiw Wyatt
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Canada Research Chairs Program, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
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2
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Lietard J, Ameur D, Somoza MM. Sequence-dependent quenching of fluorescein fluorescence on single-stranded and double-stranded DNA. RSC Adv 2022; 12:5629-5637. [PMID: 35425544 PMCID: PMC8982050 DOI: 10.1039/d2ra00534d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 02/01/2023] Open
Abstract
Fluorescein is commonly used to label macromolecules, particularly proteins and nucleic acids, but its fluorescence is known to be strongly dependent on its direct chemical environment.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Dominik Ameur
- Institute of Inorganic Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Mark M. Somoza
- Institute of Inorganic Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
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3
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Delgadillo RF, Carnes KA, Zaleta-Rivera K, Olmos O, Parkhurst LJ. A FLIM Microscopy Based on Acceptor-Detected Förster Resonance Energy Transfer. Anal Chem 2021; 93:4841-4849. [PMID: 33691398 PMCID: PMC7992049 DOI: 10.1021/acs.analchem.0c04492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/01/2021] [Indexed: 12/28/2022]
Abstract
Time-resolved donor-detected Förster resonance energy transfer (trDDFRET) allows the observation of molecular interactions of dye-labeled biomolecules in the ∼10-100 Å region. However, we can observe longer-range interactions when using time-resolved acceptor-detected FRET (trADFRET), since the signal/noise ratio can be improved when observing the acceptor emission. Therefore, we propose a new methodology based on trADFRET to construct a new fluorescence lifetime microscopy (FLIM-trADFRET) technique to observe biological machinery in the range of 100-300 Å in vivo, the last frontier in biomolecular medicine. The integrated trADFRET signal is extracted in such a way that noise is canceled, and more photons are collected, even though trADFRET and trDDFRET have the same rate of transfer. To assess our new methodology, proof of concept was demonstrated with a set of well-defined DNA scaffolds.
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Affiliation(s)
- Roberto F. Delgadillo
- Department
of Chemistry, University of Nebraska - Lincoln, Lincoln, Nebraska 68588-0304, United States
- Tecnologico
de Monterrey, School of Engineering and
Sciences, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo Leon 64849, Monterrey, Mexico
- BASF
Enzymes LLC, 3550 John
Hopkins Ct, San Diego, California 92121, United States
| | - Katie A. Carnes
- GlaxoSmithKline,
Medicinal Science and Technology, CMC Analytical − Drug Substance
and Product Analysis, King of
Prussia, Pennsylvania, 19406, United States
| | - Kathia Zaleta-Rivera
- Department
of Bioengineering, University of California
San Diego, San Diego, California, 92093-0412, United States
| | - Omar Olmos
- Tecnologico
de Monterrey, School of Engineering and
Sciences, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo Leon 64849, Monterrey, Mexico
| | - Lawrence J. Parkhurst
- Department
of Chemistry, University of Nebraska - Lincoln, Lincoln, Nebraska 68588-0304, United States
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4
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Dual-Channel Stopped-Flow Apparatus for Simultaneous Fluorescence, Anisotropy, and FRET Kinetic Data Acquisition for Binary and Ternary Biological Complexes. BIOSENSORS 2020; 10:bios10110180. [PMID: 33227895 PMCID: PMC7699296 DOI: 10.3390/bios10110180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/24/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
The Stopped-Flow apparatus (SF) tracks molecular events by mixing the reactants in sub-millisecond regimes. The reaction of intrinsically or extrinsically labeled biomolecules can be monitored by recording the fluorescence, F(t), anisotropy, r(t), polarization, p(t), or FRET, F(t)FRET, traces at nanomolar concentrations. These kinetic measurements are critical to elucidate reaction mechanisms, structural information, and even thermodynamics. In a single detector SF, or L-configuration, the r(t), p(t), and F(t) traces are acquired by switching the orientation of the emission polarizer to collect the IVV and IVH signals however it requires two-shot experiments. In a two-detector SF, or T-configuration, these traces are collected in a single-shot experiment, but it increases the apparatus’ complexity and price. Herein, we present a single-detector dual-channel SF to obtain the F(t) and r(t) traces simultaneously, in which a photo-elastic modulator oscillates by 90° the excitation light plane at a 50 kHz frequency, and the emission signal is processed by a set of electronic filters that split it into the r(t) and F(t) analog signals that are digitized and stored into separated spreadsheets by a custom-tailored instrument control software. We evaluated the association kinetics of binary and ternary biological complexes acquired with our dual-channel SF and the traditional methods; such as a single polarizer at the magic angle to acquire F(t), a set of polarizers to track F(t), and r(t), and by energy transfer quenching, F(t)FRET. Our dual-channel SF economized labeled material and yielded rate constants in excellent agreement with the traditional methods.
