1
|
Grazon C, Chern M, Lally P, Baer RC, Fan A, Lecommandoux S, Klapperich C, Dennis AM, Galagan JE, Grinstaff MW. The quantum dot vs. organic dye conundrum for ratiometric FRET-based biosensors: which one would you chose? Chem Sci 2022; 13:6715-6731. [PMID: 35756504 PMCID: PMC9172442 DOI: 10.1039/d1sc06921g] [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: 12/11/2021] [Accepted: 05/04/2022] [Indexed: 11/21/2022] Open
Abstract
Förster resonance energy transfer (FRET) is a widely used and ideal transduction modality for fluorescent based biosensors as it offers high signal to noise with a visibly detectable signal. While intense efforts are ongoing to improve the limit of detection and dynamic range of biosensors based on biomolecule optimization, the selection of and relative location of the dye remains understudied. Herein, we describe a combined experimental and computational study to systematically compare the nature of the dye, i.e., organic fluorophore (Cy5 or Texas Red) vs. inorganic nanoparticle (QD), and the position of the FRET donor or acceptor on the biomolecular components. Using a recently discovered transcription factor (TF)-deoxyribonucleic acid (DNA) biosensor for progesterone, we examine four different biosensor configurations and report the quantum yield, lifetime, FRET efficiency, IC50, and limit of detection. Fitting the computational models to the empirical data identifies key molecular parameters driving sensor performance in each biosensor configuration. Finally, we provide a set of design parameters to enable one to select the fluorophore system for future intermolecular biosensors using FRET-based conformational regulation in in vitro assays and new diagnostic devices.
Collapse
Affiliation(s)
- Chloé Grazon
- Department of Chemistry, Boston University Boston MA 02215 USA .,University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629 F-33600 Pessac France .,University Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255 F-33400 Talence France
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University Boston MA 02215 USA
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University Boston MA 02215 USA
| | - R. C. Baer
- Department of Microbiology, Boston UniversityBostonMA 02118USA,National Emerging Infectious Diseases Laboratories, Boston UniversityBostonMA 02118USA
| | - Andy Fan
- Department of Biomedical Engineering, Boston University Boston MA 02215 USA
| | | | | | - Allison M. Dennis
- Division of Materials Science and Engineering, Boston UniversityBostonMA 02215USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA
| | - James E. Galagan
- Department of Microbiology, Boston UniversityBostonMA 02118USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA,National Emerging Infectious Diseases Laboratories, Boston UniversityBostonMA 02118USA
| | - Mark W. Grinstaff
- Department of Chemistry, Boston UniversityBostonMA 02215USA,Division of Materials Science and Engineering, Boston UniversityBostonMA 02215USA,Department of Biomedical Engineering, Boston UniversityBostonMA 02215USA
| |
Collapse
|
2
|
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]
|
3
|
Billet B, Chovelon B, Fiore E, Faure P, Ravelet C, Peyrin E. Detection of small molecules by fluorescence intensity using single dye labeled aptamers and quencher transition metal ions. Biosens Bioelectron 2022; 205:114091. [PMID: 35217256 DOI: 10.1016/j.bios.2022.114091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 12/29/2022]
Abstract
We describe herein an aptamer-based sensing approach that signal the presence of small-molecule targets when fluorescent DNA probes are challenged with the Ni2+ or Co2+ quencher metal ions. Functional oligonucleotides targeting L-tyrosinamide (L-Tym), adenosine (Ade) or cocaine (Coc) were end-labeled by the Texas-Red fluorophore. A fluorescence quenching occurred upon association of these transition metal ions with the free conjugates. The formation of the target-probe complex, by the way of variations in the overall binding of quencher metal ions along the DNA strands, led to a partial restoration (for the Ade and Coc systems) or a further attenuation (for the L-Tym system) of the fluorescence intensity. The absolute signal gain varied from 40 to 180% depending on the target-probe pair investigated. The approach was also used to detect the compound Ade in a spiked biological matrix in 1 min or less. The transition metal ion-based quenching strategy is characterized by its very simple implementation, low cost, and rapid signaling.
Collapse
Affiliation(s)
- Blandine Billet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Benoit Chovelon
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Patrice Faure
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; Biochemistry, Toxicology and Pharmacology Department, Grenoble Site Nord CHU - Biology and Pathology Institute, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France
| | - Corinne Ravelet
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
| | - Eric Peyrin
- University Grenoble Alpes, DPM UMR 5063, F-38041, Grenoble, France; CNRS, DPM UMR 5063, F-38041, Grenoble, France.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
El-Shobaky A, Elshafey R, Radi AE. Spectroscopic and electrochemical approaches for the analysis of interaction between textile dye 231 and salmon sperm DNA. CAN J CHEM 2021. [DOI: 10.1139/cjc-2021-0144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA is one of the most critical targets for many artificial agents listed as carcinogens. Most of them irreversibly bind to the DNA and induce genome mutation; therefore, it is vital to study the nature of binding of these molecules to anticipate their toxicity. The interaction between the textile dye reactive red 231 and salmon sperm double-stranded DNA (ss-dsDNA) was investigated by cyclic voltammetry (CV), differential pulse voltammetry (DPV), and ultraviolet-visible spectroscopy (UV–vis spectroscopy). Changes in the anodic current signals of the dye were observed in the presence and absence of ss-dsDNA at a glassy carbon electrode (GCE) using CV. The diffusion coefficient (D) was found to be 2.2 × 10–7 and 9.5 × 10–8 cm2 s−1 from the CV data for the free dye and dye-DNA complex, respectively. Electrochemical and UV–vis spectroscopy indicated 1:1 complex formation of the dye with DNA. The binding constant (kb) between the dye and DNA was calculated to be 5.4 × 105 M–1 and 4.9 × 105 M–1 at pH 4.0 using CV and UV–vis spectroscopy, respectively. Overall, these results suggest that the dye binds to DNA through the combined effect of intercalation and electrostatic interactions. DNA damage was also detected through changes in the voltammetric behaviour of the dye.
Collapse
Affiliation(s)
- Amira El-Shobaky
- Department of Chemistry, Faculty of Science, Damietta University, Damietta 34517, Egypt
- Department of Chemistry, Faculty of Science, Damietta University, Damietta 34517, Egypt
| | - Reda Elshafey
- Department of Chemistry, Faculty of Science, Damietta University, Damietta 34517, Egypt
- Department of Chemistry, Faculty of Science, Damietta University, Damietta 34517, Egypt
| | - Abd-Elgawad Radi
- Department of Chemistry, Faculty of Science, Damietta University, Damietta 34517, Egypt
- Department of Chemistry, Faculty of Science, Damietta University, Damietta 34517, Egypt
| |
Collapse
|
6
|
Chettri A, Kruse JH, Kumar Jha K, Dröge L, Romanenko I, Neumann C, Kupfer S, Turchanin A, Rau S, Schacher FH, Dietzek B. A Molecular Photosensitizer in a Porous Block Copolymer Matrix-Implications for the Design of Photocatalytically Active Membranes. Chemistry 2021; 27:17049-17058. [PMID: 34636457 PMCID: PMC9291506 DOI: 10.1002/chem.202102377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Indexed: 11/12/2022]
Abstract
Recently, porous photocatalytically active block copolymer membranes were introduced, based on heterogenized molecular catalysts. Here, we report the integration of the photosensitizer, i. e., the light absorbing unit in an intermolecular photocatalytic system into block copolymer membranes in a covalent manner. We study the resulting structure and evaluate the orientational mobility of the photosensitizer as integral part of the photocatalytic system in such membranes. To this end we utilize transient absorption anisotropy, highlighting the temporal reorientation of the transition dipole moment probed in a femtosecond pump‐probe experiment. Our findings indicate that the photosensitizer is rigidly bound to the polymer membrane and shows a large heterogeneity of absolute anisotropy values as a function of location probed within the matrix. This reflects the sample inhomogeneity arising from different protonation states of the photosensitizer and different intermolecular interactions of the photosensitizers within the block copolymer membrane scaffold.
