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Gagliardi M, Agostini M, Lunardelli F, Miranda A, Luminare AG, Cervelli F, Gambineri F, Cecchini M. A Surface Acoustic Wave (SAW)-Based Lab-on-Chip for the Detection of Active α-Glycosidase. BIOSENSORS 2022; 12:1010. [PMID: 36421128 PMCID: PMC9688093 DOI: 10.3390/bios12111010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Enzyme detection in liquid samples is a complex laboratory procedure, based on assays that are generally time- and cost-consuming, and require specialized personnel. Surface acoustic wave sensors can be used for this application, overcoming the cited limitations. To give our contribution, in this work we present the bottom-up development of a surface acoustic wave biosensor to detect active α-glycosidase in aqueous solutions. Our device, optimized to work at an ultra-high frequency (around 740 MHz), is functionalized with a newly synthesized probe 7-mercapto-1-eptyl-D-maltoside, bringing one maltoside terminal moiety. The probe is designed ad hoc for this application and tested in-cuvette to analyze the enzymatic conversion kinetics at different times, temperatures and enzyme concentrations. Preliminary data are used to optimize the detection protocol with the SAW device. In around 60 min, the SAW device is able to detect the enzymatic conversion of the maltoside unit into glucose in the presence of the active enzyme. We obtained successful α-glycosidase detection in the concentration range 0.15-150 U/mL, with an increasing signal in the range up to 15 U/mL. We also checked the sensor performance in the presence of an enzyme inhibitor as a control test, with a signal decrease of 80% in the presence of the inhibitor. The results demonstrate the synergic effect of our SAW Lab-on-a-Chip and probe design as a valid alternative to conventional laboratory tests.
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Affiliation(s)
- Mariacristina Gagliardi
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro, 56127 Pisa, Italy
| | - Matteo Agostini
- INTA S.R.L., Intelligent Acoustics Systems, Via Nino Pisano 14, 56122 Pisa, Italy
| | - Francesco Lunardelli
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro, 56127 Pisa, Italy
- INTA S.R.L., Intelligent Acoustics Systems, Via Nino Pisano 14, 56122 Pisa, Italy
| | - Alessio Miranda
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro, 56127 Pisa, Italy
| | | | | | | | - Marco Cecchini
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro, 56127 Pisa, Italy
- INTA S.R.L., Intelligent Acoustics Systems, Via Nino Pisano 14, 56122 Pisa, Italy
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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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Mosley RJ, Talarico MV, Byrne ME. Recent applications of QCM-D for the design, synthesis, and characterization of bioactive materials. J BIOACT COMPAT POL 2021. [DOI: 10.1177/08839115211014216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The clinical translation of bioactive technologies is lacking compared to the number of novel technologies reported in the literature. This is in part due to the difficulties in characterizing bioactive materials to understand and predict their biological response. To progress the field and increase clinical success, more robust analytical techniques must be utilized when investigating novel bioactive materials. The quartz crystal microbalance with dissipation (QCM-D), a label-free sensing instrument based on an acoustic resonator, is used to quantify mass change and viscoelastic parameters from soft materials at the nanoscale, in situ, with precise temporal resolution and operation in both liquid and gaseous environments. The versatility of QCM-D has enhanced the characterization of bioactive polymers and sensing arrays for advanced applications of novel biotechnologies. In this review, we highlight exciting, recent applications of QCM-D for the investigation of bioactive materials. Attention is given to the dynamic mechanical properties of bioactive materials, discerning protein structure on surfaces, probing cell adhesion and cytoskeletal changes, and biosensing applications. We conclude that QCM-D has untapped utility in the pre-clinical investigation of bioactive materials and further utilization can improve the clinical success of novel technologies.
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Affiliation(s)
- Robert J Mosley
- Biomimetic & Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, Rowan University, Glassboro, NJ, USA
| | - Matthew V Talarico
- Biomimetic & Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, Rowan University, Glassboro, NJ, USA
| | - Mark E Byrne
- Biomimetic & Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, Rowan University, Glassboro, NJ, USA
- Department of Chemical Engineering, Rowan University, Glassboro, NJ, USA
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Zhang P, Ouyang Y, Willner I. Multiplexed and amplified chemiluminescence resonance energy transfer (CRET) detection of genes and microRNAs using dye-loaded hemin/G-quadruplex-modified UiO-66 metal-organic framework nanoparticles. Chem Sci 2021; 12:4810-4818. [PMID: 34163734 PMCID: PMC8179566 DOI: 10.1039/d0sc06744j] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/07/2021] [Indexed: 01/11/2023] Open
Abstract
Dye-loaded UiO-66 metal-organic framework nanoparticles (NMOFs) modified with catalytic hemin/G-quadruplex DNAzyme labels act as functional hybrid modules for the chemiluminescence resonance energy transfer (CRET) analysis of miRNAs (miRNA-155 or miRNA-21) or genes (p53 or BRCA1). The dye-loaded NMOFs (dye = fluorescein (Fl) or rhodamine 6G (Rh 6G)) are modified with hairpin probes that are engineered to include in their loop domains recognition sequences for the miRNAs or genes, and in their stem regions caged G-quadruplex domains. In the presence of the analytes miRNAs or genes, the hairpin structures are opened, leading, in the presence of hemin, to the self-assembly of hemin/G-quadruplex DNAzyme labels linked to the dye-loaded NMOFs. In the presence of luminol and H2O2, the hemin/G-quadruplex DNAzyme labels catalyze the generation of chemiluminescence that provides radiative energy to stimulate the process of CRET to the dye loaded in the NMOFs, resulting in the luminescence of the loaded dye without external excitation. The resulting CRET signals relate to the concentrations of the miRNAs or the genes and allow the sensitive analysis of miRNAs and genes. In addition, the DNA hairpin-functionalized dye-loaded NMOF sensing modules were further applied to develop amplified miRNA or gene CRET-based sensing platforms. The dye-loaded NMOFs were modified with hairpin probes that include in their loop domain the recognition sequences for miRNA-155 or miRNA-21 or the recognition sequences for the p53 or BRCA1 genes. Subjecting the hairpin-modified NMOFs to the respective miRNAs or genes, in the presence of two hairpins H i and H j that include in their stem regions caged G-quadruplex subunit domains, results in the analyte-triggered opening of the probe hairpin linked to the NMOFs, and the opened hairpin tethers induce the cross-opening of the hairpins H i and H j by the hybridization chain reaction, HCR, resulting in the assembly of G-quadruplex wires tethered to the NMOFs. The binding of hemin to the HCR-generated chains yields hemin/G-quadruplex DNAzyme wires that enhance, in the presence of luminol/H2O2, the CRET processes in the hybrid nanostructures. These amplification platforms lead to the amplified sensing of miRNAs and genes. By mixing the Fl- and Rh 6G-loaded hairpin-functionalized UiO NMOFs, the multiplexed CRET detection of miRNA-155, miRNA-21 and the p53 and BRCA1 genes is demonstrated.