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5
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Lee S, Kawamoto Y, Vaijayanthi T, Park J, Bae J, Kim-Ha J, Sugiyama H, Jo K. TAMRA-polypyrrole for A/T sequence visualization on DNA molecules. Nucleic Acids Res 2019; 46:e108. [PMID: 29931115 PMCID: PMC6182132 DOI: 10.1093/nar/gky531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/29/2018] [Indexed: 01/23/2023] Open
Abstract
Fluorophore-linked, sequence-specific DNA binding reagents can visualize sequence information on a large DNA molecule. In this paper, we synthesized newly designed TAMRA-linked polypyrrole to visualize adenine and thymine base pairs. A fluorescent image of the stained DNA molecule generates an intensity profile based on A/T frequency, revealing a characteristic sequence composition pattern. Computer-aided comparison of this intensity pattern with the genome sequence allowed us to determine the DNA sequence on a visualized DNA molecule from possible intensity profile pattern candidates for a given genome. Moreover, TAMRA-polypyrrole offers robust advantages for single DNA molecule detection: no fluorophore-mediated photocleavage and no structural deformation, since it exhibits a sequence-specific pattern alone without the use of intercalating dyes such as YOYO-1. Accordingly, we were able to identify genomic DNA fragments from Escherichia coli cells by aligning them to the genomic A/T frequency map based on TAMRA-polypyrrole-generated intensity profiles. Furthermore, we showed band and interband patterns of polytene chromosomal DNA stained with TAMRA-polypyrrole because it prefers to bind AT base pairs.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Thangavel Vaijayanthi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Jihyun Park
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Jaeyoung Bae
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Jeongsil Kim-Ha
- Department of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
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6
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Castro NS, Moura I, Carepo MS, Laia CA. Fluorescence anisotropy of fluorescein derivative varies according to pH: Lessons for binding studies. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2018.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Delgadillo RF, Mueser TC, Zaleta-Rivera K, Carnes KA, González-Valdez J, Parkhurst LJ. Detailed characterization of the solution kinetics and thermodynamics of biotin, biocytin and HABA binding to avidin and streptavidin. PLoS One 2019; 14:e0204194. [PMID: 30818336 PMCID: PMC6394990 DOI: 10.1371/journal.pone.0204194] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 02/01/2019] [Indexed: 01/02/2023] Open
Abstract
The high affinity (KD ~ 10−15 M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (kon) is approximately diffusion limited (109 M-1s-1) but recent single molecule and surface binding studies indicate that they are slower than expected (105 to 107 M-1s-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic cycle describes the complex formation, and if there are any functional differences between avidin and streptavidin. We have studied the biotin association by two stopped-flow methodologies using labeled and unlabeled probes: I) fluorescent probes attached to biotin and biocytin; and II) unlabeled biotin and HABA, 2-(4’-hydroxyazobenzene)-benzoic acid. Both native avidin and streptavidin are homo-tetrameric and the association data show no cooperativity between the binding sites. The kon values of streptavidin are faster than avidin but slower than expected for a diffusion limited reaction in both complexes. Moreover, the Arrhenius plots of the kon values revealed strong temperature dependence with large activation energies (6–15 kcal/mol) that do not correspond to a diffusion limited process (3–4 kcal/mol). Accordingly, we propose a simple reaction model with a single transition state for non-immobilized reactants whose forward thermodynamic parameters complete the thermodynamic cycle, in agreement with previously reported studies. Our new understanding and description of the kinetics, thermodynamics, and spectroscopic parameters for these complexes will help to improve purification efficiencies, molecule detection, and drug screening assays or find new applications.