Collapse
Affiliation(s)
- Avinash Chettri
- Department Functional Interfaces, Leibniz Institute of Photonic Technology (IPHT) e.V., Albert Einstein Straße 9, 07747, Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Jan-Hendrik Kruse
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany
| | - Keshav Kumar Jha
- Department Functional Interfaces, Leibniz Institute of Photonic Technology (IPHT) e.V., Albert Einstein Straße 9, 07747, Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Lara Dröge
- Department Functional Interfaces, Leibniz Institute of Photonic Technology (IPHT) e.V., Albert Einstein Straße 9, 07747, Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Iuliia Romanenko
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany
| | - Christof Neumann
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Stephan Kupfer
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
| | - Andrey Turchanin
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany.,Jena Center for Soft Matter (JCSM), Philosophenweg 7, 07743, Jena, Germany
| | - Sven Rau
- Institute of Inorganic Chemistry I, Ulm University, Albert Einstein Allee 11, 89081, Ulm, Germany
| | - Felix H Schacher
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.,Jena Center for Soft Matter (JCSM), Philosophenweg 7, 07743, Jena, Germany
| | - Benjamin Dietzek
- Department Functional Interfaces, Leibniz Institute of Photonic Technology (IPHT) e.V., Albert Einstein Straße 9, 07747, Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, 07743, Jena, Germany
| |
Collapse
|
7
|
Billet B, Chovelon B, Fiore E, Oukacine F, Petrillo MA, Faure P, Ravelet C, Peyrin E. Aptamer Switches Regulated by Post-Transition/Transition Metal Ions. Angew Chem Int Ed Engl 2021; 60:12346-12350. [PMID: 33742515 DOI: 10.1002/anie.202102254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Indexed: 12/11/2022]
Abstract
We introduced an aptamer switch design that relies on the ability of post-transition/transition metal ions to trigger, through their coordination to nucleobases, substantial DNA destabilization. In the absence of molecular target, the addition of one such metal ion to usual aptamer working solutions promotes the formation of an alternative, inert DNA state. Upon exposure to the cognate compound, the equilibrium is shifted towards the competent DNA form. The switching process was preferentially activated by metal ions of intermediate base over phosphate complexation preference (i.e. Pb2+ , Cd2+ ) and operated with diversely structured DNA molecules. This very simple aptamer switch scheme was applied to the detection of small organics using the fluorescence anisotropy readout mode. We envision that the approach could be adapted to a variety of signalling methods that report on changes in the surface charge density of DNA receptors.
Collapse
Affiliation(s)
- Blandine Billet
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Benoit Chovelon
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Emmanuelle Fiore
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | - Farid Oukacine
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | | | - Patrice Faure
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France.,Biochemistry, Toxicology and Pharmacology Department, Grenoble site Nord CHU- Biology and Pathology Institute, 38041, Grenoble, France
| | - Corinne Ravelet
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| | - Eric Peyrin
- DPM UMR 5063, University Grenoble Alpes, CNRS, 38041, Grenoble, France
| |
Collapse
|
8
|
Billet B, Chovelon B, Fiore E, Oukacine F, Petrillo M, Faure P, Ravelet C, Peyrin E. Aptamer Switches Regulated by Post‐Transition/Transition Metal Ions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Blandine Billet
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Benoit Chovelon
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Emmanuelle Fiore
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | - Farid Oukacine
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | | | - Patrice Faure
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
- Biochemistry, Toxicology and Pharmacology Department Grenoble site Nord CHU- Biology and Pathology Institute 38041 Grenoble France
| | - Corinne Ravelet
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| | - Eric Peyrin
- DPM UMR 5063 University Grenoble Alpes CNRS 38041 Grenoble France
| |
Collapse
|
9
|
Singh RK, Jonely M, Leslie E, Rejali NA, Noriega R, Bass BL. Transient kinetic studies of the antiviral Drosophila Dicer-2 reveal roles of ATP in self-nonself discrimination. eLife 2021; 10:65810. [PMID: 33787495 PMCID: PMC8079148 DOI: 10.7554/elife.65810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/31/2021] [Indexed: 11/25/2022] Open
Abstract
Some RIG-I-like receptors (RLRs) discriminate viral and cellular dsRNA by their termini, and Drosophila melanogaster Dicer-2 (dmDcr-2) differentially processes dsRNA with blunt or 2 nucleotide 3’-overhanging termini. We investigated the transient kinetic mechanism of the dmDcr-2 reaction using a rapid reaction stopped-flow technique and time-resolved fluorescence spectroscopy. Indeed, we found that ATP binding to dmDcr-2’s helicase domain impacts association and dissociation kinetics of dsRNA in a termini-dependent manner, revealing termini-dependent discrimination of dsRNA on a biologically relevant time scale (seconds). ATP hydrolysis promotes transient unwinding of dsRNA termini followed by slow rewinding, and directional translocation of the enzyme to the cleavage site. Time-resolved fluorescence anisotropy reveals a nucleotide-dependent modulation in conformational fluctuations (nanoseconds) of the helicase and Platform–PAZ domains that is correlated with termini-dependent dsRNA cleavage. Our study offers a kinetic framework for comparison to other Dicers, as well as all members of the RLRs involved in innate immunity.
Collapse
Affiliation(s)
- Raushan K Singh
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - McKenzie Jonely
- Department of Chemistry, University of Utah, Salt Lake City, United States
| | - Evan Leslie
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Nick A Rejali
- Department of Pathology, University of Utah, Salt Lake City, United States
| | - Rodrigo Noriega
- Department of Chemistry, University of Utah, Salt Lake City, United States
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| |
Collapse
|
10
|
Schreier VN, Loehr MO, Deng T, Lattmann E, Hajnal A, Neuhauss SC, Luedtke NW. Fluorescent dATP for DNA Synthesis In Vivo. ACS Chem Biol 2020; 15:2996-3003. [PMID: 33108866 DOI: 10.1021/acschembio.0c00654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorescent nucleoside triphosphates are powerful probes of DNA synthesis, but their potential use in living animals has been previously underexplored. Here, we report the synthesis and characterization of 7-deaza-(1,2,3-triazole)-2'-deoxyadenosine-5'-triphosphate (dATP) derivatives of tetramethyl rhodamine ("TAMRA-dATP"), cyanine ("Cy3-dATP"), and boron-dipyrromethene ("BODIPY-dATP"). Upon microinjection into live zebrafish embryos, all three compounds were incorporated into the DNA of dividing cells; however, their impact on embryonic toxicity was highly variable, depending on the exact structure of the dye. TAMRA-EdATP exhibited superior characteristics in terms of its high brightness, low toxicity, and rapid incorporation and depletion kinetics in both a vertebrate (zebrafish) and a nematode (Caenorhabditis elegans). TAMRA-EdATP allows for unprecedented, real-time visualization of DNA replication and chromosome segregation in vivo.
Collapse
Affiliation(s)
- Verena N. Schreier
- Department of Chemistry, University of Zurich, Zurich CH-8006, Switzerland
| | - Morten O. Loehr
- Department of Chemistry, University of Zurich, Zurich CH-8006, Switzerland
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Ting Deng
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Evelyn Lattmann
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Alex Hajnal
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Stephan C.F. Neuhauss
- Department of Molecular Life Sciences, University of Zurich, Zurich CH-8006, Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry, University of Zurich, Zurich CH-8006, Switzerland
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3A 0G4, Canada
| |
Collapse
|
11
|
Navien TN, Thevendran R, Hamdani HY, Tang TH, Citartan M. In silico molecular docking in DNA aptamer development. Biochimie 2020; 180:54-67. [PMID: 33086095 DOI: 10.1016/j.biochi.2020.10.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico molecular docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico molecular docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.
Collapse
Affiliation(s)
- Tholasi Nadhan Navien
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Ramesh Thevendran
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Hazrina Yusof Hamdani
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| |
Collapse
|
12
|
Zhao Q, Bai Y, Wang H. Directing a rational design of aptamer-based fluorescence anisotropy assay for sensitive detection of immunoglobulin E by site-specific binding study. Talanta 2020; 217:121018. [PMID: 32498825 DOI: 10.1016/j.talanta.2020.121018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 11/17/2022]
Abstract
Mapping aptamer-protein interactions is important for characterization and applications of aptamers against proteins. We describe here probing affinity interactions between aptamer and immunoglobulin E (IgE) with a fluorescence anisotropy (FA) approach using a series of aptamer probes having single fluorescein (FAM) label at individual nucleotide (A, C, T). Studies of binding between IgE and aptamer probes revealed several possible close-contact sites, e.g., T9, T10, T11, T13, C15, and T17 of a 37-nt aptamer with a stem-loop secondary structure. FAM labeling on these sites resulted in much higher FA values (higher than 0.230 for T10, T11, T13 and C15) of aptamer-IgE complexes than the distant sites (e.g., terminals) of aptamer probably because the bound IgE close to these sites significantly restricted local rotation of FAM. Close-contact site labeled aptamer probes with high affinity allowed to develop a more sensitive FA assay for IgE than distant site labeled aptamers. The FA assay using T10-labeled aptamer with a dissociation constant (Kd) about 0.8 nM enabled selective detection of IgE at 20 pM and large FA increase upon IgE addition. We also found A12, C14, A25, and T27 were important for IgE-aptamer binding as FAM labeling at these sites significantly reduced aptamer affinity. FA study showed the loop region of this stem-loop aptamer was crucial for affinity binding, and IgE bound to the loop. This FA method will be helpful for understanding aptamer-protein binding and making a rational design of aptamer affinity assays for proteins.