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Affiliation(s)
- Pu Zhang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Yu Ouyang
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem Jerusalem 91904 Israel
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Real-time monitoring of DNA immobilization and detection of DNA polymerase activity by a microfluidic nanoplasmonic platform. Biosens Bioelectron 2019; 142:111528. [PMID: 31362202 DOI: 10.1016/j.bios.2019.111528] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/18/2019] [Accepted: 07/20/2019] [Indexed: 12/22/2022]
Abstract
DNA polymerase catalyzes the replication of DNA, one of the key steps in cell division. The control and understanding of this reaction owns great potential for the fundamental study of DNA-enzyme interactions. In this context, we developed a label-free microfluidic biosensor platform based on the principle of localized surface plasmon resonance (LSPR) to detect the DNA-polymerase reaction in real-time. Our microfluidic LSPR chip integrates a polydimethylsiloxane (PDMS) channel bonded with a nanoplasmonic substrate, which consists of densely packed mushroom-like nanostructures with silicon dioxide stems (~40 nm) and gold caps (~22 nm), with an average spacing of 19 nm. The LSPR chip was functionalized with single-stranded DNA (ssDNA) template (T30), spaced with hexanedithiol (HDT) in a molar ratio of 1:1. The DNA primer (P8) was then attached to T30, and the second strand was subsequently elongated by DNA polymerase assembling nucleotides from the surrounding fluid. All reaction steps were detected in-situ inside the microfluidic LSPR chip, at room temperature, in real-time, and label-free. In addition, the sensor response was successfully correlated with the amount of DNA and HDT molecules immobilized on the LSPR sensor surface. Our platform represents a benchmark in developing microfluidic LSPR chips for DNA-enzyme interactions, further driving innovations in biosensing technologies.
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Wang Y, Gu L, Xu F, Xin F, Ma J, Jiang M, Fang Y. Chemoenzymatic Synthesis of Branched Glycopolymer Brushes as the Artificial Glycocalyx for Lectin Specific Binding. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4445-4452. [PMID: 30845797 DOI: 10.1021/acs.langmuir.8b03704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The artificial glycocalyx fabricated by carbohydrates is of interest because it provides a platform to simulate the cell membranes that widely exist in the nature, and thus enable extensive applications to be implantable in bioengineering. Here, we present a green strategy combining two polymerization techniques, surface-initiated atom transfer radical polymerization (SI-ATRP) and enzyme-catalyzed elongation of polysaccharide, for fabricating densely packed branched glycopolymer brushes on the gold surface as the artificial glycocalyx. In this strategy, SI-ATRP is first performed to graft a linear polymer chain for anchoring maltose, which can be used as an enzyme acceptor for dextransucrase (DSase). Under DSase, a branched polysaccharide is efficiently formed through elongation of a sucrose substrate. Undoubtedly, enzymatic transglycosylation has unique advantages, such as being green, regio-, and stereo-selective, etc. The process of DSase-catalyzed polysaccharide is well monitored by a quartz crystal microbalance, and the grafting density of the glycopolymer brushes is estimated to be 0.7 chain nm-2 with 23.0 nm dry thickness. The polysaccharide brushes display a branched structure consisting of α-d-glucose residues with 5% of α-1,3-linked shorter chain branches, and the branched structure is well characterized by X-ray photoelectron spectroscopy, time-of-flight secondary ion mass spectrometry, Fourier transform infrared/mirror reflection, water contact angle analysis, and atomic force microscopy. Compared with the linear maltose-anchored brushes, the branched glycopolymer analog prepared here shows high specific binding capacity of concanavalin A recognition, which should be of use in biomedical application.
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Zhou Z, Luo G, Wulf V, Willner I. Application of DNA Machineries for the Barcode Patterned Detection of Genes or Proteins. Anal Chem 2018; 90:6468-6476. [PMID: 29737162 DOI: 10.1021/acs.analchem.7b04916] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The study introduces an analytical platform for the detection of genes or aptamer-ligand complexes by nucleic acid barcode patterns generated by DNA machineries. The DNA machineries consist of nucleic acid scaffolds that include specific recognition sites for the different genes or aptamer-ligand analytes. The binding of the analytes to the scaffolds initiate, in the presence of the nucleotide mixture, a cyclic polymerization/nicking machinery that yields displaced strands of variable lengths. The electrophoretic separation of the resulting strands provides barcode patterns for the specific detection of the different analytes. Mixtures of DNA machineries that yield, upon sensing of different genes (or aptamer ligands), one-, two-, or three-band barcode patterns are described. The combination of nucleic acid scaffolds acting, in the presence of polymerase/nicking enzyme and nucleotide mixture, as DNA machineries, that generate multiband barcode patterns provide an analytical platform for the detection of an individual gene out of many possible genes. The diversity of genes (or other analytes) that can be analyzed by the DNA machineries and the barcode patterned imaging is given by the Pascal's triangle. As a proof-of-concept, the detection of one of six genes, that is, TP53, Werner syndrome, Tay-Sachs normal gene, BRCA1, Tay-Sachs mutant gene, and cystic fibrosis disorder gene by six two-band barcode patterns is demonstrated. The advantages and limitations of the detection of analytes by polymerase/nicking DNA machineries that yield barcode patterns as imaging readout signals are discussed.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Guofeng Luo
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Verena Wulf
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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8
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Walsh MT, Huang X. Measurement of incorporation kinetics of non-fluorescent native nucleotides by DNA polymerases using fluorescence microscopy. Nucleic Acids Res 2017; 45:e175. [PMID: 29036327 PMCID: PMC5716174 DOI: 10.1093/nar/gkx833] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/11/2017] [Indexed: 01/10/2023] Open
Abstract
We describe a method for measuring the single-turnover incorporation kinetics of non-fluorescent native nucleotides by DNA polymerases. Time-lapse total internal reflection fluorescence (TIRF) microscopy is used to directly measure the kinetics of single-base nucleotide incorporation into primed DNA templates covalently attached to the surface of a glass coverslip using a fixed ratio of a native nucleotide and a corresponding fluorescently labeled nucleotide over a series of total nucleotide concentrations. The presence of a labeled nucleotide allows for the kinetics of competitive incorporation reactions by DNA polymerase to be monitored. The single-turnover catalytic rate constants and Michaelis constants of the incorporation of the native nucleotides can be determined by modeling the kinetics of the parallel competitive reactions. Our method enables the measurements of the kinetics parameters of incorporation of native or other non-fluorescent nucleotides without using a rapid stopped-flow or quench-flow instrument and the generally more involved and less quantitative post-reaction analysis of the reaction products. As a demonstration of our method, we systematically determined the single-turnover incorporation kinetics of all four native nucleotides and a set of Cy3-labeled nucleotides by the Klenow fragment of Escherichia coli DNA polymerase I.