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Affiliation(s)
- Roberto F. Delgadillo
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (RFD); (LJP)
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, United States of America
| | - Kathia Zaleta-Rivera
- Department of Bioengineering, University of California San Diego, San Diego, California, United States of America
| | - Katie A. Carnes
- GlaxoSmithKline, Medicinal Science and Technology, R&D, King of Prussia, Pennsylvania, United States of America
| | - José González-Valdez
- Tecnologico de Monterrey, School of Engineering and Science, NL, Monterrey, Mexico
| | - Lawrence J. Parkhurst
- Department of Chemistry, University of Nebraska—Lincoln, Lincoln, Nebraska, United States of America
- * E-mail: (RFD); (LJP)
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8
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Sun J, Zhao J, Wang L, Li H, Yang F, Yang X. Inner Filter Effect-Based Sensor for Horseradish Peroxidase and Its Application to Fluorescence Immunoassay. ACS Sens 2018; 3:183-190. [PMID: 29260859 DOI: 10.1021/acssensors.7b00830] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Being an important model peroxidase, horseradish peroxidase (HRP) has been thoroughly understood, and the detection of HRP is not only directly related to peroxidase-triggered catalytic process, but also linked to the development of HRP-based enzyme-linked immunosorbent assay (ELISA). Herein, we have reported an unconventional fluorescent sensor for convenient assay of HRP activity based on the HRP-catalyzed specific conversion of p-phenylenediamine (PPD) into chromogenic PPDox with H2O2 as the oxidizing agent, accompanied by the fluorescence quenching effect on fluorescein. By combining UV-vis absorption spectrum, isothermal titration calorimetry, and fluorescence lifetime analysis, we have confirmed the inner filter effect as a main quenching mechanism in our proposed fluorescent assay. According to the intrinsic sensitivity of fluorescent sensor and high selectivity, our PPD/fluorescein-based sensing system can be utilized for real-time monitoring of the HRP activity in real biological samples. Furthermore, the unambiguous response mechanism and excellent sensing performance encourage us to extend such HRP assay into the HRP-based fluorescent ELISA, which has a broad prospect of application in fluorescent diagnosis of hepatocellular carcinoma (HCC) by sensing alpha-fetoprotein, the well-known serologic HCC marker.
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Affiliation(s)
- Jian Sun
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jiahui Zhao
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Hongwei Li
- State
Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, Jilin 130012, China
| | - Fan Yang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiurong Yang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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9
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Gordon SE, Senning EN, Aman TK, Zagotta WN. Transition metal ion FRET to measure short-range distances at the intracellular surface of the plasma membrane. ACTA ACUST UNITED AC 2016; 147:189-200. [PMID: 26755772 PMCID: PMC4727948 DOI: 10.1085/jgp.201511530] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/21/2015] [Indexed: 11/20/2022]
Abstract
A novel method is presented to measure short distances in cell plasma membranes using transition metal ion FRET with metal ions bound to introduced sites in the membrane. Biological membranes are complex assemblies of lipids and proteins that serve as platforms for cell signaling. We have developed a novel method for measuring the structure and dynamics of the membrane based on fluorescence resonance energy transfer (FRET). The method marries four technologies: (1) unroofing cells to isolate and access the cytoplasmic leaflet of the plasma membrane; (2) patch-clamp fluorometry (PCF) to measure currents and fluorescence simultaneously from a membrane patch; (3) a synthetic lipid with a metal-chelating head group to decorate the membrane with metal-binding sites; and (4) transition metal ion FRET (tmFRET) to measure short distances between a fluorescent probe and a transition metal ion on the membrane. We applied this method to measure the density and affinity of native and introduced metal-binding sites in the membrane. These experiments pave the way for measuring structural rearrangements of membrane proteins relative to the membrane.