Collapse
Affiliation(s)
- Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yunlong Bai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
13
|
Minagawa H, Shimizu A, Kataoka Y, Kuwahara M, Kato S, Horii K, Shiratori I, Waga I. Fluorescence Polarization-Based Rapid Detection System for Salivary Biomarkers Using Modified DNA Aptamers Containing Base-Appended Bases. Anal Chem 2020; 92:1780-1787. [PMID: 31855403 DOI: 10.1021/acs.analchem.9b03450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The field of care testing toward the analysis of blood and saliva lacks nowadays simple test techniques for biomarkers. In this study, we have developed a novel nucleobase analog, Ugu, which is a uracil derivative bearing a guanine base at the 5-position. Moreover, we attempted the development of aptamers that can bind to secretory immunoglobulin A (SIgA), which has been examined as a stress marker in human saliva. It was observed that the acquired aptamer binds strongly and selectively to the SIgA dimer (Kd = 13.6 nM) without binding to the IgG and IgA monomers of human serum. Reduction of the aptamer length (41 mer) successfully improved 4-fold the binding affinity (Kd = 3.7 nM), compared to the original, longer aptamer (78 mer). Furthermore, the development of a simple detection system for human saliva samples by fluorescence polarization was investigated, using the reported human salivary α-amylase (sAA) and the SIgA-binding aptamer. Comparison of the present method with conventional enzyme-linked immunosorbent assay techniques highlighted a significant Pearson's correlation of 0.94 and 0.83 when targeting sAA and SIgA, respectively. It is thus strongly suggested that a new simple test of stress markers in human saliva can be quantified quickly without bound/free (B/F) separation.
Collapse
Affiliation(s)
- Hirotaka Minagawa
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| | - Akihisa Shimizu
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| | - Yuka Kataoka
- Graduate School of Integrated Basic Sciences , Nihon University , 3-25-40 Sakurajosui, Setagaya-ku , Tokyo 156-8550 , Japan
| | - Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences , Nihon University , 3-25-40 Sakurajosui, Setagaya-ku , Tokyo 156-8550 , Japan
| | - Shintaro Kato
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| | - Katsunori Horii
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| | - Ikuo Shiratori
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| | - Iwao Waga
- NEC Solution Innovators, Ltd. , 1-18-7, Shinkiba, Koto-ku , Tokyo 136-8627 , Japan
| |
Collapse
|
14
|
Starukhin AN, Nelson DK, Eurov DA, Kurdyukov DA, Golubev VG. Manifestation of fluorophore segmental motion in carbon dots in steady-state fluorescence experiments. Phys Chem Chem Phys 2020; 22:8401-8408. [DOI: 10.1039/d0cp00056f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Perrin plot of carbon dots in aqueous glycerol solutions of different viscosity at T = 298 K.
Collapse
|
15
|
Wu Y, Belmonte I, Sykes KS, Xiao Y, White RJ. Perspective on the Future Role of Aptamers in Analytical Chemistry. Anal Chem 2019; 91:15335-15344. [PMID: 31714748 PMCID: PMC10184572 DOI: 10.1021/acs.analchem.9b03853] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
It has been almost 30 years since the invention of Systematic Evolution of Ligands by Exponential Enrichment (SELEX) methodology and the description of the first aptamers. In retrospect over the past 30 years, advances in aptamer development and application have demonstrated that aptamers are potentially useful reagents that can be employed in diverse areas within analytical chemistry, biotechnology, biomedicine, and molecular biology. While often touted as artificial antibodies with an ability to be selected for any target, aptamer development, unfortunately, lags behind development of analytical methodologies that employ aptamers, hindering deeper integration into the application of analytical tool development. This perspective covers recent advances in SELEX methodology for improving efficiency of the SELEX procedure and enhancing affinity and specificity of the selected aptamers, what we view as a critical barrier in the future role of aptamers in analytical chemistry. We discuss postselection modifications that can be used for enhancing performance of the selected aptamers in an analytical device by including understanding intermolecular interaction forces in the binding domain. While highlighting promising properties of aptamers that enable several analytical advances, we provide discussion on the challenges of penetration of aptamers in the analytical field.
Collapse
Affiliation(s)
- Yao Wu
- Department of Chemistry , University of Cincinnati , Cincinnati , Ohio 45221 , United States
| | - Israel Belmonte
- Department of Chemistry , University of Cincinnati , Cincinnati , Ohio 45221 , United States
| | - Kiana S Sykes
- Department of Chemistry , University of Cincinnati , Cincinnati , Ohio 45221 , United States
| | - Yi Xiao
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Ryan J White
- Department of Chemistry , University of Cincinnati , Cincinnati , Ohio 45221 , United States.,Department of Electrical Engineering and Computer Science , University of Cincinnati , Cincinnati , Ohio 45221 , United States
| |
Collapse
|
16
|
Mariam J, Krishnamoorthy G, Anand R. Use of 6‐Methylisoxanthopterin, a Fluorescent Guanine Analog, to Probe Fob1‐Mediated Dynamics at the Stalling Fork Barrier DNA Sequences. Chem Asian J 2019; 14:4760-4766. [DOI: 10.1002/asia.201901061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/19/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Jessy Mariam
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
| | | | - Ruchi Anand
- Department of ChemistryIndian Institute of Technology Bombay Powai Mumbai 400076 Maharashtra India
| |
Collapse
|
17
|
Thongyod W, Buranachai C, Pengpan T, Punwong C. Fluorescence quenching by photoinduced electron transfer between 7-methoxycoumarin and guanine base facilitated by hydrogen bonds: an in silico study. Phys Chem Chem Phys 2019; 21:16258-16269. [PMID: 31304496 DOI: 10.1039/c9cp02037c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, the effects of hydrogen bond (H-bond) formation on fluorescence quenching of 7-methoxycoumarin (7MC) via photo-induced electron transfer from a guanine base (Gua) are investigated using a combined quantum mechanics/molecular mechanics simulation. The electronic structure is calculated by the floating occupation molecular orbital complete active space configuration interaction modification on a semiempirical method. Then the full multiple spawning method is employed for the dynamics simulations on multiple electronic states. The methods employed here are validated by simulating direct dynamics of 7MC (without Gua) and compared with available experimental results. Our computational results are in good agreement with the previously reported experimental results in terms of spectroscopic properties of 7MC. In the case of a H-bonded 7MC-Gua complex, the results from constrained dynamics simulations and single-point calculations suggest that the electron transfer occurs on the second excited state and it depends not only on the H-bond length but also on the intermolecular planarity between 7MC and Gua. Moreover, a proton coupled electron transfer can occur at ≈1 Å of H-bond length, where a proton from Gua is also transferred together with the electron to 7MC. The obtained simulations are expected to be greatly beneficial for designing effective fluorescently labeled nucleotide probes as well as providing information for precise fluorescence signal interpretation.
Collapse
Affiliation(s)
- Wutthinan Thongyod
- Department of Physics, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand. and Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Songkhla 90112, Thailand
| | - Chittanon Buranachai
- Department of Physics, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand. and Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Songkhla 90112, Thailand
| | - Teparksorn Pengpan
- Department of Physics, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand.
| | - Chutintorn Punwong
- Department of Physics, Faculty of Science, Prince of Songkla University, Songkhla 90112, Thailand.
| |
Collapse
|
18
|
Velmurugu Y, Vivas P, Connolly M, Kuznetsov SV, Rice PA, Ansari A. Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein. Nucleic Acids Res 2019; 46:1741-1755. [PMID: 29267885 PMCID: PMC5829579 DOI: 10.1093/nar/gkx1215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1–10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.
Collapse
Affiliation(s)
- Yogambigai Velmurugu
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Serguei V Kuznetsov
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Phoebe A Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
| |
Collapse
|
19
|
Rath C, Burger J, Norval L, Kraemer SD, Gensch N, van der Kooi A, Reinemann C, O'Sullivan C, Svobodova M, Roth G. Comparison of different label-free imaging high-throughput biosensing systems for aptamer binding measurements using thrombin aptamers. Anal Biochem 2019; 583:113323. [PMID: 31129134 DOI: 10.1016/j.ab.2019.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/10/2019] [Accepted: 05/16/2019] [Indexed: 01/18/2023]
Abstract
To enable the analysis of several hundreds to thousands of interactions in parallel, high-throughput systems were developed. We used established thrombin aptamer assays to compare three such high-throughput imaging systems as well as analysis software and user influence. In addition to our own iRIf-system, we applied bscreen and IBIS-MX96. As non-imaging reference systems we used Octet-RED96, Biacore3000, and Monolith-NT.115. In this study we measured 1378 data points. Our results show that all systems are suitable for analyzing binding kinetics, but the kinetic constants as well as the ranking of the selected aptamers depend significantly on the applied system and user. We provide an insight into the signal generation principles, the systems and the results generated for thrombin aptamers. It should contribute to the awareness that binding constants cannot be determined as easily as other constants. Since many parameters like surface chemistry, biosensor type and buffer composition may change binding behavior, the experimenter should be aware that a system and assay dependent KD is determined. Frequently, certain conditions that are best suited for a given biosensing system cannot be transferred to other systems. Therefore, we strongly recommend using at least two different systems in parallel to achieve meaningful results.