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Affiliation(s)
- Matthew T Walsh
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - Xiaohua Huang
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
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Suzuki H, Kaneko A, Yamamoto T, Nambo M, Hirasawa I, Umehara T, Yoshida H, Park SY, Tamura K. Binding Properties of Split tRNA to the C-terminal Domain of Methionyl-tRNA Synthetase of Nanoarchaeum equitans. J Mol Evol 2017; 84:267-278. [PMID: 28589220 DOI: 10.1007/s00239-017-9796-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/30/2017] [Indexed: 11/28/2022]
Abstract
The C-terminal domain of methionyl-tRNA synthetase (MetRS-C) from Nanoarchaeum equitans is homologous to a tRNA-binding protein consisting of 111 amino acids (Trbp111) from Aquifex aeolicus. The crystal structure of MetRS-C showed that it existed as a homodimer, and that each monomer possessed an oligonucleotide/oligosaccharide-binding fold (OB-fold). Analysis using a quartz crystal microbalance indicated that MetRS-C freshly isolated from N. equitans was bound to tRNA. However, binding of the split 3'-half tRNA species was stronger than that of the 5'-half species. The T-loop and the 3'-end regions of the split 3'-half tRNA were found to be responsible for the binding. The minimum structure for binding to MetRS-C might be a minihelix-like stem-loop with single-stranded 3'-terminus. After successive duplications of such a small hairpin structure with the assistance of a Trbp-like structure, the interaction of the T-loop region of the 3'-half with a Trbp-like structure could have been evolutionarily replaced by RNA-RNA interactions, along with many combinational tertiary interactions, to form the modern tRNA structure.
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Affiliation(s)
- Hidemichi Suzuki
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Akihiro Kaneko
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Taro Yamamoto
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Mahoko Nambo
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Ito Hirasawa
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Takuya Umehara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Hisashi Yoshida
- Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sam-Yong Park
- Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan. .,Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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Yin Y, Sasaki S, Taniguchi Y. Recognition and Excision Properties of 8-Halogenated-7-Deaza-2′-Deoxyguanosine as 8-Oxo-2′-Deoxyguanosine Analogues and Fpg and hOGG1 Inhibitors. Chembiochem 2015; 16:1190-8. [DOI: 10.1002/cbic.201402690] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Indexed: 11/12/2022]
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Fang Y, Wu J, Xu ZK. Dextransucrase-catalyzed elongation of polysaccharide brushes with immobilized mono-/di-saccharides as acceptors. Chem Commun (Camb) 2015; 51:129-32. [PMID: 25383964 DOI: 10.1039/c4cc06137c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A quartz crystal microbalance (QCM) was used to monitor dextransucrase (DSase)-catalyzed polysaccharide elongation on the glucose-/maltose-ended self-assembly monolayer (SAM) surfaces. Kinetic parameters of the enzymatic elongation indicate that maltose is a promising substrate acceptor for DSase.
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Affiliation(s)
- Yan Fang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China.
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Poturnayova A, Snejdarkova M, Babelova L, Korri-Youssoufi H, Hianik T. Comparative Analysis of Cellular Prion Detection by Mass-Sensitive Immunosensors. ELECTROANAL 2014. [DOI: 10.1002/elan.201400049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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The influence of nucleotide sequence and temperature on the activity of thermostable DNA polymerases. J Mol Diagn 2014; 16:305-13. [PMID: 24607271 DOI: 10.1016/j.jmoldx.2014.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/17/2014] [Accepted: 01/24/2014] [Indexed: 11/23/2022] Open
Abstract
Extension rates of a thermostable, deletion-mutant polymerase were measured from 50°C to 90°C using a fluorescence activity assay adapted for real-time PCR instruments. Substrates with a common hairpin (6-base loop and a 14-bp stem) were synthesized with different 10-base homopolymer tails. Rates for A, C, G, T, and 7-deaza-G incorporation at 75°C were 81, 150, 214, 46, and 120 seconds(-1). Rates for U were half as fast as T and did not increase with increasing concentration. Hairpin substrates with 25-base tails from 0% to 100% GC content had maximal extension rates near 60% GC and were predicted from the template sequence and mononucleotide incorporation rates to within 30% for most sequences. Addition of dimethyl sulfoxide at 7.5% increased rates to within 1% to 17% of prediction for templates with 40% to 90% GC. When secondary structure was designed into the template region, extension rates decreased. Oligonucleotide probes reduced extension rates by 65% (5'-3' exo-) and 70% (5'-3' exo+). When using a separate primer and a linear template to form a polymerase substrate, rates were dependent on both the primer melting temperature (Tm) and the annealing/extension temperature. Maximum rates were observed from Tm to Tm - 5°C with little extension by Tm + 5°C. Defining the influence of sequence and temperature on polymerase extension will enable more rapid and efficient PCR.
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14
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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15
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Montgomery JL, Wittwer CT. Influence of PCR reagents on DNA polymerase extension rates measured on real-time PCR instruments. Clin Chem 2013; 60:334-40. [PMID: 24081987 DOI: 10.1373/clinchem.2013.212829] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Radioactive DNA polymerase activity methods are cumbersome and do not provide initial extension rates. A simple extension rate assay would enable study of basic assumptions about PCR and define the limits of rapid PCR. METHODS A continuous assay that monitors DNA polymerase extension using noncovalent DNA dyes on common real-time PCR instruments was developed. Extension rates were measured in nucleotides per second per molecule of polymerase. To initiate the reaction, a nucleotide analog was heat activated at 95 °C for 5 min, the temperature decreased to 75 °C, and fluorescence monitored until substrate exhaustion in 30-90 min. RESULTS The assay was linear with time for over 40% of the reaction and for polymerase concentrations over a 100-fold range (1-100 pmol/L). Extension rates decreased continuously with increasing monovalent cation concentrations (lithium, sodium, potassium, cesium, and ammonium). Melting-temperature depressors had variable effects. DMSO increased rates up to 33%, whereas glycerol had little effect. Betaine, formamide, and 1,2-propanediol decreased rates with increasing concentrations. Four common noncovalent DNA dyes inhibited polymerase extension. Heat-activated nucleotide analogs were 92% activated after 5 min, and hot start DNA polymerases were 73%-90% activated after 20 min. CONCLUSIONS Simple DNA extension rate assays can be performed on real-time PCR instruments. Activity is decreased by monovalent cations, DNA dyes, and most melting temperature depressors. Rational inclusion of PCR components on the basis of their effects on polymerase extension is likely to be useful in PCR, particularly rapid-cycle or fast PCR.