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Affiliation(s)
- Sharona E Gordon
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Eric N Senning
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Teresa K Aman
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - William N Zagotta
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
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10
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Xiong X, Huang J, Wang X. DNA binding studies of hematoxylin-Dy(ш) complex by spectrometry using acridine orange as a probe. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 33:730-45. [PMID: 25295749 DOI: 10.1080/15257770.2014.931589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The interaction of a hematoxylin(HE)-Dy(Ш) complex with herring sperm DNA(hsDNA) was studied using acridine orange(AO) as a probe by UV-vis absorption, circular dichroism(CD), fluorescence spectroscopy and viscosity measurements. From the results of the probe experiment, we found that the HE-Dy(Ш) complex could compete with AO for intercalating into hsDNA. The binding constants of the HE-Dy(Ш) complex to hsDNA was obtained by the double reciprocal method and indicated that the affinity between hsDNA and the complex is weaker than that between hsDNA and classical intercalators. The thermodynamic parameters(ΔH°, ΔG°, ΔS°) were calculated from the UV-vis absorption data measured at two different temperatures. Further experimental results suggested that there exist groove binding and partial intercalation binding between hsDNA and HE-Dy(Ш) complex.
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Affiliation(s)
- Xiaoli Xiong
- a College of Chemistry and Materials Science , Sichuan Normal University , Chengdu , P.R.China
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11
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Flory JD, Shinde S, Lin S, Liu Y, Yan H, Ghirlanda G, Fromme P. PNA-peptide assembly in a 3D DNA nanocage at room temperature. J Am Chem Soc 2013; 135:6985-93. [PMID: 23521013 DOI: 10.1021/ja400762c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteins and peptides fold into dynamic structures that access a broad functional landscape; however, designing artificial polypeptide systems is still a great challenge. Conversely, DNA engineering is now routinely used to build a wide variety of 2D and 3D nanostructures from hybridization based rules, and their functional diversity can be significantly expanded through site specific incorporation of the appropriate guest molecules. Here we demonstrate a new approach to rationally design 3D nucleic acid-amino acid complexes using peptide nucleic acid (PNA) to assemble peptides inside a 3D DNA nanocage. The PNA-peptides were found to bind to the preassembled DNA nanocage in 5-10 min at room temperature, and assembly could be performed in a stepwise fashion. Biophysical characterization of the DNA-PNA-peptide complex was performed using gel electrophoresis as well as steady state and time-resolved fluorescence spectroscopy. Based on these results we have developed a model for the arrangement of the PNA-peptides inside the DNA nanocage. This work demonstrates a flexible new approach to leverage rationally designed nucleic acid (DNA-PNA) nanoscaffolds to guide polypeptide engineering.