Collapse
Affiliation(s)
- Christin Rath
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany; Faculty for Biology, Biology 3, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany; Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79104, Freiburg, Germany; BioCopy GmbH, 79110 Freiburg, Germany.
| | - Juergen Burger
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany; BioCopy GmbH, 79110 Freiburg, Germany.
| | - Leo Norval
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany.
| | - Stefan Daniel Kraemer
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany; Faculty for Biology, Biology 3, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.
| | - Nicole Gensch
- Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany.
| | | | - Christine Reinemann
- Helmholtz Centre for Environmental Research GmbH (UFZ), Permoserstr. 15, 04318, Leipzig, Germany.
| | - Ciara O'Sullivan
- Departament d'Enginyería Química, Universitat Rovira i Virgili, 43007, Tarragona, Spain; Institució Catalana de Recerca i Estudis Avançats, 08010, Barcelona, Spain.
| | - Marketa Svobodova
- Departament d'Enginyería Química, Universitat Rovira i Virgili, 43007, Tarragona, Spain.
| | - Guenter Roth
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany; Faculty for Biology, Biology 3, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany; Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79104, Freiburg, Germany; BioCopy GmbH, 79110 Freiburg, Germany.
| |
Collapse
|
20
|
Schröder T, Scheible MB, Steiner F, Vogelsang J, Tinnefeld P. Interchromophoric Interactions Determine the Maximum Brightness Density in DNA Origami Structures. NANO LETTERS 2019; 19:1275-1281. [PMID: 30681342 DOI: 10.1021/acs.nanolett.8b04845] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
An ideal point light source is as small and as bright as possible. For fluorescent point light sources, homogeneity of the light sources is important as well as that the fluorescent units inside the light source maintain their photophysical properties, which is compromised by dye aggregation. Here we propose DNA origami as a rigid scaffold to arrange dye molecules in a dense pixel array with high control of stoichiometry and dye-dye interactions. In order to find the highest labeling density in a DNA origami structure without influencing dye photophysics, we alter the distance of two ATTO647N dyes in single base pair steps and probe the dye-dye interactions on the single-molecule level. For small distances strong quenching in terms of intensity and fluorescence lifetime is observed. With increasing distance, we observe reduced quenching and molecular dynamics. However, energy transfer processes in the weak coupling regime still have a significant impact and can lead to quenching by singlet-dark-state-annihilation. Our study fills a gap of studying the interactions of dyes relevant for superresolution microscopy with dense labeling and for single-molecule biophysics. Incorporating these findings in a 3D DNA origami object will pave the way to bright and homogeneous DNA origami nanobeads.
Collapse
Affiliation(s)
- Tim Schröder
- Department Chemie and Center for NanoScience , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5-13 Haus E , 81377 Muenchen , Germany
| | - Max B Scheible
- GATTAquant GmbH , Am Schlosshof 8 , 91355 Hiltpoltstein , Germany
| | - Florian Steiner
- Department Chemie and Center for NanoScience , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5-13 Haus E , 81377 Muenchen , Germany
| | - Jan Vogelsang
- Department Chemie and Center for NanoScience , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5-13 Haus E , 81377 Muenchen , Germany
| | - Philip Tinnefeld
- Department Chemie and Center for NanoScience , Ludwig-Maximilians-Universitaet Muenchen , Butenandtstrasse 5-13 Haus E , 81377 Muenchen , Germany
| |
Collapse
|
21
|
Cai S, Yan J, Xiong H, Liu Y, Peng D, Liu Z. Investigations on the interface of nucleic acid aptamers and binding targets. Analyst 2019; 143:5317-5338. [PMID: 30357118 DOI: 10.1039/c8an01467a] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA of 20-100 nucleotides in length that have attracted substantial scientific interest due to their ability to specifically bind to target molecules via the formation of three-dimensional structures. Compared to traditional protein antibodies, aptamers have several advantages, such as their small size, high binding affinity, specificity, flexible structure, being chemical synthesizable and modifiable, good biocompatibility, high stability and low immunogenicity, which all contribute to their widely applications in the biomedical field. To date, much progress has been made in the study and applications of aptamers, however, detailed information on how aptamers bind to their targets is still scarce. Over the past few decades, many methods have been introduced to investigate the aptamer-target binding process, such as measuring the main kinetic or thermodynamic parameters, detecting the structural changes of the binding complexes, etc. Apart from traditional physicochemical methods, various types of molecular docking programs have been applied to simulate the aptamer-target interactions, while these simulations also have limitations. To facilitate the further research on the interactions, herein, we provide a brief review to illustrate the recent advances in the study of aptamer-target interactions. We summarize the binding targets of aptamers, such as small molecules, macromolecules, and even cells. Their binding constants (KD) are also summarized. Methods to probe the aptamer-target binding process, such as surface plasmon resonance (SPR), circular dichroism spectroscopy (CD), isothermal titration calorimetry (ITC), footprinting assay, truncation and mutation assay, nuclear magnetic resonance spectroscopy (NMR), X-ray crystallography and molecular docking simulation are indicated. The binding forces mediating the aptamer-target interactions, such as hydrogen bonding, electrostatic interaction, the hydrophobic effect, π-π stacking and van der Waals forces are summarized. The challenges and future perspectives are also discussed.
Collapse
Affiliation(s)
- Shundong Cai
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, PR China.
| | | | | | | | | | | |
Collapse
|
22
|
Ingargiola A, Weiss S, Lerner E. Monte Carlo Diffusion-Enhanced Photon Inference: Distance Distributions and Conformational Dynamics in Single-Molecule FRET. J Phys Chem B 2018; 122:11598-11615. [PMID: 30252475 DOI: 10.1021/acs.jpcb.8b07608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is utilized to study the structure and dynamics of many biomolecules, such as proteins, DNA, and their various complexes. The structural assessment is based on the well-known Förster relationship between the measured efficiency of energy transfer between a donor (D) and an acceptor (A) dye and the distance between them. Classical smFRET analysis methods called photon distribution analysis (PDA) take into account photon shot-noise, D-A distance distribution, and, more recently, interconversion between states in order to extract accurate distance information. It is known that rapid D-A distance fluctuations on the order of the D lifetime (or shorter) can increase the measured mean FRET efficiency and thus decrease the estimated D-A distance. Nonetheless, this effect has been so far neglected in smFRET experiments, potentially leading to biases in estimated distances. Here we introduce a PDA approach dubbed Monte Carlo diffusion-enhanced photon inference (MC-DEPI). MC-DEPI recolor detected photons of smFRET experiments taking into account dynamics of D-A distance fluctuations, multiple interconverting states, and photoblinking. Using this approach, we show how different underlying conditions may yield identical FRET histograms and how the additional information from fluorescence decays helps in distinguishing between the different conditions. We also introduce a machine learning fitting approach for retrieving the D-A distance distribution, decoupled from the above-mentioned effects. We show that distance interpretation of smFRET experiments of even the simplest dsDNA is nontrivial and requires decoupling the effects of rapid D-A distance fluctuations on FRET in order to avoid systematic biases in the estimation of the D-A distance distribution.