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Affiliation(s)
- Jesse L Montgomery
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT
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16
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Montgomery JL, Rejali N, Wittwer CT. Stopped-flow DNA polymerase assay by continuous monitoring of dNTP incorporation by fluorescence. Anal Biochem 2013; 441:133-9. [PMID: 23872003 DOI: 10.1016/j.ab.2013.07.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/03/2013] [Accepted: 07/06/2013] [Indexed: 11/29/2022]
Abstract
DNA polymerase activity was measured by a stopped-flow assay that monitors polymerase extension using an intercalating dye. Double-stranded DNA formation during extension of a hairpin substrate was monitored at 75°C for 2 min. Rates were determined in nucleotides per second per molecule of polymerase (nt/s) and were linear with time and polymerase concentration from 1 to 50 nM. The concentrations of 15 available polymerases were quantified and their extension rates determined in 50 mM Tris, pH 8.3, 0.5 mg/ml BSA, 2 mM MgCl₂, and 200 μM each dNTP as well as their commercially recommended buffers. Native Taq polymerases had similar extension rates of 10-45 nt/s. Three alternative polymerases showed faster speeds, including KOD (76 nt/s), Klentaq I (101 nt/s), and KAPA2G (155 nt/s). Fusion polymerases including Herculase II and Phusion were relatively slow (3-13 nt/s). The pH optimum for Klentaq extension was between 8.5 and 8.7 with no effect of Tris concentration. Activity was directly correlated to the MgCl2 concentration and inversely correlated to the KCl concentration. This continuous assay is relevant to PCR and provides accurate measurement of polymerase activity using a defined template without the need of radiolabeled substrates.
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Affiliation(s)
- Jesse L Montgomery
- Department of Pathology, University of Utah, Salt Lake City, UT 84132, USA
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Binding kinetics of human cellular prion detection by DNA aptamers immobilized on a conducting polypyrrole. Anal Bioanal Chem 2013; 405:2505-14. [PMID: 23318762 DOI: 10.1007/s00216-012-6665-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 12/12/2012] [Accepted: 12/13/2012] [Indexed: 10/27/2022]
Abstract
We developed a biosensor based on the surface plasmon resonance (SPR) method for the study of the binding kinetics and detection of human cellular prions (PrP(C)) using DNA aptamers as bioreceptors. The biosensor was formed by immobilization of various biotinylated DNA aptamers on a surface of conducting polypyrrole modified by streptavidin. We demonstrated that PrP(C) interaction with DNA aptamers could be followed by measuring the variation of the resonance angle. This was studied using DNA aptamers of various configurations, including conventional single-stranded aptamers that contained a rigid double-stranded supporting part and aptamer dimers containing two binding sites. The kinetic constants determined by the SPR method suggest strong interaction of PrP(C) with various DNA aptamers depending on their configuration. SPR aptasensors have a high selectivity to PrP(C) and were regenerable by a brief wash in 0.1 M NaOH. The best limit of detection (4 nM) has been achieved with this biosensor based on DNA aptamers with one binding site but containing a double-stranded supporting part.
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Furusawa H, Uemura K, Yoshimine H, Okahata Y. In situ monitoring of a trace intermediate during DNA phosphorylation by T4 polynucleotide kinase for transient kinetic studies. Analyst 2012; 137:1334-7. [DOI: 10.1039/c2an16273c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Fang Y, Xu W, Wu J, Xu ZK. Enzymatic transglycosylation of PEG brushes by β-galactosidase. Chem Commun (Camb) 2012; 48:11208-10. [DOI: 10.1039/c2cc35369e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Cheng CI, Chang YP, Chu YH. Biomolecular interactions and tools for their recognition: focus on the quartz crystal microbalance and its diverse surface chemistries and applications. Chem Soc Rev 2012; 41:1947-71. [DOI: 10.1039/c1cs15168a] [Citation(s) in RCA: 170] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Real-time monitoring of a stepwise transcription reaction on a quartz-crystal microbalance. Anal Biochem 2011; 421:732-41. [PMID: 22182728 DOI: 10.1016/j.ab.2011.11.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/18/2011] [Accepted: 11/19/2011] [Indexed: 11/23/2022]
Abstract
We monitored real-time DNA transcription by T7 RNAP using a 27-MHz DNA-immobilized quartz-crystal microbalance (QCM) in buffer solution to investigate the stepwise reaction of transcription. We designed a template double-stranded DNA that consisted of a T7 promoter, a stall position (15 bp downstream from the promoter), and a 73-bp transcription region. Based on the frequency (mass) changes of the template-immobilized QCM in response to the addition of T7 RNAP and monomers of NTP, we obtained the kinetic parameters of each step of the T7 RNAP reactions: the enzyme-binding rate (k(on)) to and the dissociation rate (k(off)) from the promoter, the proceeding rate (k(for)) from the promoter to the forward stall position, the polymerization rate (k(cat)) of RNA along DNA, and the release rate (k(r)) from the end of the template DNA. We found that k(cat) (120 s⁻¹) was extremely large compared with k(off) (0.014 s⁻¹), k(for) (0.062 s⁻¹), and k(r) (0.014 s⁻¹), revealing that the rate-limiting steps of T7 RNAP involve the binding to the promoter, the movement to the stall position, and the release from DNA. These kinetic parameters were compared with values for other DNA-binding enzymes.