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Affiliation(s)
- Justin D Flory
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, Arizona 85287, United States
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12
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Zhang XF, Li F. Interaction of graphene with excited and ground state rhodamine revealed by steady state and time resolved fluorescence. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.06.025] [Citation(s) in RCA: 26] [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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13
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Preus S, Wilhelmsson LM. Advances in quantitative FRET-based methods for studying nucleic acids. Chembiochem 2012; 13:1990-2001. [PMID: 22936620 DOI: 10.1002/cbic.201200400] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Indexed: 01/02/2023]
Abstract
Förster resonance energy transfer (FRET) is a powerful tool for monitoring molecular distances and interactions at the nanoscale level. The strong dependence of transfer efficiency on probe separation makes FRET perfectly suited for "on/off" experiments. To use FRET to obtain quantitative distances and three-dimensional structures, however, is more challenging. This review summarises recent studies and technological advances that have improved FRET as a quantitative molecular ruler in nucleic acid systems, both at the ensemble and at the single-molecule levels.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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14
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Pinheiro AV, Nangreave J, Jiang S, Yan H, Liu Y. Steric crowding and the kinetics of DNA hybridization within a DNA nanostructure system. ACS NANO 2012; 6:5521-5530. [PMID: 22559169 DOI: 10.1021/nn301448y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The ability to generate precisely designed molecular networks and modulate the surrounding environment is vital for fundamental studies of chemical reactions. DNA nanotechnology simultaneously affords versatility and modularity for the construction of tailored molecular environments. We systematically studied the effects of steric crowding on the hybridization of a 20 nucleotide (nt) single-stranded DNA (ssDNA) target to a complementary probe strand extended from a rectangular six-helix tile, where the number and character of the surrounding strands influence the molecular environment of the hybridization site. The hybridization events were monitored through an increase in the quantum yield of a single reporter fluorophore (5-carboxyfluorescein) upon hybridization of the 20-nt ssDNA, an effect previously undocumented in similar systems. We observed that as the hybridization site moved from outer to inner positions along the DNA tile, the hybridization rate constant decreased. A similar rate decrease was observed when noncomplementary single- and double-stranded DNA flanked the hybridization site. However, base-pairing interactions between the hybridization site of the probe and the surrounding DNA resulted in a reduction in the reaction kinetics. The decreases in the hybridization rate constants can be explained by the reduced probability of successful nucleation of the invading ssDNA target to the complementary probe.
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Affiliation(s)
- Andre V Pinheiro
- The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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15
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Ranjit S, Levitus M. Probing the interaction between fluorophores and DNA nucleotides by fluorescence correlation spectroscopy and fluorescence quenching. Photochem Photobiol 2012; 88:782-91. [PMID: 22364288 DOI: 10.1111/j.1751-1097.2012.01121.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated the association interactions between the fluorescent dyes TAMRA, Cy3B and Alexa-546 and the DNA deoxynucleoside monophosphates by means of fluorescence quenching and fluorescence correlation spectroscopy (FCS). The interactions of Cy3B and TAMRA with the nucleotides produce a decrease in the apparent diffusion coefficient of the dyes, which result in a shift toward longer times in the FCS autocorrelation decays. Our results with Cy3B demonstrate the existence of Cy3B-nucleotide interactions that do not affect the fluorescence intensity or lifetime of the dye significantly. The same is true for TAMRA in the presence of dAMP, dCMP and dTMP. In contrast, the diffusion coefficient of Alexa 546 remains practically unchanged even at high concentrations of nucleotide. These results demonstrate that interactions between this dye and the four dNMPs are not significant. The presence of the negatively charged sulfonates and the bulky chlorine atoms in the phenyl group of Alexa 546 possibly prevent strong interactions that are otherwise possible for TAMRA. The characterization of dye-DNA interactions is important in biophysical research because they play an important role in the interpretation of energy transfer experiments, and because they can potentially affect the structure and dynamics of the DNA.