Collapse
Affiliation(s)
- Antonino Ingargiola
- Department of Chemistry and Biochemistry , University of California Los Angeles , Los Angeles , California , United States
| | - Shimon Weiss
- Department of Chemistry and Biochemistry , University of California Los Angeles , Los Angeles , California , United States
| | - Eitan Lerner
- Department of Chemistry and Biochemistry , University of California Los Angeles , Los Angeles , California , United States.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences , The Hebrew University , Jerusalem , Israel
| |
Collapse
|
23
|
Lisi S, Fiore E, Scarano S, Pascale E, Boehman Y, Ducongé F, Chierici S, Minunni M, Peyrin E, Ravelet C. Non-SELEX isolation of DNA aptamers for the homogeneous-phase fluorescence anisotropy sensing of tau Proteins. Anal Chim Acta 2018; 1038:173-181. [DOI: 10.1016/j.aca.2018.07.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 02/07/2023]
|
24
|
Sun L, Zhao Q. Direct fluorescence anisotropy approach for aflatoxin B1 detection and affinity binding study by using single tetramethylrhodamine labeled aptamer. Talanta 2018; 189:442-450. [PMID: 30086944 DOI: 10.1016/j.talanta.2018.07.036] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/07/2018] [Accepted: 07/11/2018] [Indexed: 12/20/2022]
Abstract
The discovery of aptamers for aflatoxin B1 (AFB1), one of toxic carcinogens, has allowed to develop aptamer-based sensors and assays for aflatoxin. In this work, we reported a direct fluorescence anisotropy (FA) assay for investigation of aptamer-AFB1 binding and detection of AFB1 with the aptamer having single tetramethylrhodamine (TMR) label on a specific site. From a series of labeling sites of a 50-mer aptamer, we screened out the aptamer with TMR labeling at the 26th T, capable of generating good and large FA-decreasing response to AFB1. By using the T26-labeled 50-mer aptamer probe in FA analysis, we determined the affinity and selectivity of aptamer, and identified the crucial region of aptamer and optimum experimental conditions for strong binding. The aptamer could be further truncated to as short as 26 nucleotides in length, and this shorter aptamer possessed a simple stem-loop secondary structure and retained good binding affinity. Nucleotides in the loop region of the aptamer were conserved and important for affinity recognition. We achieved FA detection of AFB1 with a detection limit about 2 nM by using the TMR-labeled aptamer probe. The cross reactivity of aflatoxin B1, aflatoxin B2, aflatoxin M1, aflatoxin M2, aflatoxin G1, and aflatoxin G2 with aptamer were estimated to be 100%, 61%, 23%, 21%, 6.3%, 6.5%, respectively. The aptamer probe presented good selectivity over other mycotoxins and showed potential in complex sample analysis. This study of affinity binding between aptamer and aflatoxins will be helpful for developing other aptamer-based assays and sensors for aflatoxins.
Collapse
Affiliation(s)
- Linlin Sun
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
25
|
Kinetic Basis of the Bifunctionality of SsoII DNA Methyltransferase. Molecules 2018; 23:molecules23051192. [PMID: 29772716 PMCID: PMC6100179 DOI: 10.3390/molecules23051192] [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: 04/06/2018] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 12/04/2022] Open
Abstract
Type II restriction–modification (RM) systems are the most widespread bacterial antiviral defence mechanisms. DNA methyltransferase SsoII (M.SsoII) from a Type II RM system SsoII regulates transcription in its own RM system in addition to the methylation function. DNA with a so-called regulatory site inhibits the M.SsoII methylation activity. Using circular permutation assay, we show that M.SsoII monomer induces DNA bending of 31° at the methylation site and 46° at the regulatory site. In the M.SsoII dimer bound to the regulatory site, both protein subunits make equal contributions to the DNA bending, and both angles are in the same plane. Fluorescence of TAMRA, 2-aminopurine, and Trp was used to monitor conformational dynamics of DNA and M.SsoII under pre-steady-state conditions by stopped-flow technique. Kinetic data indicate that M.SsoII prefers the regulatory site to the methylation site at the step of initial protein–DNA complex formation. Nevertheless, in the presence of S-adenosyl-l-methionine, the induced fit is accelerated in the M.SsoII complex with the methylation site, ensuring efficient formation of the catalytically competent complex. The presence of S-adenosyl-l-methionine and large amount of the methylation sites promote efficient DNA methylation by M.SsoII despite the inhibitory effect of the regulatory site.
Collapse
|
26
|
Perrier S, Guieu V, Chovelon B, Ravelet C, Peyrin E. Panoply of Fluorescence Polarization/Anisotropy Signaling Mechanisms for Functional Nucleic Acid-Based Sensing Platforms. Anal Chem 2018. [PMID: 29513518 DOI: 10.1021/acs.analchem.7b04593] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescence polarization/anisotropy is a very popular technique that is widely used in homogeneous-phase immunoassays for the small molecule quantification. In the present Feature, we discuss how the potential of this signaling approach considerably expanded during the last 2 decades through the implementation of a myriad of original transducing strategies that use functional nucleic acid recognition elements as a promising alternative to antibodies.
Collapse
Affiliation(s)
- Sandrine Perrier
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Valérie Guieu
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Benoit Chovelon
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France.,Département de Biochimie, Toxicologie et Pharmacologie , CHU de Grenoble Site Nord-Institut de Biologie et de Pathologie , F-38041 Grenoble , France
| | - Corinne Ravelet
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| | - Eric Peyrin
- University Grenoble Alpes , DPM UMR 5063, F-38041 Grenoble , France.,CNRS , DPM UMR 5063, F-38041 Grenoble , France
| |
Collapse
|
27
|
Oh T, Kim S, Choi JY, Chang H, Heller MJ. Enhancement of fluorescent resonant energy transfer and the antenna effect in DNA structures with multiple fluorescent dyes. RSC Adv 2017. [DOI: 10.1039/c7ra01470h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This study examines the use of surfactants and metal cations to enhance the long range fluorescent resonant energy transfer (FRET) and the antenna effect from three TAMRA donor dyes to one Texas Red acceptor dye conjugated in dsDNA structure.
Collapse
Affiliation(s)
- Taeseok Oh
- Materials Science and Engineering Program
- University of California
- San Diego
- USA
- Department of NanoEngineering
| | - Sejung Kim
- Department of NanoEngineering
- University of California
- San Diego
- USA
| | - Jae-Young Choi
- Department of NanoEngineering
- University of California
- San Diego
- USA
| | - Haeun Chang
- Department of NanoEngineering
- University of California
- San Diego
- USA
| | | |
Collapse
|
28
|
Pei X, Huang H, Chen Y, Li C, Liu F, Li N. Modulating fluorescence anisotropy of dye-labeled DNA without involving mass amplification. Talanta 2016; 154:567-73. [DOI: 10.1016/j.talanta.2016.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/05/2016] [Accepted: 01/08/2016] [Indexed: 11/25/2022]
|
29
|
Oh T, Choi JY, Heller MJ. Enhanced fluorescent resonant energy transfer of DNA conjugates complexed with surfactants and divalent metal ions. Analyst 2016; 141:2371-5. [PMID: 26985458 DOI: 10.1039/c5an02516h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dimerization and resultant quenching of donor and acceptor dyes conjugated on DNA causes loss of fluorescent resonant energy transfer (FRET) efficiency. However, when complexed with surfactants and divalent metal ions, sheathing effects insulate and shield the DNA structures, reducing dimerization and quenching which leads to significant enhancement of FRET efficiency.
Collapse
Affiliation(s)
- Taeseok Oh
- Materials Science and Engineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | | | | |
Collapse
|
30
|
Perrier S, Bouilloud P, De Oliveira Coelho G, Henry M, Peyrin E. Small molecule aptamer assays based on fluorescence anisotropy signal-enhancer oligonucleotides. Biosens Bioelectron 2016; 82:155-61. [PMID: 27085946 DOI: 10.1016/j.bios.2016.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/23/2016] [Accepted: 04/04/2016] [Indexed: 12/24/2022]
Abstract
Herein, we design novel fluorescence anisotropy (FA) aptamer sensing platforms dedicated to small molecule detection. The assay strategy relied on enhanced fluctuations of segmental motion dynamics of the aptamer tracer mediated by an unlabelled, partially complementary oligonucleotide. The signal-enhancer oligonucleotide (SEO) essentially served as a free probe fraction revealer. By targeting specific regions of the signalling functional nucleic acid, the SEO binding to the unbound aptamer triggered perturbations of both the internal DNA flexibility and the localized dye environment upon the free probe to duplex structure transition. This potentiating effect determined increased FA variations between the duplex and target bound states of the aptameric probe. FA assay responses were obtained with both pre-structured (adenosine) and unstructured (tyrosinamide) aptamers and with dyes of different photochemical properties (fluorescein and texas red). The multiplexed analysis ability was further demonstrated through the simultaneous multicolour detection of the two small targets. The FA method appears to be especially simple, sensitive and widely applicable.
Collapse
Affiliation(s)
- Sandrine Perrier
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Prisca Bouilloud
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Gisella De Oliveira Coelho
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Mickael Henry
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France.
| |
Collapse
|
31
|
Oh T, Takahashi T, Kim S, Heller MJ. CTAB enhancement of FRET in DNA structures. JOURNAL OF BIOPHOTONICS 2016; 9:49-54. [PMID: 26530400 DOI: 10.1002/jbio.201500221] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 09/20/2015] [Accepted: 10/13/2015] [Indexed: 06/05/2023]
Abstract
The effect of cetyl-trimethylammonium bromide (CTAB) on enhancing the fluorescence resonance energy transfer (FRET) between two dye-conjugated DNA strands was studied using fluorescence emission spectroscopy and dynamic light scattering (DLS). For hybridized DNA where one strand is conjugated with a TAMRA donor and the other with a TexasRed acceptor, increasing the concentration of CTAB changes the fluorescence emission properties and improves the FRET transfer efficiency through changes in the polarity of the solvent, neutralization of the DNA backbone and micelle formation. For the DNA FRET system without CTAB, the DNA hybridization leads to contact quenching between TAMRA donor and TexasRed acceptor producing reduced donor emission and only a small increase in acceptor emission. At 50 µM CTAB, however, the sheathing and neutralization of the dye-conjugated dsDNA structure significantly reduces quenching by DNA bases and dye interactions, producing a large increase in FRET efficiency, which is almost four fold higher than without CTAB.
