1
|
Wang TY, Rukundo JL, Mao Z, Krylov SN. Maximizing the Accuracy of Equilibrium Dissociation Constants for Affinity Complexes: From Theory to Practical Recommendations. ACS Chem Biol 2024. [PMID: 39121869 DOI: 10.1021/acschembio.4c00259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
The equilibrium dissociation constant (Kd) is a major characteristic of affinity complexes and one of the most frequently determined physicochemical parameters. Despite its significance, the values of Kd obtained for the same complex under similar conditions often exhibit considerable discrepancies and sometimes vary by orders of magnitude. These inconsistencies highlight the susceptibility of Kd determination to large systematic errors, even when random errors are small. It is imperative to both minimize and quantitatively assess the systematic errors inherent in Kd determination. Traditionally, Kd values are determined through nonlinear regression of binding isotherms. This analysis utilizes three variables: concentrations of two reactants and a fraction R of unbound limiting reactant. The systematic errors in Kd arise directly from systematic errors in these variables. Therefore, to maximize the accuracy of Kd, this study thoroughly analyzes the sources of systematic errors within the three variables, including (i) non-additive signals to calculate R, (ii) mis-calibrated experimental instruments, (iii) inaccurate calibration parameters, (iv) insufficient incubation time, (v) unsaturated binding isotherm, (vi) impurities in the reactants, and (vii) solute adsorption onto surfaces. Through this analysis, we illustrate how each source contributes to inaccuracies in the determination of Kd and propose strategies to minimize these contributions. Additionally, we introduce a method for quantitatively assessing the confidence intervals of systematic errors in concentrations, a crucial step toward quantitatively evaluating the accuracy of Kd. While presenting original findings, this paper also reiterates the fundamentals of Kd determination, hence guiding researchers across all proficiency levels. By shedding light on the sources of systematic errors and offering strategies for their mitigation, our work will help researchers enhance the accuracy of Kd determination, thereby making binding studies more reliable and the conclusions drawn from such studies more robust.
Collapse
Affiliation(s)
- Tong Ye Wang
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Jean-Luc Rukundo
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Zhiyuan Mao
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N Krylov
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| |
Collapse
|
2
|
Smith HE, Mackenzie AM, Seddon C, Mould R, Kalampouka I, Malakar P, Needham SR, Beis K, Bell JD, Nunn A, Botchway SW. The use of NADH anisotropy to investigate mitochondrial cristae alignment. Sci Rep 2024; 14:5980. [PMID: 38472304 DOI: 10.1038/s41598-024-55780-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Life may be expressed as the flow of electrons, protons, and other ions, resulting in large potential difference. It is also highly photo-sensitive, as a large proportion of the redox capable molecules it relies on are chromophoric. It is thus suggestive that a key organelle in eukaryotes, the mitochondrion, constantly adapt their morphology as part of the homeostatic process. Studying unstained in vivo nano-scale structure in live cells is technically very challenging. One option is to study a central electron carrier in metabolism, reduced nicotinamide adenine dinucleotide (NADH), which is fluorescent and mostly located within mitochondria. Using one and two-photon absorption (340-360 nm and 730 nm, respectively), fluorescence lifetime imaging and anisotropy spectroscopy of NADH in solution and in live cells, we show that mitochondria do indeed appear to be aligned and exhibit high anisotropy (asymmetric directionality). Aqueous solution of NADH showed an anisotropy of ~ 0.20 compared to fluorescein or coumarin of < 0.1 and 0.04 in water respectively and as expected for small organic molecules. The anisotropy of NADH also increased further to 0.30 in the presence of proteins and 0.42 in glycerol (restricted environment) following two-photon excitation, suggesting more ordered structures. Two-photon NADH fluorescence imaging of Michigan Cancer Foundation-7 (MCF7) also showed strong anisotropy of 0.25 to 0.45. NADH has a quantum yield of fluorescence of 2% compared to more than 40% for photoionisation (electron generation), when exposed to light at 360 nm and below. The consequence of such highly ordered and directional NADH patterns with respect to electron ejection upon ultra-violet (UV) excitation could be very informative-especially in relation to ascertaining the extent of quantum effects in biology, including electron and photonic cascade, communication and modulation of effects such as spin and tunnelling.
Collapse
Affiliation(s)
- Holly E Smith
- UKRI, STFC, Central Laser Facility, Rutherford Appleton Laboratory, Oxfordshire, OX11 0QX, UK
| | - Alasdair M Mackenzie
- UKRI, STFC, Central Laser Facility, Rutherford Appleton Laboratory, Oxfordshire, OX11 0QX, UK
| | - Chloe Seddon
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, OX11 0FA, UK
| | - Rhys Mould
- School of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, W1W 6UW, UK
| | - Ifi Kalampouka
- School of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, W1W 6UW, UK
| | - Partha Malakar
- UKRI, STFC, Central Laser Facility, Rutherford Appleton Laboratory, Oxfordshire, OX11 0QX, UK
| | - Sarah R Needham
- UKRI, STFC, Central Laser Facility, Rutherford Appleton Laboratory, Oxfordshire, OX11 0QX, UK
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, OX11 0FA, UK
| | - Jimmy D Bell
- School of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, W1W 6UW, UK
| | - Alistair Nunn
- School of Life Sciences, Research Centre for Optimal Health, University of Westminster, London, W1W 6UW, UK
| | - Stanley W Botchway
- UKRI, STFC, Central Laser Facility, Rutherford Appleton Laboratory, Oxfordshire, OX11 0QX, UK.
| |
Collapse
|
3
|
Priyanka, Maiti S. Co-assembly-mediated biosupramolecular catalysis: thermodynamic insights into nucleobase specific (oligo)nucleotide attachment and cleavage. J Mater Chem B 2023; 11:10383-10394. [PMID: 37874292 DOI: 10.1039/d3tb01747h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Gaining control over the stability and cleavage of phosphoester and phosphodiester remains a matter of interest for their application in biotechnology to oligonucleotide-based therapeutics. Herein, we report an efficient unactivated phosphoester hydrolysis (stable mono/di/tri/cyclic nucleotide to nucleoside conversion) via a biosupramolecular system comprising of a non-covalent complex of enzyme, alkaline phosphatase (ALP), and Zn(II)-metallosurfactant. We also demonstrate the nucleobase selective activation or inhibition of ALP-mediated oligonucleotide digestion process using that complex. The higher binding affinity of Zn(II)-containing headgroup with phosphate-containing substrate enhanced the effective substrate concentration surrounding the enzyme, which, in turn, results in a drastic decrease in the Michaelis constant (KM), along with an increase in the turnover (kcat). The catalytic activation or inhibition of nucleobase-specific oligonucleotide digestion depends on the hydration, localization of the substrates, and viscosity of the resultant co-assembly upon substrate binding with the enzyme-metallosurfactant complex. Additionally, through isothermal titration calorimetry experiment, we demonstrate enthalpy-entropy change during both the supramolecular binding of (oligo)nucleotides and simultaneous activation/inhibition in catalytic cleavage. Overall, it showed the possible modularity of Zn(II)-mediated biosupramolecular interaction, describing intrinsic thermodynamic aspects in developing complex biocatalytic circuits with nucleobase-specific oligonucleotides inputs, which are relevant in designing nucleic acid-based cargo for drug delivery and bioimaging.
Collapse
Affiliation(s)
- Priyanka
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India.
| |
Collapse
|
4
|
Zhang Y, Yan P, Tang H, Zhang J. Rapid detection of tear lactoferrin for diagnosis of dry eyes by using fluorescence polarization-based aptasensor. Sci Rep 2023; 13:15179. [PMID: 37704755 PMCID: PMC10499909 DOI: 10.1038/s41598-023-42484-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 09/11/2023] [Indexed: 09/15/2023] Open
Abstract
Differentiating dry eye disease (DED) from allergic or viral conjunctivitis rapidly and accurately is important to ensure prompt diagnosis and treatment. Tear lactoferrin (LF), a multi-functional glycoprotein found in tears, decreases significantly in patients with DED, and has been considered as a DED diagnostic biomarker. Measuring tear LF level, however, takes time and requires the use of bulky instruments. Herein, a homogeneous carbon nanostructure-based aptasensor with high sensitivity and selectivity has been developed by applying fluorescence polarization (FP) technology. The FP of carbon dots (CDs) bioconjugated with LF aptamers (CDs-aptamer) is 21.2% higher than that of CDs, which can be further amplified (1.81 times) once interacting with graphene oxide nanosheets (GONS). In the presence of LF, GONS separates from CDs-aptamer because of the stronger binding affinity between CDs-aptamer to LF, resulting in the decrease of FP value. A linear relationship is observed between FP value and LF concentration in spiked tear samples from 0.66 to 3.32 mg/mL. The selectivity of the aptasensor has been investigated by measuring other proteins. The results indicate that the FP-based aptasensor is a cost-effective method with high sensitivity and selectivity in detection of tear LF.
Collapse
Affiliation(s)
- Yingqi Zhang
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON, N6A 5B9, Canada
| | - Peng Yan
- Kensington Eye Institute, Toronto Western Hospital, Kensington Eye Institute, 600-340 College St, Toronto, ON, M5T 3A9, Canada
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, M5T 3A9, Canada
| | - Howyn Tang
- School of Biomedical Engineering, University of Western Ontario, London, ON, N6A 5B9, Canada
| | - Jin Zhang
- Department of Chemical and Biochemical Engineering, University of Western Ontario, London, ON, N6A 5B9, Canada.