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Affiliation(s)
- Suman Ranjit
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ, USA
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16
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Linck L, Kapusta P, Resch-Genger U. Spectroscopic and photophysical properties of dUTP and internally DNA bound fluorophores for optimized signal detection in biological formats. Photochem Photobiol 2012; 88:867-75. [PMID: 22360746 DOI: 10.1111/j.1751-1097.2012.01119.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Efficient signal generation in DNA-based assays requires understanding of the influence of fluorophore's interactions on the spectroscopic properties. The resulting changes in fluorescence intensity, quantum yield, emission anisotropy, and fluorescence lifetime provide straightforward tools for the study of molecular dynamics and interaction between labels and nucleic acids. Searching for bright fluorescent reporters for rolling circle amplification (RCA) as efficient signal enhancement strategy for biological formats, we investigated the spectroscopic properties of seven dyes: cyanines, rhodamines, and BODIPYs. They spectrally resemble Cy3, the most frequently used fluorophore in biodetection formats, and are measured in six samples (free dye, dye-dUTP, internally labeled ssDNA and dsDNA-single- and triple-labeled) using steady-state and time-resolved fluorometry. Special emphasis was dedicated to characterizing the nature of the interaction of these fluorophores differing in dye class, charge, and rigidity. Our results suggest dye charge and structure as main factors governing the dye's interactions, with DY-555 and Cy3B presenting the best candidates for our envisaged signal amplification strategy. This label comparison underlines the importance of a proper understanding of structure-property relations and dye-biomolecule interactions for reporter choice and presents a road map towards the design and interpretation of experiments using these labels on DNA of known sequence.
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Affiliation(s)
- Lena Linck
- BAM Federal Institute for Materials Research and Testing, Berlin, Germany
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17
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Segal M, Fischer B. Analogues of uracil nucleosides with intrinsic fluorescence (NIF-analogues): synthesis and photophysical properties. Org Biomol Chem 2012; 10:1571-80. [PMID: 22222762 DOI: 10.1039/c1ob06536j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Uridine cannot be utilized as fluorescent probe due to its extremely low quantum yield. For improving the uracil fluorescence characteristics we extended the natural chromophore at the C5 position by coupling substituted aromatic rings directly or via an alkenyl or alkynyl linker to create fluorophores. Extension of the uracil base was achieved by treating 5-I-uridine with the appropriate boronic acid under the Suzuki coupling conditions. Analogues containing an alkynyl linker were obtained from 5-I-uridine and the suitable boronic acid in a Sonogashira coupling reaction. The uracil fluorescent analogues proposed here were designed to satisfy the following requirements: a minimal chemical modification at a position not involved in base-pairing, resulting in relatively long absorption and emission wavelengths and high quantum yield. 5-((4-Methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6b, was found to be a promising fluorescent probe. Probe 6b exhibits a quantum yield that is 3000-fold larger than that of the natural chromophore (Φ 0.12), maximum emission (478 nm) which is 170 nm red shifted as compared to uridine, and a Stokes shift of 143 nm. In addition, since probe 6b adopts the anti conformation and S sugar puckering favored by B-DNA, it makes a promising nucleoside analogue to be incorporated in an oligonucleotide probe for detection of genetic material.
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Affiliation(s)
- Meirav Segal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 52900, Israel
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Lei J, Wang L, Zhang J. Superbright multifluorescent core-shell mesoporous nanospheres as trackable transport carrier for drug. ACS NANO 2011; 5:3447-3455. [PMID: 21446756 DOI: 10.1021/nn103254g] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A novel kind of monodisperse core-shell silica nanosphere composed of a fluorescent solid core and a mesoporous shell has been successfully fabricated. These nanospheres exhibit multifluorescent signals under a single-wavelength excitation as a result of the solid silica core that is doped with three kinds of dyes and that can produce effective fluorescence resonance energy transfer. The fluorescent signal of a single nanosphere is about 700 times brighter than its constituent fluorophores. X-ray diffraction, transmission electron microscopy, and N(2) adsorption-desorption isotherms reveal that these nanospheres possess abundant mesopores in the shell. Combining the advantages of extremely bright multifluorescent signals excited with a single wavelength and an abundant mesoporous system, this core-shell silica nanosphere is designed for the simultaneous monitoring of fluorescence of in vivo multiple-target drug transport. Experiments on drug loading and release in addition to studies on cell uptake reveal that these nanospheres not only show good drug storage and sustained release capacity but also demonstrate biocompatibility and mutlifluorescent labeling capacity for biological systems.
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Affiliation(s)
- Juying Lei
- Key Lab for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
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