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Chu J, González-López M, Cockroft SL, Amorin M, Ghadiri MR. Real-time monitoring of DNA polymerase function and stepwise single-nucleotide DNA strand translocation through a protein nanopore. Angew Chem Int Ed Engl 2010; 49:10106-9. [PMID: 21105031 PMCID: PMC3132071 DOI: 10.1002/anie.201005460] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | | | - M. Reza Ghadiri
- Departments of Chemistry and Molecule Biology and the Skaggs Institute of Chemical Biology The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Chu J, González-López M, Cockroft SL, Amorin M, Ghadiri MR. Real-Time Monitoring of DNA Polymerase Function and Stepwise Single-Nucleotide DNA Strand Translocation through a Protein Nanopore. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201005460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Detection of a complementary couple of single-stranded DNAs by use of a quartz crystal device for determination of bacteria. J Biosci Bioeng 2010; 111:242-5. [PMID: 21041116 DOI: 10.1016/j.jbiosc.2010.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 10/06/2010] [Accepted: 10/06/2010] [Indexed: 11/21/2022]
Abstract
Preliminary experiments were carried out for the DNA detection targeting a complementary couple of single-stranded DNAs originating from Nitrobacter winogradskyi. The target DNAs were detected successfully with a quartz crystal unit bearing probe DNAs, based on the oscillation frequency decrease due to hybridization of the probe and target DNAs.
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Mori T, Ohtsuka T, Okahata Y. Kinetic analyses of bindings of Shiga-like toxin to clustered and dispersed Gb3 glyco-arrays on a quartz-crystal microbalance. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:14118-14125. [PMID: 20666463 DOI: 10.1021/la102260k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
One-, two-, four-, and eight-branched globotriaosyl saccharides (Gb(3): Gal-alpha1,4-Gal-beta1,4-Glc), whose reducing ends were biotinylated, were prepared (1Gb(3)-bio, 2Gb(3)-bio, 4Gb(3)-bio, and 8Gb(3)-bio, respectively). They are dispersively immobilized as a glyco-array in the matrix of biotinylated maltotriose (Glc(3)-bio) on a streptavidin-covered 27 MHz quartz-crystal microbalance (QCM). The binding kinetics of the verotoxin B subunit (VTB) to various branched Gb(3)-bio ligands in the Glc(3)-bio matrix could be obtained from frequency decreases (mass increases) of the QCM. VTB can recognize the Gb(3) unit but not the Glc(3) unit, where VTB is a pentamer having five binding sites for one Gb(3) unit per each B subunit (having a total of 15 binding sites for Gb(3)). By changing the Gb(3) multivalency, the Gb(3) packing density, and the Gb(3) cluster size in the Glc(3) matrix, association constants (K(a)), maximum amounts bound (Delta m(max)), and binding and dissociation rate constants (k(on) and k(off)) were obtained. When 15 sites of VTB were recognized by 16 Gb(3) units, K(a) was 100 times larger than that when 15 sites of VTB were recognized by only 2 Gb(3) units, with a 6-fold-larger k(on) and a 25-fold-smaller k(off). When the Gb(3) multivalency was changed by covering with two 1Gb(3)-bio, 2Gb(3)-bio, 4Gb(3)-bio, or 8Gb(3)-bio ligands on two pockets of one streptavidin, the K(a) values increased with increasing branch number from one to eight. When the Gb(3) cluster size was changed from eight 1Gb(3)-bio units to one 8Gb(3)-bio unit in the matrix, the K(a) values increased but the Delta m(max) values decreased with increasing cluster size from eight 1Gb(3)-bio units to one 8Gb(3)-bio unit. This is the first example of systematically obtaining all kinetic parameters of sugar-binding proteins to sugars on a glyco-array by changing the sugar multivalency, the sugar packing density, and the sugar cluster size in the matrix.
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Affiliation(s)
- Toshiaki Mori
- Japan Science and Technology Agency-Precursory Research for Embryonic Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501 Japan.
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Mori T, Toyoda M, Ohtsuka T, Okahata Y. Kinetic analyses for bindings of concanavalin A to dispersed and condensed mannose surfaces on a quartz crystal microbalance. Anal Biochem 2009; 395:211-6. [DOI: 10.1016/j.ab.2009.08.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2009] [Revised: 08/13/2009] [Accepted: 08/19/2009] [Indexed: 11/25/2022]
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Takahashi S, Iida M, Furusawa H, Shimizu Y, Ueda T, Okahata Y. Real-time monitoring of cell-free translation on a quartz-crystal microbalance. J Am Chem Soc 2009; 131:9326-32. [PMID: 19518055 DOI: 10.1021/ja9019947] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The efficiency of protein synthesis is often regulated post-transcriptionally by sequences within the mRNA. To investigate the reactions of protein translation, we established a system that allowed real-time monitoring of protein synthesis using a cell-free translation mixture and a 27 MHz quartz-crystal microbalance (QCM). Using an mRNA that encoded a fusion polypeptide comprising the streptavidin-binding peptide (SBP) tag, a portion of Protein D as a spacer, and the SecM arrest sequence, we could follow the binding of the SBP tag, while it was displayed on the 70S ribosome, to a streptavidin-modified QCM over time. Thus, we could follow a single turnover of protein synthesis as a change in mass. This approach allowed us to evaluate the effects of different antibiotics and mRNA sequences on the different steps of translation. From the results of this study, we have determined that both the formation of the initiation complex from the 70S ribosome, mRNA, and fMet-tRNA(fMet) and the accommodation of the second aminoacyl-tRNA to the initiation complex are rate-limiting steps in protein synthesis.
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Affiliation(s)
- Shuntaro Takahashi
- Department of Biomolecular Engineering, Tokyo Institute of Technology, B-53, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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Höpfner M, Rothe U, Bendas G. Biosensor-based evaluation of liposomal behavior in the target binding process. J Liposome Res 2008; 18:71-82. [PMID: 18348073 DOI: 10.1080/08982100801894000] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In this study we evaluated the quartz crystal microbalance (QCM) as a biosensor for a real-time investigation of liposomal binding, under dynamic flow conditions, onto target proteins immobilized at the sensor. The mass-sensitive frequency changes of quartz sensors allow for a quantification of the liposomal binding process. Furthermore, simultaneous damping analysis gives an insight into liposomal behavior, such as the degree of liposomal deformation or spreading at the target surface. In this study a series of liposomes was evaluated, differing in the kind and concentration of ligands interacting with appropriate target proteins. It became evident that an increase in homing device concentration accelerated deformation and flattening of liposomes, triggering a fusion process. Furthermore, liposomal deformation corresponded with the binding affinity of target molecules, comparing biotin/avidin with E-selectin/ligand interactions. Deformation could be emphasized using dioleoylphosphatidylethanolamine (DOPE) as a fusiogenic membrane component, while sterical stabilization by polyethylenglycol (PEG-PE) appeared in a low degree of deformation. Consequently, the online detection of liposomal target binding by QCM is an excellent facility to control and predict the liposomal behavior at the target site for increasing therapeutic potency.