- School of Biomedical Engineering, University of Western Ontario, London, ON, N6A 5B9, Canada.
| |
Collapse
|
5
|
Wan Y, Zong C, Li X, Wang A, Li Y, Yang T, Bao Q, Dubow M, Yang M, Rodrigo LA, Mao C. New Insights for Biosensing: Lessons from Microbial Defense Systems. Chem Rev 2022; 122:8126-8180. [PMID: 35234463 DOI: 10.1021/acs.chemrev.1c01063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.
Collapse
Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Chengli Zong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, 1700 Fourth Street, Byers Hall 303C, San Francisco, California 94158, United States
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Yan Li
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Michael Dubow
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Université Paris-Saclay, Campus C.N.R.S, Bâtiment 12, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Ledesma-Amaro Rodrigo
- Imperial College Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| |
Collapse
|
6
|
Li Y, Yu H, Zhao Q. Aptamer fluorescence anisotropy assays for detection of aflatoxin B1 and adenosine triphosphate using antibody to amplify signal change. RSC Adv 2022; 12:7464-7468. [PMID: 35424710 PMCID: PMC8982223 DOI: 10.1039/d2ra00843b] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 12/21/2022] Open
Abstract
Fluorescence polarization/anisotropy (FP/FA) is an attractive technology for determining small molecules in homogeneous solution based on rotation changes of a fluorescent reporter. Binding induced conformation change is a specific property of aptamers. This property has been integrated into aptamer based FA assays for small molecules. In this work, we reported aptamer FA assays for aflatoxin B1 (AFB1) and adenosine triphosphate (ATP) by using antibody conjugated complementary DNA at the 3′ end and a fluorescein (FAM)-labeled aptamer at the 5′ end. The hybridization of aptamer and cDNA induced a FAM label close to the large-sized antibody, which restricts the local rotation of FAM and gives high FA signal. With the addition of target, the aptamer probe binds with the target, and the aptamer–cDNA duplex is inhibited, causing FA signal decreases. This method achieved detection of 25 pM AFB1 and 1 μM ATP, respectively. The assay is promising for application. Aptamer fluorescence anisotropy assays for small molecules (aflatoxin B1 and ATP) using antibody to amplify signal change.![]()
Collapse
Affiliation(s)
- Yapiao Li
- 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
| | - Hao Yu
- 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.,School of Environment, Hangzhou Institute for Advanced Study, UCAS Hangzhou 310000 China
| |
Collapse
|
7
|
Assays to Estimate the Binding Affinity of Aptamers. Talanta 2022; 238:122971. [PMID: 34857318 DOI: 10.1016/j.talanta.2021.122971] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023]
Abstract
Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.
Collapse
|
8
|
Schmidl D, Jonasson NSW, Menke A, Schneider S, Daumann L. Spectroscopic and in vitro investigations of Fe2+/α-Ketoglutarate-dependent enzymes involved in nucleic acid repair and modification. Chembiochem 2022; 23:e202100605. [PMID: 35040547 PMCID: PMC9401043 DOI: 10.1002/cbic.202100605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/14/2022] [Indexed: 11/08/2022]
Abstract
The activation of molecular oxygen for the highly selective functionalization and repair of DNA and RNA nucleobases is achieved by α-ketoglutarate (α-KG)/iron-dependent dioxygenases. Enzymes of special interest are the human homologs AlkBH of Escherichia coli EcAlkB and ten-eleven translocation (TET) enzymes. These enzymes are involved in demethylation or dealkylation of DNA and RNA, although additional physiological functions are continuously being revealed. Given their importance, studying enzyme-substrate interactions, turnover and kinetic parameters is pivotal for the understanding of the mode of action of these enzymes. Diverse analytical methods, including X-ray crystallography, UV/Vis absorption, electron paramagnetic resonance (EPR), circular dichroism (CD) and NMR spectroscopy have been employed to study the changes in the active site and the overall enzyme structure upon substrate, cofactor and inhibitor addition. Several methods are now available to assess activity of these enzymes. By discussing limitations and possibilities of these techniques for EcAlkB, AlkBH and TET we aim to give a comprehensive synopsis from a bioinorganic point of view, addressing researchers from different disciplines working in the highly interdisciplinary and rapidly evolving field of epigenetic processes and DNA/RNA repair and modification.
Collapse
Affiliation(s)
- David Schmidl
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Niko S W Jonasson
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Annika Menke
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Sabine Schneider
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Lena Daumann
- Ludwig-Maximilians-Universität München, Department of Chemistry, Butenandtstr. 5-13, 81377, München, GERMANY
| |
Collapse
|
9
|
Jain P, Aida T, Motosuke M. Fluorescence Anisotropy as a Temperature-Sensing Molecular Probe Using Fluorescein. MICROMACHINES 2021; 12:1109. [PMID: 34577751 PMCID: PMC8469510 DOI: 10.3390/mi12091109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/08/2021] [Accepted: 09/12/2021] [Indexed: 01/28/2023]
Abstract
Fluorescence anisotropy, a technique to study the folding state of proteins or affinity of ligands, is used in this present work as a temperature sensor, to measure the microfluidic temperature field, by adding fluorophore in the liquid. Fluorescein was used as a temperature-sensing probe, while glycerol-aq. ammonia solution was used as a working fluid. Fluorescence anisotropy of fluorescein was measured by varying various parameters. Apart from this, a comparison of fluorescence anisotropy and fluorescence intensity is also performed to demonstrate the validity of anisotropy to be applied in a microfluidic field with non-uniform liquid thickness. Viscosity dependence and temperature dependence on the anisotropy are also clarified; the results indicate an appropriate selection of relation between molecule size and viscosity is important to obtain a large temperature coefficient in anisotropy. Furthermore, a practical calibration procedure of the apparatus constant is proposed. In addition, the potential of temperature imaging is confirmed by the measurement of temperature distribution under focused laser heating.
Collapse
Affiliation(s)
- Puneet Jain
- Department of Mechanical Engineering, Faculty of Engineering, Tokyo University of Science, 6-3-1, Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; (T.A.); (M.M.)
| | - Takuya Aida
- Department of Mechanical Engineering, Faculty of Engineering, Tokyo University of Science, 6-3-1, Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; (T.A.); (M.M.)
| | - Masahiro Motosuke
- Department of Mechanical Engineering, Faculty of Engineering, Tokyo University of Science, 6-3-1, Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; (T.A.); (M.M.)
- Water Frontier Research Center, Research Institute for Science and Technology, Tokyo University of Science, 1-3, Kagurazaka, Shinjuku-ku, Tokyo 125-8585, Japan
| |
Collapse
|
10
|
Shepherd JW, Payne-Dwyer AL, Lee JE, Syeda A, Leake MC. Combining single-molecule super-resolved localization microscopy with fluorescence polarization imaging to study cellular processes. JPHYS PHOTONICS 2021. [DOI: 10.1088/2515-7647/ac015d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Super-resolution microscopy has catalyzed valuable insights into the sub-cellular, mechanistic details of many different biological processes across a wide range of cell types. Fluorescence polarization spectroscopy tools have also enabled important insights into cellular processes through identifying orientational changes of biological molecules typically at an ensemble level. Here, we combine these two biophysical methodologies in a single home-made instrument to enable the simultaneous detection of orthogonal fluorescence polarization signals from single fluorescent protein molecules used as common reporters on the localization of proteins in cellular processes. These enable measurement of spatial location to a super-resolved precision better than the diffraction-limited optical resolution, as well as estimation of molecular stoichiometry based on the brightness of individual fluorophores. In this innovation we have adapted a millisecond timescale microscope used for single-molecule detection to enable splitting of fluorescence polarization emissions into two separate imaging channels for s- and p-polarization signals, which are imaged onto separate halves of the same high sensitivity back-illuminated CMOS camera detector. We applied this fluorescence polarization super-resolved imaging modality to a range of test fluorescent samples relevant to the study of biological processes, including purified monomeric green fluorescent protein, single combed DNA molecules, and protein assemblies and complexes from live Escherichia coli and Saccharomyces cerevisiae cells. Our findings are qualitative but demonstrate promise in showing how fluorescence polarization and super-resolved localization microscopy can be combined on the same sample to enable simultaneous measurements of polarization and stoichiometry of tracked molecular complexes, as well as the translational diffusion coefficient.
Collapse
|
11
|
Ligand Discovery: High-Throughput Binding: Fluorescence Polarization (Anisotropy). Methods Mol Biol 2021. [PMID: 33877601 DOI: 10.1007/978-1-0716-1197-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
High-throughput assays based on fluorescence polarization (or fluorescence anisotropy) technology have often been employed for primary hit-finding in drug discovery. These binding assays provide a homogeneous format and consistent performance and offer advantages over some other optical methods. Developments in assay design and improvements in fluorescent probes have enabled the application of the technique to even complex biological systems. Here we describe the practical considerations for development of FP assays applied in high-throughput screening, including fluorophore selection, assay design, data analysis, and approaches for detecting compound interference.
Collapse
|
12
|
Fernandes DA, Fernandes DD, Malik A, Gomes GNW, Appak-Baskoy S, Berndl E, Gradinaru CC, Kolios MC. Multifunctional nanoparticles as theranostic agents for therapy and imaging of breast cancer. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2021; 218:112110. [PMID: 33865007 DOI: 10.1016/j.jphotobiol.2020.112110] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/13/2020] [Accepted: 12/18/2020] [Indexed: 11/26/2022]
Abstract
Over the last decade, there has been significant developments in nanotechnology, in particular for combined imaging and therapeutic applications (theranostics). The core or shell of nanoemulsions (NEs) can be loaded with various therapeutic agents, including drugs with low solubility for effective treatment, or various imaging agents for specific imaging modalities (e.g., MRI, fluorescence). In this work, perfluorohexane (PFH) NEs were synthesized for theranostic applications and were coupled to silica coated gold nanoparticles (scAuNPs) to increase the generation of PFH bubbles upon laser induced vaporization (i.e., optical droplet vaporization). The localized heat generated from the absorption properties of these nanoparticles (used to provide photoacoustic signals) can also be used to treat cancer without significantly damaging nearby healthy tissues. The theranostic potential of these PFH-NEs for contrast imaging of tumors and as a drug-delivery vehicle for therapeutic purposes were demonstrated for both in vitro and in vivo systems using a combination of photoacoustic, ultrasound and fluorescence imaging modalities. The ability of PFH-NEs to couple with scAuNPs, attach to the membranes of cancer cells and internalize within cancer cells, are encouraging for targeted chemotherapeutic applications for directly inducing cancer cell death via vaporization in clinical settings.