Collapse
Affiliation(s)
- Taeseok Oh
- Materials Science and Engineering Program, University of California, San Diego, 9500, Gilman Dr., La Jolla, CA 92093, USA
| | - Tsukasa Takahashi
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, 9500, Gilman Dr., La Jolla, CA 92093, USA
| | - Sejung Kim
- Materials Science and Engineering Program, University of California, San Diego, 9500, Gilman Dr., La Jolla, CA 92093, USA
| | - Michael J Heller
- Department of NanoEngineering, University of California, San Diego, 9500, Gilman Dr., La Jolla, CA 92093, USA.
| |
Collapse
|
32
|
Nardo L, Lamperti M, Salerno D, Cassina V, Missana N, Bondani M, Tempestini A, Mantegazza F. Effects of non-CpG site methylation on DNA thermal stability: a fluorescence study. Nucleic Acids Res 2015; 43:10722-33. [PMID: 26354864 PMCID: PMC4678853 DOI: 10.1093/nar/gkv884] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/21/2015] [Indexed: 11/14/2022] Open
Abstract
Cytosine methylation is a widespread epigenetic regulation mechanism. In healthy mature cells, methylation occurs at CpG dinucleotides within promoters, where it primarily silences gene expression by modifying the binding affinity of transcription factors to the promoters. Conversely, a recent study showed that in stem cells and cancer cell precursors, methylation also occurs at non-CpG pairs and involves introns and even gene bodies. The epigenetic role of such methylations and the molecular mechanisms by which they induce gene regulation remain elusive. The topology of both physiological and aberrant non-CpG methylation patterns still has to be detailed and could be revealed by using the differential stability of the duplexes formed between site-specific oligonucleotide probes and the corresponding methylated regions of genomic DNA. Here, we present a systematic study of the thermal stability of a DNA oligonucleotide sequence as a function of the number and position of non-CpG methylation sites. The melting temperatures were determined by monitoring the fluorescence of donor-acceptor dual-labelled oligonucleotides at various temperatures. An empirical model that estimates the methylation-induced variations in the standard values of hybridization entropy and enthalpy was developed.
Collapse
Affiliation(s)
- Luca Nardo
- Department of Health Sciences, University of Milano Bicocca, Via Cadore 48, Monza, MB 20900, Italy
| | - Marco Lamperti
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, Como, CO 22100, Italy
| | - Domenico Salerno
- Department of Health Sciences, University of Milano Bicocca, Via Cadore 48, Monza, MB 20900, Italy
| | - Valeria Cassina
- Department of Health Sciences, University of Milano Bicocca, Via Cadore 48, Monza, MB 20900, Italy
| | - Natalia Missana
- Department of Health Sciences, University of Milano Bicocca, Via Cadore 48, Monza, MB 20900, Italy
| | - Maria Bondani
- Institute for Photonics and Nanotechnology, National Research Council, Via Valleggio 11, Como, CO 22100, Italy
| | - Alessia Tempestini
- LENS-Department of Physics and Astronomy, University of Firenze, Via Sansone 1, Sesto Fiorentino, FI 50019, Italy
| | - Francesco Mantegazza
- Department of Health Sciences, University of Milano Bicocca, Via Cadore 48, Monza, MB 20900, Italy
| |
Collapse
|
33
|
Urmann K, Tenenbaum E, Walter JG, Segal E. Porous Silicon Biosensors Employing Emerging Capture Probes. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-20346-1_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
34
|
Yin L, Wang W, Wang S, Zhang F, Zhang S, Tao N. How does fluorescent labeling affect the binding kinetics of proteins with intact cells? Biosens Bioelectron 2015; 66:412-6. [PMID: 25486538 PMCID: PMC4836836 DOI: 10.1016/j.bios.2014.11.036] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 11/25/2022]
Abstract
Fluorescent labeling is a mainstream technology for detecting molecular binding. Despite the importance, few studies have been devoted to quantitatively examine the effect of labeling on the molecular binding processes. Here we present a quantitative study on the binding kinetics of fluorescent-labeled and un-labeled molecules (lectin proteins) with glycoproteins on the membrane of cells using surface plasmon resonance imaging (SPRi) technique. The study shows that fluorescent labeling has a significant influence on the binding behaviors of proteins, especially the association processes, and the influence depends sensitively on the charge of fluorescent labels. It further shows that the labels also affect the local distribution of probe proteins, due to the inhomogeneous surface charge distribution of the cell membrane. Our work indicates that fluorescent labeling in general affects the binding behaviors, but proper design of the label will help to minimize its effect.
Collapse
Affiliation(s)
- Linliang Yin
- College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China; Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Shaopeng Wang
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Fenni Zhang
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shengtao Zhang
- College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China.
| | - Nongjian Tao
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| |
Collapse
|
35
|
Huang H, Wei H, Zou M, Xu X, Xia B, Liu F, Li N. Modulating fluorescence anisotropy of terminally labeled double-stranded DNA via the interaction between dye and nucleotides for rational design of DNA recognition based applications. Anal Chem 2015; 87:2748-54. [PMID: 25671552 DOI: 10.1021/ac504028n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Effective signal enhancement for fluorescence anisotropy in a simple manner is most desirable for fluorescence anisotropy method development. This work aimed to provide insights into the fluorescence anisotropy of terminally labeled double-stranded DNA (dsDNA) to facilitate a facile and universal design strategy for DNA recognition based applications. We demonstrated that fluorescence anisotropy of dsDNA could be regulated by the nature of dyes, the molecular volume, and the end structure of dsDNA. Fluorescence anisotropy ascended with the increased number of base pairs up to 18 bp and leveled off thereafter, indicating the molecular volume was not the only factor responsible for fluorescence anisotropy. By choosing dyes with the positively charged center, high fluorescence anisotropy signal was obtained due to the confinement of the segmental motion of dyes through the electrostatic interaction. By properly designing the end structure of dsDNA, fluorescence anisotropy could be further improved by enlarging the effective overall rotational volume, as supported by two-dimensional (2D) (1)H-(1)H nuclear Overhauser enhancement spectroscopy (NOESY). With the successful enhancement of the fluorescence anisotropy for terminally labeled dsDNA, simple and universal designs were demonstrated by sensing of major classes of analytes from macromolecules (DNA and protein) to small molecules (cocaine).
Collapse
Affiliation(s)
- Hongduan Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, ‡Beijing NMR Center, and §College of Life Sciences, Peking University , Beijing, 100871, China
| | | | | | | | | | | | | |
Collapse
|
36
|
Zhou S, Anupam R, Hines JV. Fluorescence anisotropy: analysis of tRNA binding to the T box riboswitch antiterminator RNA. Methods Mol Biol 2015; 1240:143-52. [PMID: 25352143 DOI: 10.1007/978-1-4939-1896-6_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Fluorescence anisotropy can be utilized in drug discovery screening assays to identify compounds that disrupt medicinally important RNA-macromolecular complexes. Here we describe the application of this technique to monitor tRNA binding to T box riboswitch antiterminator RNA.
Collapse
Affiliation(s)
- S Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, 45701, USA
| | | | | |
Collapse
|
37
|
Fluorescence assays for monitoring RNA-ligand interactions and riboswitch-targeted drug discovery screening. Methods Enzymol 2014; 550:363-83. [PMID: 25605395 DOI: 10.1016/bs.mie.2014.10.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Riboswitches and other noncoding regulatory RNA are intriguing targets for the development of therapeutic agents. A significant challenge in the drug discovery process, however, is the identification of potent compounds that bind the target RNA specifically and disrupt its function. Essential to this process is an effectively designed cascade of screening assays. A screening cascade for identifying compounds that target the T box riboswitch antiterminator element is described. In the primary assays, moderate to higher throughput screening of compound libraries is achieved by combining the sensitivity of fluorescence techniques with functionally relevant assays. Active compounds are then validated and the binding to target RNA further characterized in secondary assays. The cascade of assays monitor ligand-induced changes in the steady-state fluorescence of an attached dye or internally incorporated 2-aminopurine; the fluorescence anisotropy of an RNA complex; and, the thermal denaturation fluorescence profile of a fluorophore-quencher labeled RNA. While the assays described have been developed for T box riboswitch-targeted drug discovery, the fluorescence methods and screening cascade design principles can be applied to drug discovery efforts targeted toward other medicinally relevant noncoding RNA.