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Affiliation(s)
- Matthias Höpfner
- Department of Physiological Chemistry, Medical Faculty, University Halle, Germany
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Furusawa H, Takano H, Okahata Y. Transient kinetic studies of protein hydrolyses by endo- and exo-proteases on a 27 MHz quartz-crystal microbalance. Org Biomol Chem 2008; 6:727-31. [DOI: 10.1039/b717171d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Terada T, Mizobata M, Kawakami S, Yamashita F, Hashida M. Optimization of tumor-selective targeting by basic fibroblast growth factor-binding peptide grafted PEGylated liposomes. J Control Release 2007; 119:262-70. [PMID: 17467100 DOI: 10.1016/j.jconrel.2007.01.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 01/22/2007] [Accepted: 01/24/2007] [Indexed: 12/01/2022]
Abstract
We have previously shown that the peptide, KRTGQYKLC (bFGF), is recognized by fibroblast growth factor (FGF) receptor (FGFR) via binding to basic FGF (bFGF), and is capable of being used for drug delivery to tumors highly expressing FGFR and bFGF. However, although the binding and uptake of the liposomes (bFGFp-liposomes) modified by the peptide increased in the presence of bFGF, the modification induced non-specific uptake. To overcome this problem, here, we prepared bFGFp-liposomes including mPEG-DSPE. The 5 and 10% mPEG(5000)/ and 10% mPEG(3000)/bFGFp-liposomes reduced most of the interaction with erythrocytes and the uptake by macrophages, suggesting the sustained blood circulation of bFGFp grafted PEGylated liposomes. Furthermore, 10% mPEG(3000)/bFGFp-liposomes produced a significant increase in uptake in NIH3T3, A549, and B16BL6 cells with the expression of FGFR following pre-incubation with bFGF, but no increase in CHO-K1 cells lacking FGFR expression. Taken together, these results lead us to believe that bFGFp grafted PEGylated liposomes possess the functions of both PEGylated stealth liposomes and the tumor-targeting liposomes. This strategy could be applied to the development of novel tumor-selective drug delivery systems.
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Affiliation(s)
- Takeshi Terada
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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Abstract
In the present study, we have used the QCM-D technology to study the replication of surface attached oligonucleotide template strands using Escherichia coli DNA polymerase I (Klenow fragment, KF). Changes in resonance frequency (F) and energy dissipation (D) for DNA hybridization and polymerization were recorded at multiple harmonics. Formation of the polymerase/DNA complex led to a significant decrease in energy dissipation, which is consistent with a conformational change induced upon enzyme binding. This interpretation was further strengthened by a data analysis using a Voigt-based viscoelastic model. The analysis revealed a significant increase in shear viscosity and shear modulus during KF binding, whereas the viscoelastic properties of single- and double-stranded templates were almost identical. During the actual DNA synthesis, an initial increase in rigidity (shear viscosity) was followed by a gradual decrease that has two components corresponding to the release of enzyme and to the presence of the catalytically active enzyme/substrate complex. The corresponding decrease in surface concentration was found to underestimate the rate of enzyme release due to viscously coupled water that compensates for the loss in enzyme mass. Furthermore, the modeling elucidates that significant changes in both F and D originate from variations in the viscoelastic properties, which means that changes in F alone should be used with care for estimations of coupled mass and kinetics. Therefore, the modeled temporal variation in effective thickness, being proportional to coupled mass and, thus, independent of structural changes, was used to estimate the catalytic constants of the polymerization reaction. The reported work is the first example providing this type of structural information for the catalytic action of an enzyme, thereby demonstrating the potential of the technique for advanced analysis of complex biological reactions, including proper analysis of enzyme kinetics.
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Takahashi S, Matsuno H, Furusawa H, Okahata Y. Monitoring of EcoRV Digestions on a DNA-immobilized Quartz Crystal Microbalance. CHEM LETT 2007. [DOI: 10.1246/cl.2007.230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Takahashi S, Matsuno H, Furusawa H, Okahata Y. Kinetic analyses of divalent cation-dependent EcoRV digestions on a DNA-immobilized quartz crystal microbalance. Anal Biochem 2007; 361:210-7. [PMID: 17217909 DOI: 10.1016/j.ab.2006.11.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 11/15/2006] [Accepted: 11/17/2006] [Indexed: 11/18/2022]
Abstract
Enzymatic digestion with a type IIP restriction endonuclease EcoRV was investigated on a DNA-immobilized 27-MHz quartz crystal microbalance (QCM). Real-time observations of both the enzyme binding process and the DNA cleavage process of EcoRV were followed by frequency (mass) changes on the QCM, which were dependent on divalent cations such as Ca(2+) or Mg(2+). In the presence of Ca(2+), the site-specific binding of EcoRV to DNA could be observed, without the catalytic process. On the other hand, in the presence of Mg(2+), both the binding of the enzyme to the specific DNA (mass increase) and the site-specific cleavage reaction (mass decrease) could be observed continuously from QCM frequency changes. From time courses of frequency (mass) changes, each kinetic parameter, namely binding rate constants (k(on)), dissociation rate constants (k(off)), dissociation constants (K(d)) of EcoRV to DNA, and catalytic rate constant (k(cat)) of the cleavage reaction, could be determined. The binding kinetic parameters of EcoRV in the presence of Ca(2+) were consistent with those of the binding process followed by the cleavage process in the presence of Mg(2+). The k(cat) value obtained by the QCM method was also consistent with that obtained by other methods. This study is the first to simultaneously determine k(on), k(off), and k(cat) for a type IIP restriction endonuclease on one device.
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Affiliation(s)
- Shuntaro Takahashi
- Department of Biomolecular Engineering, Frontier Collaborative Research Center, Tokyo Institute of Technology and CREST, Japan Science and Technology Corp., 4259 Nagatsuta, Yokohama 226-8501, Japan
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Cooper MA, Singleton VT. A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactions. J Mol Recognit 2007; 20:154-84. [PMID: 17582799 DOI: 10.1002/jmr.826] [Citation(s) in RCA: 294] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The widespread exploitation of biosensors in the analysis of molecular recognition has its origins in the mid-1990s following the release of commercial systems based on surface plasmon resonance (SPR). More recently, platforms based on piezoelectric acoustic sensors (principally 'bulk acoustic wave' (BAW), 'thickness shear mode' (TSM) sensors or 'quartz crystal microbalances' (QCM)), have been released that are driving the publication of a large number of papers analysing binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights salient theoretical and practical aspects of the technologies that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and lipidic and polymeric interfaces. Key differentiators between optical and acoustic sensing modalities are also reviewed.