Collapse
Affiliation(s)
- Donald A Fernandes
- Department of Chemistry & Biology, Ryerson University, Toronto, ON M5B 2K3, Canada; Institute for Biomedical Engineering, Science and Technology (iBEST), a partnership between Ryerson University and St. Michael's Hospital, Toronto, ON M5B 1T8, Canada; Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, ON, M5B 1T8, Canada.
| | - Dennis D Fernandes
- Department of Physics, University of Toronto, Toronto, ON M5S 1A7, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Aimen Malik
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Gregory-Neal W Gomes
- Department of Physics, University of Toronto, Toronto, ON M5S 1A7, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Sila Appak-Baskoy
- Department of Chemistry & Biology, Ryerson University, Toronto, ON M5B 2K3, Canada; Institute for Biomedical Engineering, Science and Technology (iBEST), a partnership between Ryerson University and St. Michael's Hospital, Toronto, ON M5B 1T8, Canada; Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, ON, M5B 1T8, Canada
| | - Elizabeth Berndl
- Institute for Biomedical Engineering, Science and Technology (iBEST), a partnership between Ryerson University and St. Michael's Hospital, Toronto, ON M5B 1T8, Canada; Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, ON, M5B 1T8, Canada; Department of Physics, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Claudiu C Gradinaru
- Department of Physics, University of Toronto, Toronto, ON M5S 1A7, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada.
| | - Michael C Kolios
- Institute for Biomedical Engineering, Science and Technology (iBEST), a partnership between Ryerson University and St. Michael's Hospital, Toronto, ON M5B 1T8, Canada; Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Toronto, ON, M5B 1T8, Canada; Department of Physics, Ryerson University, Toronto, ON M5B 2K3, Canada.
| |
Collapse
|
13
|
Ligand modulation of the conformational dynamics of the A 2A adenosine receptor revealed by single-molecule fluorescence. Sci Rep 2021; 11:5910. [PMID: 33723285 PMCID: PMC7960716 DOI: 10.1038/s41598-021-84069-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of transmembrane proteins, making them an important target for therapeutics. Activation of these receptors is modulated by orthosteric ligands, which stabilize one or several states within a complex conformational ensemble. The intra- and inter-state dynamics, however, is not well documented. Here, we used single-molecule fluorescence to measure ligand-modulated conformational dynamics of the adenosine A2A receptor (A2AR) on nanosecond to millisecond timescales. Experiments were performed on detergent-purified A2R in either the ligand-free (apo) state, or when bound to an inverse, partial or full agonist ligand. Single-molecule Förster resonance energy transfer (smFRET) was performed on detergent-solubilized A2AR to resolve active and inactive states via the separation between transmembrane (TM) helices 4 and 6. The ligand-dependent changes of the smFRET distributions are consistent with conformational selection and with inter-state exchange lifetimes ≥ 3 ms. Local conformational dynamics around residue 2296.31 on TM6 was measured using fluorescence correlation spectroscopy (FCS), which captures dynamic quenching due to photoinduced electron transfer (PET) between a covalently-attached dye and proximal aromatic residues. Global analysis of PET-FCS data revealed fast (150-350 ns), intermediate (50-60 μs) and slow (200-300 μs) conformational dynamics in A2AR, with lifetimes and amplitudes modulated by ligands and a G-protein mimetic (mini-Gs). Most notably, the agonist binding and the coupling to mini-Gs accelerates and increases the relative contribution of the sub-microsecond phase. Molecular dynamics simulations identified three tyrosine residues (Y112, Y2887.53, and Y2907.55) as being responsible for the dynamic quenching observed by PET-FCS and revealed associated helical motions around residue 2296.31 on TM6. This study provides a quantitative description of conformational dynamics in A2AR and supports the idea that ligands bias not only GPCR conformations but also the dynamics within and between distinct conformational states of the receptor.
Collapse
|
14
|
Abdelsattar AS, Mansour Y, Aboul-Ela F. The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding. Chembiochem 2021; 22:1499-1516. [PMID: 33351206 DOI: 10.1002/cbic.202000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/19/2020] [Indexed: 12/24/2022]
Abstract
The effects of ligand binding on biomolecular conformation are crucial in drug design, enzyme mechanisms, the regulation of gene expression, and other biological processes. Descriptive models such as "lock and key", "induced fit", and "conformation selection" are common ways to interpret such interactions. Another historical model, linked equilibria, proposes that the free-energy landscape (FEL) is perturbed by the addition of ligand binding energy for the bound population of biomolecules. This principle leads to a unified, quantitative theory of ligand-induced conformation change, building upon the FEL concept. We call the map of binding free energy over biomolecular conformational space the "binding affinity landscape" (BAL). The perturbed FEL predicts/explains ligand-induced conformational changes conforming to all common descriptive models. We review recent experimental and computational studies that exemplify the perturbed FEL, with emphasis on RNA. This way of understanding ligand-induced conformation dynamics motivates new experimental and theoretical approaches to ligand design, structural biology and systems biology.
Collapse
Affiliation(s)
- Abdallah S Abdelsattar
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Youssef Mansour
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Fareed Aboul-Ela
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| |
Collapse
|
15
|
Wang X, Qian S, Wang D, Wang C, Qin H, Peng L, Lu W, Zhang Y, Qing G. Self-assembly gel-based dynamic response system for specific recognition of N-acetylneuraminic acid. J Mater Chem B 2021; 9:4690-4699. [PMID: 34076032 DOI: 10.1039/d1tb00627d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Sialic acids located at the terminal end of glycans are densely attached to cell surfaces and play crucial and distinctive roles in a variety of physiological and pathological processes, such as neural development, cell-cell interactions, autoimmunity and cancers. However, due to the subtle structural differences of sialic acid species and the complicated composition of glycans, the precise recognition of sialylated glycans is difficult. Here, a fluorescent dynamic response system based on a pyrene-conjugated histidine (PyHis) supramolecular gel is proposed. Driven by π-π stacking and intermolecular hydrogen bonds, PyHis exhibits a strong self-assembly ability and forms stable gels. It is found that introduction of N-acetylneuraminic acid (a typical sialic acid) can prevent this self-assembly process, whereas other monosaccharides or sialic acid analogs have no significant effect on it. Interestingly, a sialylated glycan also has a remarkable inhibitory effect on the gel formation, which highlights the high selectivity of the gel dynamic response system. Analysis of the mechanism reveals that the sialic acid or sialylated glycan can interact closely with two PyHis molecules stacked together in the assemblies via hydrogen bonding interactions, thereby preventing the ordered accumulation of the gelators. It is worth noting that the high-efficiency sialic acid recognition effect is not observed at the single molecule level but at the supramolecular level, indicating the unique superiority of the supramolecular self-assembly system in biomolecular recognition and response. This work shows the promising prospects of using supramolecular gels in assembly engineering, regenerative medicine, tumour cell sorting and cancer diagnosis.
Collapse
Affiliation(s)
- Xue Wang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan, 430070, P. R. China and Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.
| | - Shengxu Qian
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.
| | - Dongdong Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.
| | - Cunli Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.
| | - Haijuan Qin
- Research Centre of Modern Analytical Technology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Lang Peng
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China. and College of Chemistry and Chemical Engineering, Wuhan Textile University, 1 Sunshine Road, Wuhan 430200, P. R. China
| | - Wenqi Lu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.
| | - Yahui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.
| | - Guangyan Qing
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China. and College of Chemistry and Chemical Engineering, Wuhan Textile University, 1 Sunshine Road, Wuhan 430200, P. R. China
| |
Collapse
|
16
|
An in vitro investigation into the protective and genotoxic effects of myricetin bulk and nano forms in lymphocytes of MGUS patients and healthy individuals. Toxicol Lett 2020; 327:33-40. [DOI: 10.1016/j.toxlet.2020.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/11/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
|
17
|
Bai Y, Shu T, Su L, Zhang X. Functional nucleic acid-based fluorescence polarization/anisotropy biosensors for detection of biomarkers. Anal Bioanal Chem 2020; 412:6655-6665. [PMID: 32601896 DOI: 10.1007/s00216-020-02754-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/27/2020] [Accepted: 06/03/2020] [Indexed: 01/03/2023]
Abstract
The sensitive and selective detection of biomarkers plays a crucial role in disease diagnostics, drug discovery, and early screening of cancers. The achievement of this goal highly depends on the continuous development of biosensing technologies. Among them, fluorescence anisotropy/polarization (FA/FP) analysis receives increasing interest due to the advantage of simple operation, fast response, and no background interference. In recent decades, great progress has been achieved in FA/FP sensors thanks to the development of functional nucleic acids (FNAs) including aptamers and nucleic acid enzymes. This review focuses on FNA-based FA/FP sensors for the quantitative detection of biomarkers, such as nucleic acid, small molecules, and proteins. The design strategies, recognition elements, and practical applications are fully highlighted. The article also discusses the challenges of applying FNA-based FA/FP sensors in the next generation and the potential solutions along with future prospects. Graphical abstract.