Collapse
|
38
|
Höfig H, Gabba M, Poblete S, Kempe D, Fitter J. Inter-dye distance distributions studied by a combination of single-molecule FRET-filtered lifetime measurements and a weighted accessible volume (wAV) algorithm. Molecules 2014; 19:19269-91. [PMID: 25429558 PMCID: PMC6270743 DOI: 10.3390/molecules191219269] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 11/03/2014] [Accepted: 11/06/2014] [Indexed: 11/16/2022] Open
Abstract
Förster resonance energy transfer (FRET) is an important tool for studying the structural and dynamical properties of biomolecules. The fact that both the internal dynamics of the biomolecule and the movements of the biomolecule-attached dyes can occur on similar timescales of nanoseconds is an inherent problem in FRET studies. By performing single-molecule FRET-filtered lifetime measurements, we are able to characterize the amplitude of the motions of fluorescent probes attached to double-stranded DNA standards by means of flexible linkers. With respect to previously proposed experimental approaches, we improved the precision and the accuracy of the inter-dye distance distribution parameters by filtering out the donor-only population with pulsed interleaved excitation. A coarse-grained model is employed to reproduce the experimentally determined inter-dye distance distributions. This approach can easily be extended to intrinsically flexible proteins allowing, under certain conditions, to decouple the macromolecule amplitude of motions from the contribution of the dye linkers.
Collapse
Affiliation(s)
- Henning Höfig
- Physikalisches Institut (IA), RWTH Aachen University, Otto-Blumenthal-Straße, 52074 Aachen, Germany.
| | - Matteo Gabba
- Institute of Complex Systems (ICS-5), Molecular Biophysics, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
| | - Simón Poblete
- Institute of Complex Systems (ICS-2), Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
| | - Daryan Kempe
- Physikalisches Institut (IA), RWTH Aachen University, Otto-Blumenthal-Straße, 52074 Aachen, Germany.
| | - Jörg Fitter
- Physikalisches Institut (IA), RWTH Aachen University, Otto-Blumenthal-Straße, 52074 Aachen, Germany.
| |
Collapse
|
39
|
Hartmann A, Krainer G, Schlierf M. Different fluorophore labeling strategies and designs affect millisecond kinetics of DNA hairpins. Molecules 2014; 19:13735-54. [PMID: 25255759 PMCID: PMC6271894 DOI: 10.3390/molecules190913735] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/21/2014] [Accepted: 08/26/2014] [Indexed: 11/18/2022] Open
Abstract
Changes in molecular conformations are one of the major driving forces of complex biological processes. Many studies based on single-molecule techniques have shed light on conformational dynamics and contributed to a better understanding of living matter. In particular, single-molecule FRET experiments have revealed unprecedented information at various time scales varying from milliseconds to seconds. The choice and the attachment of fluorophores is a pivotal requirement for single-molecule FRET experiments. One particularly well-studied millisecond conformational change is the opening and closing of DNA hairpin structures. In this study, we addressed the influence of base- and terminal-labeled fluorophores as well as the fluorophore DNA interactions on the extracted kinetic information of the DNA hairpin. Gibbs free energies varied from ∆G0 = −3.6 kJ/mol to ∆G0 = −0.2 kJ/mol for the identical DNA hairpin modifying only the labeling scheme and design of the DNA sample. In general, the base-labeled DNA hairpin is significantly destabilized compared to the terminal-labeled DNA hairpin and fluorophore DNA interactions additionally stabilize the closed state of the DNA hairpin. Careful controls and variations of fluorophore attachment chemistry are essential for a mostly undisturbed measurement of the underlying energy landscape of biomolecules.
Collapse
Affiliation(s)
- Andreas Hartmann
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany.
| | - Georg Krainer
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany.
| | - Michael Schlierf
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany.
| |
Collapse
|
40
|
Rao AN, Grainger DW. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE. Biomater Sci 2014; 2:436-471. [PMID: 24765522 PMCID: PMC3992954 DOI: 10.1039/c3bm60181a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.
Collapse
Affiliation(s)
- Archana N. Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
| | - David W. Grainger
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112 USA
| |
Collapse
|
41
|
Gray RD, Trent JO, Chaires JB. Folding and unfolding pathways of the human telomeric G-quadruplex. J Mol Biol 2014; 426:1629-50. [PMID: 24487181 DOI: 10.1016/j.jmb.2014.01.009] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/06/2014] [Accepted: 01/07/2014] [Indexed: 11/30/2022]
Abstract
Sequence analogs of human telomeric DNA such as d[AGGG(TTAGGG)3] (Tel22) fold into monomeric quadruplex structures in the presence of a suitable cation. To investigate the pathway for unimolecular quadruplex formation, we monitored the kinetics of K(+)-induced folding of Tel22 by circular dichroism (CD), intrinsic 2-aminopurine fluorescence, and fluorescence resonance energy transfer (FRET). The results are consistent with a four-step pathway U ↔ I1 ↔ I2 ↔ I3 ↔ F where U and F represent unfolded and folded conformational ensembles and I1, I2, and I3 are intermediates. Previous kinetic studies have shown that I1 is formed in a rapid pre-equilibrium and may consist of an ensemble of "prefolded" hairpin structures brought about by cation-induced electrostatic collapse of the DNA. The current study shows that I1 converts to I2 with a relaxation time τ1=0.1s at 25 °C in 25 mM KCl. The CD spectrum of I2 is characteristic of an antiparallel quadruplex that could form as a result of intramolecular fold-over of the I1 hairpins. I3 is relatively slowly formed (τ2≈3700s) and has CD and FRET properties consistent with those expected of a triplex structure as previously observed in equilibrium melting studies. I3 converts to F with τ3≈750s. Identical pathways with different kinetic constants involving a rapidly formed antiparallel intermediate were observed with oligonucleotides forming mixed parallel/antiparallel hybrid-1 and hybrid-2 topologies {e.g. d[TTGGG(TTAGGG)3A] and d[TAGGG(TTAGGG)3TT]}. Aspects of the kinetics of unfolding were also monitored by the spectroscopic methods listed above and by time-resolved fluorescence lifetime measurements using a complementary strand trap assay. These experiments reveal a slow, rate-limiting step along the unfolding pathway.
Collapse
Affiliation(s)
- Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - John O Trent
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Jonathan B Chaires
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA.
| |
Collapse
|
42
|
Busson MP, Bidault S. Selective excitation of single molecules coupled to the bright mode of a plasmonic cavity. NANO LETTERS 2014; 14:284-8. [PMID: 24303895 DOI: 10.1021/nl403963y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Plasmon-based optical antennas featuring a nanometer-sized gap can enhance the photophysical properties of solid-state quantum emitters by several orders of magnitude at room temperature. However, controlling the position and orientation of an isolated emitter in a metallic resonator, at the nanometer scale, has only been achieved in scanning probe geometries. Using radially polarized cylindrical vector beams and DNA-assembled gold nanoparticle dimers, we demonstrate the reproducible interaction of single dye molecules with the bright longitudinal mode of a plasmonic cavity, achieving decay rate enhancements of 2 orders of magnitude. These results demonstrate that interfacing efficiently isolated quantum emitters and optical nanoantennas is possible on a large scale.
Collapse
Affiliation(s)
- Mickaël P Busson
- Institut Langevin, ESPCI ParisTech, CNRS UMR 7587, 1 rue Jussieu, 75005 Paris, France
| | | |
Collapse
|
43
|
Zhao Q, Lv Q, Wang H. Identification of allosteric nucleotide sites of tetramethylrhodamine-labeled aptamer for noncompetitive aptamer-based fluorescence anisotropy detection of a small molecule, ochratoxin A. Anal Chem 2013; 86:1238-45. [PMID: 24354298 DOI: 10.1021/ac4035532] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aptamer-based fluorescence anisotropy (FA) assay combines the advantages of affinity aptamers in good stability, easy generation, and facile labeling and the benefits of FA in homogeneous analysis, such as robustness, simplicity, and high reproducibility. By using a fluorophore-labeled aptamer, FA detection of a small molecule is not as easy as detection of protein because the binding of a small molecule cannot cause significant increase of molecular weight of the dye-labeled aptamer. The intramolecular interaction between labeled tetramethylrhodamine (TMR) and DNA aptamer bases dramatically affects the local rotation and FA of TMR. This intramolecular interaction can be altered by aptamer conformation change upon target binding, leading to a significant change of FA of TMR. Taking this unique feature of a TMR-labeled aptamer, we described a noncompetitive aptamer-based fluorescence anisotropy assay for detection of small molecules by using ochratoxin A (OTA) as a model. We successfully identified the specific TMR-labeling sites of aptamers with sensitive FA response to OTA from the 5'-end, 3'-end and the internal thymine (T) bases. The aptamer with a TMR labeled on the 10th T base exhibited a remarkable FA reduction response to OTA (Δr = 0.078), without requiring any proteins or nanomaterials as FA signal enhancers. This FA approach for OTA showed high sensitivity with a detection limit of 3 nM, a dynamic range from 3 nM to 3 μM, and good selectivity over the tested compounds with similar structures to OTA. The new strategy allowed the detection of OTA in diluted red wine and urine samples.