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Affiliation(s)
- Matthew A Cooper
- Akubio Ltd., 181 Cambridge Science Park, Cambridge, United Kingdom, UK.
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Manaka Y, Kudo Y, Yoshimine H, Kawasaki T, Kajikawa K, Okahata Y. Simultaneous anomalous reflection and quartz-crystal microbalance measurements of protein bindings on a gold surface. Chem Commun (Camb) 2007:3574-6. [DOI: 10.1039/b708901e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ozeki T, Morita M, Yoshimine H, Furusawa H, Okahata Y. Hydration and Energy Dissipation Measurements of Biomolecules on a Piezoelectric Quartz Oscillator by Admittance Analyses. Anal Chem 2006; 79:79-88. [PMID: 17194124 DOI: 10.1021/ac060873x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
By using a 27-MHz piezoelectric quartz oscillator connected with a vector network analyzer, we obtained resonance frequency decreases (-DeltaFwater) and energy dissipation increases (DeltaDwater) during binding of biotinylated bovine serum albumin, biotinylated ssDNA, biotinylated dsDNA, and biotinylated pullulan to a NeutrAvidin-immobilized 27-MHz quartz crystal microbalance (QCM) plate in aqueous solution, as well as in the wet air phase (98% humidity, -DeltaFwet and DeltaDwet) and in the dry air phase (-DeltaFair and DeltaDair). -DeltaFwater indicates the total mass of the molecule, bound water, and vibrated water in aqueous solutions. -DeltaFwet indicates the total mass of the molecule and bound water. -DeltaFair simply shows the real mass of the molecule on the QCM. In terms of results, (-DeltaFwet)/(-DeltaFair) values indicated the bound water ratios per unit biomolecular mass were on the order of pullulan (2.1-2.2) > DNAs = proteins (1.4-1.6) > polystyrene (1.0). The (-DeltaFwater)/(-DeltaFair) values indicated the hydrodynamic water (bound and vibrated water) ratios per unit biomolecular mass were on the order of dsDNA (6.5) > ssDNA = pullulan (3.5-4.4) > proteins (2.4-2.5) > polystyrene (1.0). Energy dissipation parameters per unit mass in water (DeltaDwater/(-DeltaFair)) were on the order of pullulan > dsDNA > ssDNA > proteins > polystyrene. Energy dissipation in the wet and dry air phases (DeltaDwet and DeltaDair) were negligibly small, which indicates even these biomolecules act as elastic membranes in the air phase (without aqueous solution). We obtained a good linear relationship between [(-DeltaFwater)/(-DeltaFair) - 1], which is indicative of hydration and DeltaDwater/(-DeltaFair) of proteins. The aforementioned values suggest that the energy dissipation of proteins was mainly caused by hydration and that proteins themselves are elastic molecules without energy dissipation in aqueous solutions. On the contrary, plots in cases of denatured proteins, DNAs, and pullulans were relatively deviant toward the large hydration and energy dissipation from the theoretical line as perfect elastic materials, meaning that the large energy dissipation occurs because of viscoelastic properties of denatured proteins, linear DNAs, and pullulans in the water phase, in addition to energy dissipation due to the hydration of molecules. These two parameters could characterize various biomolecules with structural properties in aqueous solutions.
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Affiliation(s)
- Tomomitsu Ozeki
- Department of Biomolecular Engineering, Frontier Collaborative Research Center, Tokyo Institute of Technology and CREST, Japan Science and Technology Corporation (JST), 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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Rodríguez Seguí S, Pla M, Minic J, Pajot‐Augy E, Salesse R, Hou Y, Jaffrezic‐Renault N, Mills CA, Samitier J, Errachid A. Detection of Olfactory Receptor I7 Self‐Assembled Multilayer Formation and Immobilization Using a Quartz Crystal Microbalance. ANAL LETT 2006. [DOI: 10.1080/00032710600714030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Matsuno H, Furusawa H, Okahata Y. Kinetic study of phosphorylation-dependent complex formation between the kinase-inducible domain (KID) of CREB and the KIX domain of CBP on a quartz crystal microbalance. Chemistry 2006; 10:6172-8. [PMID: 15515068 DOI: 10.1002/chem.200400030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report quantitative analysis of peptide-peptide interactions on a 27 MHz quartz crystal microbalance (QCM) in aqueous solution. The KID (kinase-inducible domain) of transcription factor CREB (cyclic AMP response element binding protein) is known to interact with the KIX domain of coactivator CBP (CREB binding protein), facilitated by phosphorylation at Ser-133 of the KID. The KIX domain peptide (86 aa) was immobilized on the QCM gold electrode surface by means of a poly(ethylene glycol) spacer. Binding of the KID peptide (46 aa) to the KIX peptide was detected by frequency decreases (mass increases) of the QCM. Both maximum binding amount (Deltammax) and association constants (Ka) obtained from the QCM measurements increased as a result of phosphorylation of Ser-133 of the KID peptide. The Ka values for KIX peptide to the phosphorylated (pKID) and unphosphorylated KID peptides were (93+/-2) x 10(3) and (5+/-1) x 10(3) M(-1), respectively. This difference was explained by the dissociation rate constant (k(-1)) of the pKID being 20 times smaller than that of the KID, while association rate constants (k1) were independent of phosphorylation.
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Affiliation(s)
- Hisao Matsuno
- Department of Biomolecular Engineering, Tokyo Institute of Technology and CREST, JST, 4259 Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
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Hoshino Y, Kawasaki T, Okahata Y. Effect of Ultrasound on DNA Polymerase Reactions: Monitoring on a 27-MHz Quartz Crystal Microbalance. Biomacromolecules 2006; 7:682-5. [PMID: 16529399 DOI: 10.1021/bm050738e] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Effects of ultrasound irradiation on DNA polymerase (Klenow fragment, KF) reactions were studied on the template/primer DNA-immobilized quartz crystal microbalance (QCM). Under ultrasound irradiation, binding of KF to the DNA was suppressed due to the decrease of the binding rate constant (k(1)) and the increase of the dissociation rate constant (k(-)(1)). The catalytic elongation rate (k(cat)) was increased, but the stability of the KF/DNA/monomer ternary complex (K(m)) was decreased by the ultrasound irradiation. Ultrasound effects are discussed in correlation with the conformation changes of domain structures in KF.