Collapse
Affiliation(s)
- Yunlong Bai
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Tong Shu
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China. .,Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou, 510640, Guangdong, China.
| | - Lei Su
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China. .,School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, Guangdong, China.
| |
Collapse
|
18
|
Faisal Z, Vörös V, Fliszár-Nyúl E, Lemli B, Kunsági-Máté S, Csepregi R, Kőszegi T, Zsila F, Poór M. Probing the Interactions of Ochratoxin B, Ochratoxin C, Patulin, Deoxynivalenol, and T-2 Toxin with Human Serum Albumin. Toxins (Basel) 2020; 12:toxins12060392. [PMID: 32545742 PMCID: PMC7354631 DOI: 10.3390/toxins12060392] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 01/03/2023] Open
Abstract
Ochratoxins, patulin, deoxynivalenol, and T-2 toxin are mycotoxins, and common contaminants in food and drinks. Human serum albumin (HSA) forms complexes with certain mycotoxins. Since HSA can affect the toxicokinetics of bound ligand molecules, the potential interactions of ochratoxin B (OTB), ochratoxin C (OTC), patulin, deoxynivalenol, and T-2 toxin with HSA were examined, employing spectroscopic (fluorescence, UV, and circular dichroism) and ultrafiltration techniques. Furthermore, the influence of albumin on the cytotoxicity of these xenobiotics was also evaluated in cell experiments. Fluorescence studies showed the formation of highly stable OTB–HSA and OTC–HSA complexes. Furthermore, fluorescence quenching and circular dichroism measurements suggest weak or no interaction of patulin, deoxynivalenol, and T-2 toxin with HSA. In ultrafiltration studies, OTB and OTC strongly displaced the Sudlow’s site I ligand warfarin, while other mycotoxins tested did not affect either the albumin binding of warfarin or naproxen. The presence of HSA significantly decreased or even abolished the OTB- and OTC-induced cytotoxicity in cell experiments; however, the toxic impacts of patulin, deoxynivalenol, and T-2 toxin were not affected by HSA. In summary, the complex formation of OTB and OTC with albumin is relevant, whereas the interactions of patulin, deoxynivalenol, and T-2 toxin with HSA may have low toxicological importance.
Collapse
Affiliation(s)
- Zelma Faisal
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (Z.F.); (V.V.); (E.F.-N.)
- János Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary; (B.L.); (S.K.-M.); (R.C.); (T.K.)
| | - Virág Vörös
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (Z.F.); (V.V.); (E.F.-N.)
- János Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary; (B.L.); (S.K.-M.); (R.C.); (T.K.)
| | - Eszter Fliszár-Nyúl
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (Z.F.); (V.V.); (E.F.-N.)
- János Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary; (B.L.); (S.K.-M.); (R.C.); (T.K.)
| | - Beáta Lemli
- János Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary; (B.L.); (S.K.-M.); (R.C.); (T.K.)
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary
| | - Sándor Kunsági-Máté
- János Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary; (B.L.); (S.K.-M.); (R.C.); (T.K.)
- Institute of Organic and Medicinal Chemistry, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary
| | - Rita Csepregi
- János Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary; (B.L.); (S.K.-M.); (R.C.); (T.K.)
- Department of Laboratory Medicine, University of Pécs, Medical School, Ifjúság útja 13, H-7624 Pécs, Hungary
| | - Tamás Kőszegi
- János Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary; (B.L.); (S.K.-M.); (R.C.); (T.K.)
- Department of Laboratory Medicine, University of Pécs, Medical School, Ifjúság útja 13, H-7624 Pécs, Hungary
| | - Ferenc Zsila
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok krt. 2, H-1117 Budapest, Hungary;
| | - Miklós Poór
- Department of Pharmacology, Faculty of Pharmacy, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (Z.F.); (V.V.); (E.F.-N.)
- János Szentágothai Research Centre, Ifjúság útja 20, H-7624 Pécs, Hungary; (B.L.); (S.K.-M.); (R.C.); (T.K.)
- Correspondence: ; Tel.: +36-536-000 (ext. 35052)
| |
Collapse
|
19
|
Aptamer binding assays and molecular interaction studies using fluorescence anisotropy - A review. Anal Chim Acta 2020; 1125:267-278. [PMID: 32674773 DOI: 10.1016/j.aca.2020.05.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/16/2020] [Accepted: 05/23/2020] [Indexed: 12/26/2022]
Abstract
Binding of nucleic acid aptamers to specific targets and detection with fluorescence anisotropy (FA) or fluorescence polarization (FP) take advantage of the complementary features of aptamers and the fluorescence techniques. We review recent advances in affinity binding assays using aptamers and FA/FP, with an emphasis on studies of molecular interactions and identification of binding sites. Aptamers provide several benefits, including the ease of labelling fluorophores on specific sites, binding-induced changes in aptamer structures, hybridization of the aptamers to complementary sequences, changes in molecular volume upon binding of the aptamer to its target, and adsorption of aptamers onto nanomaterials. Some of these benefits have been utilized for FA/FP assays. Once the aptamer binds to its target, the resulting changes in molecular volume (size), structure, local rotation of the fluorophore, and/or the fluorescence lifetime influence changes to the FA/FP values. Measurements of these fluorescence anisotropy/polarization changes have provided insights into the molecular interactions, such as the binding affinity and the site of binding. Studies of molecular interactions conducted in homogeneous solutions, as well as those with separations, e.g., capillary electrophoresis, have been summarized in this review. Studies on mapping the position of binding in aptamers at the single nucleotide level have demonstrated a unique benefit of the FA/FP techniques and pointed to an exciting direction for future research.
Collapse
|
20
|
Li Y, Zhang N, Wang H, Zhao Q. Fluorescence Anisotropy-Based Signal-Off and Signal-On Aptamer Assays Using Lissamine Rhodamine B as a Label for Ochratoxin A. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4277-4283. [PMID: 32182058 DOI: 10.1021/acs.jafc.0c00549] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ochratoxin A (OTA), a common mycotoxin, has attracted great concern as many foodstuffs can suffer from OTA contamination; OTA causes harmful effects on human and animals. Rapid and sensitive detection of OTA is demanded in many fields for agricultural product quality, food safety, and health. Aptamer fluorescence polarization/anisotropy (FP/FA) assays integrate advantages of nucleic acid aptamers (e.g., easy preparation, high stability, and low cost) and FP/FA analysis (e.g., high sensitivity, rapidity, simplicity, and robustness). Here, we report the preparation of lissamine rhodamine B labeled OTA and developed competitive aptamer fluorescence anisotropy (FA) assays for OTA with signal-off or signal-on responses by using this fluorescently labeled probe. In the signal-off FA assay, the binding between the fluorescent probe and aptamer gave a large FA signal due to molecular volume increase, and the fluorescent probe was displaced from the aptamer in the presence of OTA target, causing FA to decrease. To further enhance the FA change in the signal-off assay, large-sized streptavidin was conjugated on the aptamer, and this assay allowed for a detection limit of 2.5 nM and a more remarkable FA decrease. Furthermore, we found that the fluorescent probe could interact with Tween 20, which caused the fluorescent probe to show a higher FA value than that of the aptamer-fluorescent probe complex. A signal-on FA assay was achieved in the binding buffer containing 0.1% Tween 20, with a detection limit of 10 nM. Signal-off and signal-on FA methods both were selective and enabled detection of OTA spiked in red wine samples, showing capability for target analysis in complex sample matrix.
Collapse
Affiliation(s)
- Yapiao Li
- 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
| | - Ning Zhang
- 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
| | - 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
|
21
|
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
|
22
|
Sandoval JE, Reich NO. The R882H substitution in the human de novo DNA methyltransferase DNMT3A disrupts allosteric regulation by the tumor supressor p53. J Biol Chem 2019; 294:18207-18219. [PMID: 31640986 DOI: 10.1074/jbc.ra119.010827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/18/2019] [Indexed: 12/14/2022] Open
Abstract
A myriad of protein partners modulate the activity of the human DNA methyltransferase 3A (DNMT3A), whose interactions with these other proteins are frequently altered during oncogenesis. We show here that the tumor suppressor p53 decreases DNMT3A activity by forming a heterotetramer complex with DNMT3A. Mutational and modeling experiments suggested that p53 interacts with the same region in DNMT3A as does the structurally characterized DNMT3L. We observed that the p53-mediated repression of DNMT3A activity is blocked by amino acid substitutions within this interface, but surprisingly, also by a distal DNMT3A residue, R882H. DNMT3A R882H occurs frequently in various cancers, including acute myeloid leukemia, and our results suggest that the effects of R882H and other DNMT3A mutations may go beyond changes in DNMT3A methylation activity. To further understand the dynamics of how protein-protein interactions modulate DNMT3A activity, we determined that p53 has a greater affinity for DNMT3A than for DNMT3L and that p53 readily displaces DNMT3L from the DNMT3A:DNMT3L heterotetramer. Interestingly, this occurred even when the preformed DNMT3A:DNMT3L complex was actively methylating DNA. The frequently identified p53 substitutions (R248W and R273H), whereas able to regulate DNMT3A function when forming the DNMT3A:p53 heterotetramer, no longer displaced DNMT3L from the DNMT3A:DNMT3L heterotetramer. The results of our work highlight the complex interplay between DNMT3A, p53, and DNMT3L and how these interactions are further modulated by clinically derived mutations in each of the interacting partners.