Collapse
Affiliation(s)
- Qiang Zhao
- Research Institute of Environmental Science, Shanxi University , Taiyuan, Shanxi Province, 030006, People's Republic of China
| | | | | |
Collapse
|
44
|
Liu C, Liang G, Liu Z, Zu L. Time-Resolved Fluorescence Anisotropy Study of the Interaction Between DNA and a Peptide Truncated from the p53 Protein Core Domain. J Fluoresc 2013; 24:533-9. [DOI: 10.1007/s10895-013-1322-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 11/07/2013] [Indexed: 11/28/2022]
|
45
|
Techen A, Czapla S, Möllnitz K, Budach D, Wessig P, Kumke MU. Synthesis and Spectroscopic Characterization of Fluorophore-Labeled Oligospiroketal Rods. Helv Chim Acta 2013. [DOI: 10.1002/hlca.201200616] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
46
|
Rao AN, Vandencasteele N, Gamble LJ, Grainger DW. High-resolution epifluorescence and time-of-flight secondary ion mass spectrometry chemical imaging comparisons of single DNA microarray spots. Anal Chem 2012; 84:10628-36. [PMID: 23150996 DOI: 10.1021/ac3019334] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA microarray assay performance is commonly compromised by spot-spot probe and signal variations as well as heterogeneity within printed microspots. Accurate metrics for captured DNA target signal rely upon uniform spot distribution of both probe and target DNA to yield reliable hybridized signal. While often presumed, this is neither easily achieved nor often proven experimentally. High-resolution imaging techniques were used to determine spot heterogeneity in identical DNA array microspots comprising varied ratios of unlabeled and dye-labeled DNA probes contact-printed onto commercial arraying surfaces. Epifluorescence imaging data for individual array microspots were correlated with time-of-flight secondary ion mass spectrometry (TOF-SIMS) chemical state imaging of the same spots. Epifluorescence imaging intensity distinguished varying DNA density distributed both within a given spot and from spot to spot. TOF-SIMS chemical analysis confirmed these heterogeneous printed DNA distributions by tracking bound Cy3 dye, DNA base, and phosphate specific ion fragments often correlating to fluorescence patterns within identical spots. TOF-SIMS ion fragments originating from probe DNA and Cy3 dye are enriched in microspot centers, correlating with high fluorescence intensity regions. Both TOF-SIMS and epifluorescence support Marangoni flow effects on spot drying, with high-density DNA-Cy3 located in spot centers and nonhomogeneous DNA distribution within printed spots. Microspot image dimensional analysis results for DNA droplet spreading show differing DNA densities across printed spots. The study directly supports different DNA probe chemical and spatial microenvironments within spots that yield spot-spot signal variations known to affect DNA target hybridization efficiencies and kinetics. These variations critically affect probe-target duplex formation and DNA array signal generation.
Collapse
Affiliation(s)
- Archana N Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112-5820, USA
| | | | | | | |
Collapse
|
47
|
Chen T, Fu L, Zu L. Steady-state and time-resolved fluorescence of tetramethylrhodamine attached to DNA: correlation with DNA sequences. LUMINESCENCE 2012; 28:860-4. [DOI: 10.1002/bio.2446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 08/30/2012] [Accepted: 09/06/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Tingting Chen
- Department of Chemistry; Beijing Normal University; Beijing 100875 People's Republic of China
| | - Leixiaomeng Fu
- Department of Chemistry; Beijing Normal University; Beijing 100875 People's Republic of China
| | - Lily Zu
- Department of Chemistry; Beijing Normal University; Beijing 100875 People's Republic of China
| |
Collapse
|
48
|
Yoo L, Ahn KY, Ahn JY, Laurell T, Lee YM, Yoo PJ, Lee J. A simple one-step assay platform based on fluorescence quenching of macroporous silicon. Biosens Bioelectron 2012; 41:477-83. [PMID: 23083907 DOI: 10.1016/j.bios.2012.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/27/2012] [Accepted: 09/09/2012] [Indexed: 01/24/2023]
Abstract
We synthesized 3D macroporous silicon through a simple electrochemical dissolution process and systematically estimated its protein adsorption and effect on fluorescence emission. Compared with conventional 2D polystyrene plate, the macroporous silicon showed a superior protein adsorption capacity and significant fluorescence quenching effect. We developed a 3D macroporous silicon-based adenosine assay system through the following fabrication process: streptavidin molecules that have been immobilized on the surface of macroporous silicon are attached with biotin-linked and adenosine-specific DNA aptamer, followed by hybridization between the attached aptamer and fluorescent chemical (carboxytetramethylrhodamine/CTMR) that is conjugated with a short complementary DNA sequence. In the absence of adenosine, the aptamer-CTMR complexes remain closely attached to the surface of porous silicon, hence fluorescence being significantly quenched. Upon binding to adenosine, the DNA aptamer is subject to structure switching that leads to dissociation of CTMR from DNA aptamer, and consequently the CTMR fluorescence is restored, indicating a simple one-step assay of adenosine. Compared to the conventional 2D PS and ZnO nanorods-based assays, adenosine at much lower (sub-micromolar) concentration was successfully detected through the 3D macroporous silicon-based assay. The three-dimensionally and densely immobilized aptamer probes and effective fluorescence quenching on the surface of macroporous silicon enables adenosine to be detected at lower levels. Although the adenosine detection is reported here as a proof-of-concept, the developed macroporous silicon-based simple one-step assay platform can be applied in general to fluorescence quenching -based detection of many other biomolecules.
Collapse
Affiliation(s)
- Lina Yoo
- Department of Chemical and Biological Engineering, College of Engineering Korea University, Anam-Dong 5-1, Seoul 136-713, Republic of Korea
| | | | | | | | | | | | | |
Collapse
|
49
|
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.
Collapse
Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | | |
Collapse
|
50
|
Zhu Z, Ravelet C, Perrier S, Guieu V, Fiore E, Peyrin E. Single-stranded DNA binding protein-assisted fluorescence polarization aptamer assay for detection of small molecules. Anal Chem 2012; 84:7203-11. [PMID: 22793528 DOI: 10.1021/ac301552e] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Here, we describe a new fluorescence polarization aptamer assay (FPAA) strategy which is based on the use of the single-stranded DNA binding (SSB) protein from Escherichia coli as a strong FP signal enhancer tool. This approach relied on the unique ability of the SSB protein to bind the nucleic acid aptamer in its free state but not in its target-bound folded one. Such a feature was exploited by using the antiadenosine (Ade)-DNA aptamer (Apt-A) as a model functional nucleic acid. Two fluorophores (fluorescein and Texas Red) were introduced into different sites of Apt-A to design a dozen fluorescent tracers. In the absence of the Ade target, the binding of the labeled aptamers to SSB governed a very high fluorescence anisotropy increase (in the 0.130-0.200 range) as the consequence of (i) the large global diffusion difference between the free and SSB-bound tracers and (ii) the restricted movement of the dye in the SSB-bound state. When the analyte was introduced into the reaction system, the formation of the folded tertiary structure of the Ade-Apt-A complex triggered the release of the labeled nucleic acids from the protein, leading to a strong decrease in the fluorescence anisotropy. The key factors involved in the fluorescence anisotropy change were considered through the development of a competitive displacement model, and the optimal tracer candidate was selected for the Ade assay under buffer and realistic (diluted human serum) conditions. The SSB-assisted principle was found to operate also with another aptamer system, i.e., the antiargininamide DNA aptamer, and a different biosensing configuration, i.e., the sandwich-like design, suggesting the broad usefulness of the present approach. This sensing platform allowed generation of a fluorescence anisotropy signal for aptamer probes which did not operate under the direct format and greatly improved the assay response relative to that of the most previously reported small target FPAA.
Collapse
Affiliation(s)
- Zhenyu Zhu
- Département de Pharmacochimie Moléculaire UMR 5063, Institut de Chimie Moléculaire de Grenoble FR 2607, CNRS-Université Grenoble I (Joseph Fourier), 38041 Grenoble cedex 9, France
| | | | | | | | | | | |
Collapse
|