Collapse
Affiliation(s)
- Jonathan E Sandoval
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9510
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510.
| |
Collapse
|
23
|
Wolfe AJ, Parella KJ, Movileanu L. High-Throughput Screening of Protein-Detergent Complexes Using Fluorescence Polarization Spectroscopy. ACTA ACUST UNITED AC 2019; 97:e96. [PMID: 31517448 DOI: 10.1002/cpps.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This article provides detailed protocols for a high-throughput fluorescence polarization (FP) spectroscopy approach to disentangle the interactions of membrane proteins with solubilizing detergents. Existing techniques for examining the membrane protein-detergent complex (PDC) interactions are low throughput and require high amounts of proteins. Here, we describe a 96-well analytical approach, which facilitates a scalable analysis of the PDC interactions at low-nanomolar concentrations of membrane proteins in native solutions. At detergent concentrations much greater than the equilibrium dissociation constant of the PDC, Kd , the FP anisotropy reaches a saturated value, so it is independent of the detergent concentration. On the contrary, at detergent concentrations comparable with or lower than the Kd , the FP anisotropy readout undergoes a time-dependent decrease, exhibiting a sensitive and specific detergent-dissociation signature. Our approach can also be used for determining the kinetic rate constants of association and dissociation. With further development, these protocols might be used in various arenas of membrane protein research that pertain to extraction, solubilization, and stabilization. © 2019 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Aaron J Wolfe
- Ichor Therapeutics, Inc., LaFayette, New York.,Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, New York
| | - Kyle J Parella
- Ichor Therapeutics, Inc., LaFayette, New York.,Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, New York
| | - Liviu Movileanu
- Department of Physics, Syracuse University, Syracuse, New York.,Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, New York
| |
Collapse
|
24
|
Modulation effect of core-wall ratio on the stability and antibacterial activity of cinnamaldehyde liposomes. Chem Phys Lipids 2019; 223:104790. [DOI: 10.1016/j.chemphyslip.2019.104790] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/30/2019] [Accepted: 06/26/2019] [Indexed: 11/19/2022]
|
25
|
Ma P, Ye H, Deng J, Khan IM, Yue L, Wang Z. A fluorescence polarization aptasensor coupled with polymerase chain reaction and streptavidin for chloramphenicol detection. Talanta 2019; 205:120119. [PMID: 31450463 DOI: 10.1016/j.talanta.2019.120119] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/23/2019] [Accepted: 07/03/2019] [Indexed: 01/28/2023]
Abstract
The authors describe a fluorescence polarization (FP) aptasensor based on the polymerase chain reaction (PCR) and streptavidin as dual FP amplifiers to detect chloramphenicol residues in food. Briefly, label-free aptamer was incubated with chloramphenicol and the aptamer-chloramphenicol conjugate was used as a template. Subsequently, the FAM-labeled forward primer and biotin-labeled reverse primer were added for PCR to amplify the template and the FAM-labeled primer. The molecular weight of FAM-labeled primer increased rapidly and the corresponding FP also enhanced. Finally, with the introduction of streptavidin, the PCR products and streptavidin were combined with the biotin-streptavidin interactions, resulting in much larger molecular weight. Thus, a dual amplified FP signal was obtained. Under optimal conditions, we were able to achieve a wide linear detection range of 0.001-200 nM. In addition, the designed strategy was applied to detect chloramphenicol in honey samples with high accuracy. Moreover, the strategy can be easily extended to detect other small molecules by changing the corresponding aptamers, which provide a promising avenue for the detection of small molecules by FP.
Collapse
Affiliation(s)
- Pengfei Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Hua Ye
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Jieying Deng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Lin Yue
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, PR China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, PR China; Collaborative Innovation Center of Food Safety and Quality Control of Jiangsu Province, Jiangnan University, Wuxi, 214122, China; School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116024, PR China.
| |
Collapse
|
26
|
Li Y, Zhao Q. Aptamer Structure Switch Fluorescence Anisotropy Assay for Small Molecules Using Streptavidin as an Effective Signal Amplifier Based on Proximity Effect. Anal Chem 2019; 91:7379-7384. [PMID: 31079453 DOI: 10.1021/acs.analchem.9b01253] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorescence polarization/anisotropy (FP/FA) approaches are appealing for targets sensing in homogeneous solution due to simplicity, reproducibility and sensitivity. Taking advantage of aptamers, aptamer structure switch FA methods are unique for small molecule detection based on the competition between aptamer-target binding and the hybridization of aptamer and complementary DNA (cDNA). However, usually small FA change is generated in these aptamer assays that only rely on size change caused by hybridization of an oligonucleotide because of the rapid local rotation of fluorophores and small mass change. Here we describe a simple and general aptamer structure switch FA assay for small molecules by employing a large-sized streptavidin (SA) as an effective signal amplifier based on proximity effect to reduce local rotation of fluorophore. In this design, the SA-labeled cDNA hybridizes with fluorescein (FAM)-labeled aptamer, drawing FAM close to SA and bringing a much higher FA value due to restricted local rotation of FAM. Small molecule-aptamer probe binding causes displacement of the SA-labeled cDNA and great decrease of FA. The closeness of SA to FAM in the duplex is key for this proposed strategy to produce large FA changes in target detection. Our method enabled to detect 60 pM aflatoxin B1 (AFB1), 1 nM ochratoxin A (OTA), and 0.5 μM adenosine triphosphate (ATP), respectively. This aptamer FA method combines the merits of aptamers and FA analysis, and it is promising in applications of detection of small molecules with good sensitivity.
Collapse
Affiliation(s)
- Yapiao Li
- 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
|
27
|
Camacho R, Täuber D, Scheblykin IG. Fluorescence Anisotropy Reloaded-Emerging Polarization Microscopy Methods for Assessing Chromophores' Organization and Excitation Energy Transfer in Single Molecules, Particles, Films, and Beyond. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1805671. [PMID: 30721532 DOI: 10.1002/adma.201805671] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/12/2018] [Indexed: 06/09/2023]
Abstract
Fluorescence polarization is widely used to assess the orientation/rotation of molecules, and the excitation energy transfer between closely located chromophores. Emerging since the 1990s, single molecule fluorescence spectroscopy and imaging stimulate the application of light polarization for studying molecular organization and energy transfer beyond ensemble averaging. Here, traditional fluorescence polarization and linear dichroism methods used for bulk samples are compared with techniques specially developed for, or inspired by, single molecule fluorescence spectroscopy. Techniques for assessing energy transfer in anisotropic samples, where the traditional fluorescence anisotropy framework is not readily applicable, are discussed in depth. It is shown that the concept of a polarization portrait and the single funnel approximation can lay the foundation for alternative energy transfer metrics. Examples ranging from fundamental studies of photoactive materials (conjugated polymers, light-harvesting aggregates, and perovskite semiconductors) to Förster resonant energy transfer (FRET)-based biomedical imaging are presented. Furthermore, novel uses of light polarization for super-resolution optical imaging are mentioned as well as strategies for avoiding artifacts in polarization microscopy.
Collapse
Affiliation(s)
- Rafael Camacho
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Daniela Täuber
- Chemical Physics and NanoLund, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
- Biopolarisation, Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, D-07745, Jena, Germany
- Institute of Solid State Physics, FSU Jena, Helmholtzweg 3, D-07743, Jena, Germany
| | - Ivan G Scheblykin
- Chemical Physics and NanoLund, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
| |
Collapse
|
28
|
Nucleic acid aptamers improving fluorescence anisotropy and fluorescence polarization assays for small molecules. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.11.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
29
|
Wolfe AJ, Gugel JF, Chen M, Movileanu L. Kinetics of Membrane Protein-Detergent Interactions Depend on Protein Electrostatics. J Phys Chem B 2018; 122:9471-9481. [PMID: 30251852 DOI: 10.1021/acs.jpcb.8b07889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Interactions of a membrane protein with a detergent micelle represent a fundamental process with practical implications in structural and chemical biology. Quantitative assessment of the kinetics of protein-detergent complex (PDC) interactions has always been challenged by complicated behavior of both membrane proteins and solubilizing detergents in aqueous phase. Here, we show the kinetic reads of the desorption of maltoside-containing detergents from β-barrel membrane proteins. Using steady-state fluorescence polarization (FP) anisotropy measurements, we recorded real-time, specific signatures of the PDC interactions. The results of these measurements were used to infer the model-dependent rate constants of association and dissociation of the proteomicelles. Remarkably, the kinetics of the PDC interactions depend on the overall protein charge despite the nonionic nature of the detergent monomers. In the future, this approach might be employed for high-throughput screening of kinetic fingerprints of different membrane proteins stabilized in micelles that contain mixtures of various detergents.
Collapse
Affiliation(s)
- Aaron J Wolfe
- Department of Physics , Syracuse University , 201 Physics Building , Syracuse , New York 13244-1130 , United States.,Structural Biology, Biochemistry, and Biophysics Program , Syracuse University , 111 College Place , Syracuse , New York 13244-4100 , United States
| | - Jack F Gugel
- Department of Physics , Syracuse University , 201 Physics Building , Syracuse , New York 13244-1130 , United States
| | - Min Chen
- Department of Chemistry , University of Massachusetts , 820 LGRT, 710 North Pleasant Street , Amherst , Massachusetts 01003-9336 , United States
| | - Liviu Movileanu
- Department of Physics , Syracuse University , 201 Physics Building , Syracuse , New York 13244-1130 , United States.,Structural Biology, Biochemistry, and Biophysics Program , Syracuse University , 111 College Place , Syracuse , New York 13244-4100 , United States.,Department of Biomedical and Chemical Engineering , Syracuse University , 223 Link Hall , Syracuse , New York 13244 , United States
| |
Collapse
|
30
|
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
|
31
|
Zhang O, Lu J, Ding T, Lew MD. Imaging the three-dimensional orientation and rotational mobility of fluorescent emitters using the Tri-spot point spread function. APPLIED PHYSICS LETTERS 2018; 113:031103. [PMID: 30057423 PMCID: PMC6050162 DOI: 10.1063/1.5031759] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/27/2018] [Indexed: 04/14/2023]
Abstract
Fluorescence photons emitted by single molecules contain rich information regarding their rotational motions, but adapting single-molecule localization microscopy (SMLM) to measure their orientations and rotational mobilities with high precision remains a challenge. Inspired by dipole radiation patterns, we design and implement a Tri-spot point spread function (PSF) that simultaneously measures the three-dimensional orientation and the rotational mobility of dipole-like emitters across a large field of view. We show that the orientation measurements done using the Tri-spot PSF are sufficiently accurate to correct the anisotropy-based localization bias, from 30 nm to 7 nm, in SMLM. We further characterize the emission anisotropy of fluorescent beads, revealing that both 20-nm and 100-nm diameter beads emit light significantly differently from isotropic point sources. Exciting 100-nm beads with linearly polarized light, we observe significant depolarization of the emitted fluorescence using the Tri-spot PSF that is difficult to detect using other methods. Finally, we demonstrate that the Tri-spot PSF detects rotational dynamics of single molecules within a polymer thin film that are not observable by conventional SMLM.
Collapse
Affiliation(s)
- Oumeng Zhang
- Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Jin Lu
- Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Tianben Ding
- Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Matthew D Lew
- Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| |
Collapse
|
32
|
Wolfe AJ, Gugel JF, Chen M, Movileanu L. Detergent Desorption of Membrane Proteins Exhibits Two Kinetic Phases. J Phys Chem Lett 2018; 9:1913-1919. [PMID: 29595981 PMCID: PMC5908730 DOI: 10.1021/acs.jpclett.8b00549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Gradual dissociation of detergent molecules from water-insoluble membrane proteins culminates in protein aggregation. However, the time-dependent trajectory of this process remains ambiguous because the signal-to-noise ratio of most spectroscopic and calorimetric techniques is drastically declined by the presence of protein aggregates in solution. We show that by using steady-state fluorescence polarization (FP) spectroscopy the dissociation of the protein-detergent complex (PDC) can be inspected in real time at detergent concentrations below the critical micelle concentration. This article provides experimental evidence of the coexistence of two distinct phases of the dissociations of detergent monomers from membrane proteins. We first noted a slow detergent predesolvation process, which was accompanied by a relatively modest change in the FP anisotropy, suggesting a small number of dissociated detergent monomers from the proteomicelles. This predesolvation phase was followed by a fast detergent desolvation process, which was highlighted by a major alteration in the FP anisotropy. The durations and rates of these phases were dependent on both the detergent concentration and the interfacial PDC interactions. Further development of this approach might lead to the creation of a new semiquantitative method for the assessment of the kinetics of association and dissociation of proteomicelles.
Collapse
Affiliation(s)
- Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
| | - Jack F. Gugel
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Min Chen
- Department of Chemistry, University of Massachusetts Amherst, 820 LGRT, 710 North Pleasant Street, Amherst, Massachusetts 01003-9336, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse University, 223 Link Hall, Syracuse, New York 13244, USA
| |
Collapse
|
33
|
Arad E, Malishev R, Rapaport H, Jelinek R. Membrane Determinants Affect Fibrillation Processes of β-Sheet Charged Peptides. Biomacromolecules 2017; 19:307-314. [DOI: 10.1021/acs.biomac.7b01318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elad Arad
- Department of Chemistry, ‡Avram and Stella Goldstein-Goren Department of Biotechnology
Engineering, and §Ilse Katz Institute for Nano-Science and Technology (IKI), Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Ravit Malishev
- Department of Chemistry, ‡Avram and Stella Goldstein-Goren Department of Biotechnology
Engineering, and §Ilse Katz Institute for Nano-Science and Technology (IKI), Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Hanna Rapaport
- Department of Chemistry, ‡Avram and Stella Goldstein-Goren Department of Biotechnology
Engineering, and §Ilse Katz Institute for Nano-Science and Technology (IKI), Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Raz Jelinek
- Department of Chemistry, ‡Avram and Stella Goldstein-Goren Department of Biotechnology
Engineering, and §Ilse Katz Institute for Nano-Science and Technology (IKI), Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| |
Collapse
|
34
|
Manger LH, Foote AK, Wood SL, Holden MR, Heylman KD, Margittai M, Goldsmith RH. Revealing Conformational Variants of Solution-Phase Intrinsically Disordered Tau Protein at the Single-Molecule Level. Angew Chem Int Ed Engl 2017; 56:15584-15588. [PMID: 29063723 PMCID: PMC5831721 DOI: 10.1002/anie.201708242] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/05/2017] [Indexed: 11/09/2022]
Abstract
Intrinsically disordered proteins, such as tau protein, adopt a variety of conformations in solution, complicating solution-phase structural studies. We employed an anti-Brownian electrokinetic (ABEL) trap to prolong measurements of single tau proteins in solution. Once trapped, we recorded the fluorescence anisotropy to investigate the diversity of conformations sampled by the single molecules. A distribution of anisotropy values obtained from trapped tau protein is conspicuously bimodal while those obtained by trapping a globular protein or individual fluorophores are not. Time-resolved fluorescence anisotropy measurements were used to provide an explanation of the bimodal distribution as originating from a shift in the compaction of the two different families of conformations.
Collapse
Affiliation(s)
- Lydia H Manger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Alexander K Foote
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Sharla L Wood
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Michael R Holden
- Department of Chemistry & Biochemistry, University of Denver, 2190 East Iliff Ave., Denver, CO, 80208, USA
| | - Kevin D Heylman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Martin Margittai
- Department of Chemistry & Biochemistry, University of Denver, 2190 East Iliff Ave., Denver, CO, 80208, USA
| | - Randall H Goldsmith
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| |
Collapse
|
35
|
Revealing Conformational Variants of Solution-Phase Intrinsically Disordered Tau Protein at the Single-Molecule Level. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
36
|
Wolfe AJ, Si W, Zhang Z, Blanden AR, Hsueh YC, Gugel JF, Pham B, Chen M, Loh SN, Rozovsky S, Aksimentiev A, Movileanu L. Quantification of Membrane Protein-Detergent Complex Interactions. J Phys Chem B 2017; 121:10228-10241. [PMID: 29035562 DOI: 10.1021/acs.jpcb.7b08045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although fundamentally significant in structural, chemical, and membrane biology, the interfacial protein-detergent complex (PDC) interactions have been modestly examined because of the complicated behavior of both detergents and membrane proteins in aqueous phase. Membrane proteins are prone to unproductive aggregation resulting from poor detergent solvation, but the participating forces in this phenomenon remain ambiguous. Here, we show that using rational membrane protein design, targeted chemical modification, and steady-state fluorescence polarization spectroscopy, the detergent desolvation of membrane proteins can be quantitatively evaluated. We demonstrate that depleting the detergent in the sample well produced a two-state transition of membrane proteins between a fully detergent-solvated state and a detergent-desolvated state, the nature of which depended on the interfacial PDC interactions. Using a panel of six membrane proteins of varying hydrophobic topography, structural fingerprint, and charge distribution on the solvent-accessible surface, we provide direct experimental evidence for the contributions of the electrostatic and hydrophobic interactions to the protein solvation properties. Moreover, all-atom molecular dynamics simulations report the major contribution of the hydrophobic forces exerted at the PDC interface. This semiquantitative approach might be extended in the future to include studies of the interfacial PDC interactions of other challenging membrane protein systems of unknown structure. This would have practical importance in protein extraction, solubilization, stabilization, and crystallization.
Collapse
Affiliation(s)
- Aaron J Wolfe
- Department of Physics, Syracuse University , 201 Physics Building, Syracuse, New York 13244-1130, United States.,Structural Biology, Biochemistry, and Biophysics Program, Syracuse University , 111 College Place, Syracuse, New York 13244-4100, United States
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University , Nanjing 210096, China.,Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Zhengqi Zhang
- Department of Chemistry and Biochemistry, University of Delaware , 136 Brown Laboratory, Newark, Delaware 19716, United States
| | - Adam R Blanden
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University , 4249 Weiskotten Hall, 766 Irving Av., Syracuse, New York 13210, United States
| | - Yi-Ching Hsueh
- Department of Physics, Syracuse University , 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Jack F Gugel
- Department of Physics, Syracuse University , 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Bach Pham
- Department of Chemistry, University of Massachusetts , 820 LGRT, 710 North Pleasant Street, Amherst, Massachusetts 01003-9336, United States
| | - Min Chen
- Department of Chemistry, University of Massachusetts , 820 LGRT, 710 North Pleasant Street, Amherst, Massachusetts 01003-9336, United States
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University , 4249 Weiskotten Hall, 766 Irving Av., Syracuse, New York 13210, United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware , 136 Brown Laboratory, Newark, Delaware 19716, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University , 201 Physics Building, Syracuse, New York 13244-1130, United States.,Structural Biology, Biochemistry, and Biophysics Program, Syracuse University , 111 College Place, Syracuse, New York 13244-4100, United States.,Department of Biomedical and Chemical Engineering, Syracuse University , 329 Link Hall, Syracuse, New York 13244, United States
| |
Collapse
|
37
|
Fernandes DD, Bamrah J, Kailasam S, Gomes GNW, Li Y, Wieden HJ, Gradinaru CC. Characterization of Fluorescein Arsenical Hairpin (FlAsH) as a Probe for Single-Molecule Fluorescence Spectroscopy. Sci Rep 2017; 7:13063. [PMID: 29026195 PMCID: PMC5638890 DOI: 10.1038/s41598-017-13427-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/21/2017] [Indexed: 01/27/2023] Open
Abstract
In recent years, new labelling strategies have been developed that involve the genetic insertion of small amino-acid sequences for specific attachment of small organic fluorophores. Here, we focus on the tetracysteine FCM motif (FLNCCPGCCMEP), which binds to fluorescein arsenical hairpin (FlAsH), and the ybbR motif (TVLDSLEFIASKLA) which binds fluorophores conjugated to Coenzyme A (CoA) via a phosphoryl transfer reaction. We designed a peptide containing both motifs for orthogonal labelling with FlAsH and Alexa647 (AF647). Molecular dynamics simulations showed that both motifs remain solvent-accessible for labelling reactions. Fluorescence spectra, correlation spectroscopy and anisotropy decay were used to characterize labelling and to obtain photophysical parameters of free and peptide-bound FlAsH. The data demonstrates that FlAsH is a viable probe for single-molecule studies. Single-molecule imaging confirmed dual labeling of the peptide with FlAsH and AF647. Multiparameter single-molecule Förster Resonance Energy Transfer (smFRET) measurements were performed on freely diffusing peptides in solution. The smFRET histogram showed different peaks corresponding to different backbone and dye orientations, in agreement with the molecular dynamics simulations. The tandem of fluorophores and the labelling strategy described here are a promising alternative to bulky fusion fluorescent proteins for smFRET and single-molecule tracking studies of membrane proteins.
Collapse
Affiliation(s)
- Dennis D Fernandes
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada.
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
| | - Jasbir Bamrah
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Senthilkumar Kailasam
- Alberta RNA Research & Training Institute, Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Gregory-Neal W Gomes
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Yuchong Li
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research & Training Institute, Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, T1K 3M4, Canada
| | - Claudiu C Gradinaru
- Department of Physics, University of Toronto, Toronto, Ontario, M5S 1A7, Canada.
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
| |
Collapse
|
38
|
Wolfe AJ, Hsueh YC, Blanden AR, Mohammad MM, Pham B, Thakur AK, Loh SN, Chen M, Movileanu L. Interrogating Detergent Desolvation of Nanopore-Forming Proteins by Fluorescence Polarization Spectroscopy. Anal Chem 2017; 89:8013-8020. [PMID: 28650154 PMCID: PMC5558884 DOI: 10.1021/acs.analchem.7b01339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Understanding how membrane proteins interact with detergents is of fundamental and practical significance in structural and chemical biology as well as in nanobiotechnology. Current methods for inspecting protein-detergent complex (PDC) interfaces require high concentrations of protein and are of low throughput. Here, we describe a scalable, spectroscopic approach that uses nanomolar protein concentrations in native solutions. This approach, which is based on steady-state fluorescence polarization (FP) spectroscopy, kinetically resolves the dissociation of detergents from membrane proteins and protein unfolding. For satisfactorily solubilizing detergents, at concentrations much greater than the critical micelle concentration (CMC), the fluorescence anisotropy was independent of detergent concentration. In contrast, at detergent concentrations comparable with or below the CMC, the anisotropy readout underwent a time-dependent decrease, showing a specific and sensitive protein unfolding signature. Functionally reconstituted membrane proteins into a bilayer membrane confirmed predictions made by these FP-based determinations with respect to varying refolding conditions. From a practical point of view, this 96-well analytical approach will facilitate a massively parallel assessment of the PDC interfacial interactions under a fairly broad range of micellar and environmental conditions. We expect that these studies will potentially accelerate research in membrane proteins pertaining to their extraction, solubilization, stabilization, and crystallization, as well as reconstitution into bilayer membranes.
Collapse
Affiliation(s)
- Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
| | - Yi-Ching Hsueh
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Adam R. Blanden
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Av., Syracuse, New York 13210, USA
| | - Mohammad M. Mohammad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003-9336, USA
| | - Avinash K. Thakur
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
| | - Stewart N. Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Av., Syracuse, New York 13210, USA
| | - Min Chen
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003-9336, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
| |
Collapse
|
39
|
Vinegoni C, Fumene Feruglio P, Brand C, Lee S, Nibbs AE, Stapleton S, Shah S, Gryczynski I, Reiner T, Mazitschek R, Weissleder R. Measurement of drug-target engagement in live cells by two-photon fluorescence anisotropy imaging. Nat Protoc 2017; 12:1472-1497. [PMID: 28686582 PMCID: PMC5928516 DOI: 10.1038/nprot.2017.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The ability to directly image and quantify drug-target engagement and drug distribution with subcellular resolution in live cells and whole organisms is a prerequisite to establishing accurate models of the kinetics and dynamics of drug action. Such methods would thus have far-reaching applications in drug development and molecular pharmacology. We recently presented one such technique based on fluorescence anisotropy, a spectroscopic method based on polarization light analysis and capable of measuring the binding interaction between molecules. Our technique allows the direct characterization of target engagement of fluorescently labeled drugs, using fluorophores with a fluorescence lifetime larger than the rotational correlation of the bound complex. Here we describe an optimized protocol for simultaneous dual-channel two-photon fluorescence anisotropy microscopy acquisition to perform drug-target measurements. We also provide the necessary software to implement stream processing to visualize images and to calculate quantitative parameters. The assembly and characterization part of the protocol can be implemented in 1 d. Sample preparation, characterization and imaging of drug binding can be completed in 2 d. Although currently adapted to an Olympus FV1000MPE microscope, the protocol can be extended to other commercial or custom-built microscopes.
Collapse
Affiliation(s)
- Claudio Vinegoni
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Paolo Fumene Feruglio
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, Verona, Italy
| | - Christian Brand
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sungon Lee
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- School of Electrical Engineering, Hanyang University, Ansan, Republic of Korea
| | - Antoinette E Nibbs
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Shawn Stapleton
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Sunil Shah
- Institute for Molecular Medicine, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Ignacy Gryczynski
- Institute for Molecular Medicine, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Thomas Reiner
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ralph Mazitschek
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ralph Weissleder
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
40
|
Nandi S, Malishev R, Bhunia SK, Kolusheva S, Jopp J, Jelinek R. Lipid-Bilayer Dynamics Probed by a Carbon Dot-Phospholipid Conjugate. Biophys J 2017; 110:2016-25. [PMID: 27166809 DOI: 10.1016/j.bpj.2016.04.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 03/09/2016] [Accepted: 04/04/2016] [Indexed: 12/28/2022] Open
Abstract
Elucidating the dynamic properties of membranes is important for understanding fundamental cellular processes and for shedding light on the interactions of proteins, drugs, and viruses with the cell surface. Dynamic studies of lipid bilayers have been constrained, however, by the relatively small number of pertinent molecular probes and the limited physicochemical properties of the probes. We show that a lipid conjugate comprised of a fluorescent carbon dot (C-dot) covalently attached to a phospholipid constitutes a versatile and effective vehicle for studying bilayer dynamics. The C-dot-modified phospholipids readily incorporated within biomimetic membranes, including solid-supported bilayers and small and giant vesicles, and inserted into actual cellular membranes. We employed the C-dot-phospholipid probe to elucidate the effects of polymyxin-B (a cytolytic peptide), valproic acid (a lipophilic drug), and amyloid-β (a peptide associated with Alzheimer's disease) upon bilayer fluidity and lipid dynamics through the application of various biophysical techniques.
Collapse
Affiliation(s)
- Sukhendu Nandi
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Ravit Malishev
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel
| | | | - Sofiya Kolusheva
- Ilse Katz Institute for Nanoscale Science & Technology, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Jürgen Jopp
- Ilse Katz Institute for Nanoscale Science & Technology, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Raz Jelinek
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel; Ilse Katz Institute for Nanoscale Science & Technology, Ben Gurion University of the Negev, Beer Sheva, Israel.
| |
Collapse
|
41
|
Li Y, Sun L, Zhao Q. Competitive fluorescence anisotropy/polarization assay for ATP using aptamer as affinity ligand and dye-labeled ATP as fluorescence tracer. Talanta 2017; 174:7-13. [PMID: 28738645 DOI: 10.1016/j.talanta.2017.05.077] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/18/2017] [Accepted: 05/26/2017] [Indexed: 12/26/2022]
Abstract
We developed an aptamer-based competitive fluorescence anisotropy (FA)/fluorescence polarization (FP) assay for adenosine triphosphate (ATP). Different from the traditional fluorescence polarization immunoassays for small molecules, here DNA aptamer against ATP was used as affinity ligand, and tetramethylrhodamine (TMR) labeled ATP served as fluorescent tracer. The binding between TMR-labeled ATP and aptamer gave large FA due to molecular volume increase and restricted rotation of the dye-labeled ATP. When ATP was added in solution, ATP competitively displaced the TMR-labeled ATP from aptamer affinity complex, causing decrease of FA of TMR-labeled ATP. The buffer containing MgCl2 and incubation at low temperature were preferred for large FA change in the FA assay. The FA change was further enhanced in this competitive FA assay by increasing the molecular weight of aptamer through extension of aptamer sequences or conjugating streptavidin protein on aptamer. This method allowed for the detection of ATP in the range from 0.5μM to 1mM, generating the maximum FA change about 0.187 (corresponding maximum FP change about 0.242). The detection of ATP spiked in diluted urine or serum sample was achieved, showing capability for analysis in complex sample matrix. This assay also enabled the detection of the analogues of ATP, e.g. adenosine, adenosine monophosphate (AMP), and adenosine diphosphate (ADP) with similar sensitivity. This aptamer-based competitive FA assay takes advantages of aptamer in ease of synthesis, good thermal stability, and facile modulating the molecular mass of aptamer.
Collapse
Affiliation(s)
- Yapiao Li
- 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
| | - 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
|
42
|
Sueyoshi D, Anraku Y, Komatsu T, Urano Y, Kataoka K. Enzyme-Loaded Polyion Complex Vesicles as in Vivo Nanoreactors Working Sustainably under the Blood Circulation: Characterization and Functional Evaluation. Biomacromolecules 2017; 18:1189-1196. [DOI: 10.1021/acs.biomac.6b01870] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Daiki Sueyoshi
- Graduate
School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Innovation
Center of Nanomedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Yasutaka Anraku
- Graduate
School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Innovation
Center of Nanomedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Toru Komatsu
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasuteru Urano
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Graduate
School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunori Kataoka
- Graduate
School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Graduate
School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Policy
Alternatives Research Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-1709, Japan
- Innovation
Center of Nanomedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| |
Collapse
|
43
|
Xiong Y, Jiang G, Li M, Qing G, Li X, Liang X, Sun T. Sialic Acid-Responsive Polymeric Interface Material: From Molecular Recognition to Macroscopic Property Switching. Sci Rep 2017; 7:40913. [PMID: 28084463 PMCID: PMC5234036 DOI: 10.1038/srep40913] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/12/2016] [Indexed: 12/25/2022] Open
Abstract
Biological systems that utilize multiple weak non-covalent interactions and hierarchical assemblies to achieve various bio-functions bring much inspiration for the design of artificial biomaterials. However, it remains a big challenge to correlate underlying biomolecule interactions with macroscopic level of materials, for example, recognizing such weak interaction, further transforming it into regulating material's macroscopic property and contributing to some new bio-applications. Here we designed a novel smart polymer based on polyacrylamide (PAM) grafted with lactose units (PAM-g-lactose0.11), and reported carbohydrate-carbohydrate interaction (CCI)-promoted macroscopic properties switching on this smart polymer surface. Detailed investigations indicated that the binding of sialic acid molecules with the grafted lactose units via the CCIs induced conformational transformation of the polymer chains, further resulted in remarkable and reversible switching in surface topography, wettability and stiffness. With these excellent recognition and response capacities towards sialic acid, the PAM-g-lactose0.11 further facilitated good selectivity, strong anti-interference and high adsorption capacity in the capture of sialylated glycopeptides (important biomarkers for cancers). This work provides some enlightenment for the development of biointerface materials with tunable property, as well as high-performance glycopeptide enrichment materials.
Collapse
Affiliation(s)
- Yuting Xiong
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Ge Jiang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Minmin Li
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Guangyan Qing
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226019, P.R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| |
Collapse
|
44
|
Lu Q, Zhan M, Deng L, Qing G, Sun T. Rapid and high-efficiency discrimination of different sialic acid species using dipeptide-based fluorescent sensors. Analyst 2017; 142:3564-3568. [PMID: 28872647 DOI: 10.1039/c7an00762k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A novel fluorescence sensing matrix is developed by combining six dipeptide-based fluorescent sensors, which allows rapid discrimination of different sialic acid species.
Collapse
Affiliation(s)
- Qi Lu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan 430070
- P. R. China
| | - Mimi Zhan
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan 430070
- P. R. China
| | - Lijing Deng
- West China Hospital
- Sichuan University
- Chengdu 610041
- P. R. China
| | - Guangyan Qing
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan 430070
- P. R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing
- Wuhan University of Technology
- Wuhan 430070
- P. R. China
- School of Chemistry
| |
Collapse
|
45
|
CHATTORAJ SHYAMTANU, BHATTACHARYYA KANKAN. Spatial inhomogeneity in spectra and exciton dynamics in porphyrin micro-rods and micro-brushes: Confocal microscopy. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1155-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
46
|
Perez-Gonzalez C, Lafontaine DA, Penedo JC. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem 2016; 4:33. [PMID: 27536656 PMCID: PMC4971091 DOI: 10.3389/fchem.2016.00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
Collapse
Affiliation(s)
- Cibran Perez-Gonzalez
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
| | - Daniel A. Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de SherbrookeSherbrooke, QC, Canada
| | - J. Carlos Penedo
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
- Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. AndrewsSt. Andrews, UK
| |
Collapse
|
47
|
Schrell AM, Mukhitov N, Roper MG. Multiplexing Fluorescence Anisotropy Using Frequency Encoding. Anal Chem 2016; 88:7910-5. [PMID: 27440478 DOI: 10.1021/acs.analchem.6b02131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this report, a method to multiplex fluorescence anisotropy measurements is described using frequency encoding. As a demonstration of the method, simultaneous competitive immunoassays for insulin and glucagon were performed by measuring the ratio of bound and free Cy5-insulin and FITC-glucagon in the presence of their respective antibodies. A vertically polarized 635 nm laser was pulsed at 73 Hz and used to excite Cy5-insulin, while a vertically polarized 488 nm laser pulsed at 137 Hz excited FITC-glucagon. The total emission was split into parallel and perpendicular polarizations and collected onto separate photomultiplier tubes. The signals from each channel were demodulated using a fast Fourier transform, resolving the contributions from each fluorophore. Anisotropy calculations were carried out using the magnitude of the peaks in the frequency domain. The method produced the expected shape of the calibration curves with limits of detection of 0.6 and 5 nM for insulin and glucagon, respectively. This methodology could readily be expanded to other biological systems and further multiplexed to monitor increased numbers of analytes.
Collapse
Affiliation(s)
- Adrian M Schrell
- Department of Chemistry and Biochemistry, Florida State University , 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Nikita Mukhitov
- Department of Chemistry and Biochemistry, Florida State University , 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Michael G Roper
- Department of Chemistry and Biochemistry, Florida State University , 95 Chieftain Way, Tallahassee, Florida 32306, United States
| |
Collapse
|
48
|
Bai Y, Nguyen L, Song Z, Peng S, Lee J, Zheng N, Kapoor I, Hagler LD, Cai K, Cheng J, Chan HYE, Zimmerman SC. Integrating Display and Delivery Functionality with a Cell Penetrating Peptide Mimic as a Scaffold for Intracellular Multivalent Multitargeting. J Am Chem Soc 2016; 138:9498-507. [DOI: 10.1021/jacs.6b03697] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | | | - Shaohong Peng
- Laboratory
of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong SAR, China
| | | | | | | | | | | | | | - H. Y. Edwin Chan
- Laboratory
of Drosophila Research and School of Life Sciences, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong SAR, China
| | | |
Collapse
|
49
|
Wang Z, Pei X, Li N, Tang X. Phosphate-perylene modified G-quadruplex probes for the detection of Pb 2+ using fluorescence anisotropy. J Mater Chem B 2016; 4:4330-4336. [PMID: 32263415 DOI: 10.1039/c6tb00539j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A simple and universal phosphate-perylene modification strategy was applied in the development of G-quadruplex probes with thrombin binding aptamer (TBA) and [d(TGGGT)4] (G4) sequences. A perylene moiety was inserted at different phosphate positions of oligonucleotides without a significant effect on the G-quadruplex structures. Upon binding with K+ or Pb2+, these probes showed different perylene fluorescence anisotropy responses due to the different labeling positions and G-quadruplex structures. Two probes (G4-9 and TBA-9) were successfully used in Pb2+ detection through fluorescence anisotropy. Once the complexes of Pb2+ with G4-9 or TBA-9 were formed, the rotational diffusion of the perylene moiety was limited, resulting in a significant increase in fluorescence anisotropy. Both probes showed good sensitivity to Pb2+ and their fluorescence anisotropy signals demonstrated good linear responses to the logarithm of Pb2+ concentrations and the detection limits were 24.5 nM and 30.0 nM for TBA-9 and G4-9, respectively.
Collapse
Affiliation(s)
- Zhixuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
| | | | | | | |
Collapse
|
50
|
Li X, Xiong Y, Qing G, Jiang G, Li X, Sun T, Liang X. Bioinspired Saccharide-Saccharide Interaction and Smart Polymer for Specific Enrichment of Sialylated Glycopeptides. ACS APPLIED MATERIALS & INTERFACES 2016; 8:13294-13302. [PMID: 27172767 DOI: 10.1021/acsami.6b03104] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Abnormal sialylation of proteins is highly associated with many major diseases, such as cancers and neurodegenerative diseases. However, this study is challenging owing to the difficulty in enriching trace sialylated glycopeptides (SGs) from highly complex biosamples. The key to solving this problem relies strongly on the design of novel SG receptors to capture the sialic acid (SA) moieties in a specific and tunable manner. Inspired by the saccharide-saccharide interactions in life systems, here we introduce saccharide-based SG receptors into this study. Allose (a monosaccharide) displays specific and pH-sensitive binding toward SAs. Integrating allose units into a polyacrylamide chain generates a saccharide-responsive smart copolymer (SRSC). Such design significantly improves the selectivity of SA binding; meanwhile, this binding can be intelligently triggered in a large extent by solution polarity and pH. As a result, SRSC exhibits high-performance enrichment capacity toward SGs, even under 500-fold interference of bovine serum albumins digests, which is notably higher than conventional materials. In real biosamples of HeLa cell lysates, 180 sialylated glycosylation sites (SGSs) have been identified using SRSC. This is apparently superior to those obtained by SA-binding lectins including WGA (18 SGSs) and SNA (22 SGSs). Furthermore, lactose displays good chemoselectivity toward diverse disaccharides, which indicated the good potential of lactose-based material in glycan discrimination. Subsequently, the lactose-based SRSC facilitates the stepwise isolation of O-linked or N-linked SGs with the same peptide sequence but varied glycans by CH3CN/H2O gradients. This study opens a new avenue for next generation of glycopeptide enrichment materials.
Collapse
Affiliation(s)
- Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Yuting Xiong
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Guangyan Qing
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Ge Jiang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xianqin Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology , 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, P. R. China
| |
Collapse
|