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Affiliation(s)
- Yu Hoshino
- Department of Biomolecular Engineering and Frontier Collaborative Research Center, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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40
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Tomizaki KY, Usui K, Mihara H. Protein-detecting microarrays: current accomplishments and requirements. Chembiochem 2006; 6:782-99. [PMID: 15791688 DOI: 10.1002/cbic.200400232] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The sequencing of the human genome has been successfully completed and offers the chance of obtaining a large amount of valuable information for understanding complex cellular events simply and rapidly in a single experiment. Interestingly, in addressing these proteomic studies, the importance of protein-detecting microarray technology is increasing. In the coming few years, microarray technology will become a significantly promising and indispensable research/diagnostic tool from just a speculative technology. It is clear that the protein-detecting microarray is supported by three independent but strongly related technologies (surface chemistry, detection methods, and capture agents). Firstly, a variety of surface-modification methodologies are now widely available and offer site-specific immobilization of capture agents onto surfaces in such a way as to keep the native conformation and activity. Secondly, sensitive and parallel detection apparatuses are being developed to provide highly engineered microarray platforms for simultaneous data acquisition. Lastly, in the development of capture agents, antibodies are now probably the most prominent capture agents for analyzing protein abundances. Alternative scaffolds, such as phage-displayed antibody and protein fragments, which provide the advantage of increasing diversity of proteinic capture agents, however, are under development. An approach involving recombinant proteins fused with affinity tag(s) and coupled with a highly engineered surface chemistry will provide simple production protocols and specific orientations of capture agents on the microarray formats. Peptides and other small molecules can be employed in screening highly potent ligands as well as in measuring enzymatic activities. Protein-detecting microarrays supported by the three key technologies should contribute in accelerating diagnostic/biological research and drug discovery.
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Affiliation(s)
- Kin-ya Tomizaki
- Department of Bioengineering and The COE21 Program, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B-40, 4259 Nagatsuta, Midori, Yokohama 226-8501, Japan
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41
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Huang GS, Wang MT, Hong MY. A versatile QCM matrix system for online and high-throughput bio-sensing. Analyst 2006; 131:382-7. [PMID: 16496046 DOI: 10.1039/b515722f] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 3 x 3 quartz crystal microbalance (QCM) sensor matrix, fabricated on an A-T cut quartz crystal, has the ability to detect online a variety of labeled DNA samples in a parallel and comparative fashion. The QCM matrix was equipped with a single oscillator circuit, which activated only one QCM at any given time, and was controlled by programmable time-shared electronic relays. The gold electrode had a diameter of 0.8 mm and operated at a fundamental resonating frequency of 40 MHz; the dimensions of the matrix were 1.2 cm x 1.2 cm. The sensitivity of an individual QCM was in the pictogram regime. Selected QCMs were coated with either streptavidin or the anti-DIG antibody; the specificity of their detections was monitored using various concentrations of samples of biotin- and DIG-labeled DNA. The basic design of the QCM matrix is readily expandable, without any conceivable difficulties, in both geometry and circuitry.
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Affiliation(s)
- G Steve Huang
- Institute of Nanotechnology, National Chiao Tung University, Hsinchu 300, Taiwan.
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42
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Ohtsuka K, Uemura K, Nojima T, Waki M, Takenaka S. Immobilization of RNase S-Peptide on a single-stranded DNA-fixed gold surface and effective masking of its surface by an acridinyl poly(ethylene glycol). Analyst 2006; 131:55-61. [PMID: 16365663 DOI: 10.1039/b508166a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Oligonucleotide-peptide conjugate was synthesized by coupling of RNase S-peptide to a 24-mer single-stranded DNA (ssDNA) oligonucleotide to be immobilized on its complementary ssDNA oligonucleotide-fixed gold surface of sensor chip or electrode. Immobilization of on the ssDNA-fixed gold surface through DNA duplex formation was confirmed by quartz crystal microbalance (QCM) and electrochemical measurements. After treating with a synthetic acridinyl poly(ethylene glycol) (APEG), specific interaction of S-protein with the S-peptide immobilized on the gold surface was demonstrated by QCM without nonspecific adsorption of unrelated proteins such as BSA and RNase A at the surfaces. This result suggested that the acridine parts of APEG could bind to the DNA duplex on the gold surface and the poly(ethylene glycol) parts were fastened on the surface to resist the adsorption of proteins. Thus, the combination of oligonucleotide-peptide conjugate, ssDNA-fixed chip and APEG with effective masking property provides a new tool for the analysis of specific peptide-protein interactions without disturbance by other unrelated proteins.
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Affiliation(s)
- Keiichi Ohtsuka
- Department of Materials Science, Kyushu Institute of Technology, Kitakyushu-shi 804-8550, Japan
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43
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Takakusagi Y, Kobayashi S, Sugawara F. Camptothecin binds to a synthetic peptide identified by a T7 phage display screen. Bioorg Med Chem Lett 2005; 15:4850-3. [PMID: 16122925 DOI: 10.1016/j.bmcl.2005.07.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 06/28/2005] [Accepted: 07/07/2005] [Indexed: 11/21/2022]
Abstract
An analysis of non-biotinylated camptothecin (CPT) binding to the C-20-biotinylated CPT binding peptide NSSQSARR was carried out using two methods, quartz-crystal microbalance (QCM) and surface plasmon resonance (SPR). The peptide was immobilized peptide on a sensor chip and showed a dissociation constant (KD) of approximately 0.1 microM against CPT in QCM and SPR experiments.
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Affiliation(s)
- Yoichi Takakusagi
- Genome and Drug Discovery Research Center, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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44
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Mondal S, Venkataraman V. In situ monitoring of polymerase extension rate and adaptive feedback control of PCR by using fluorescence measurements. ACTA ACUST UNITED AC 2005; 65:97-105. [PMID: 16293313 DOI: 10.1016/j.jbbm.2005.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 09/29/2005] [Accepted: 10/12/2005] [Indexed: 11/24/2022]
Abstract
Real time PCR detection systems based on fluorescence detection from intercalating dyes (such as SYBR Green I) typically take only single point measurements during every cycle to quantify the amplification. In this process key information about enzymatic kinetics is lost. In this work we measure SYBR Green I fluorescence intensity every 0.5 s within a cycle during PCR in polypropylene tubes. We observe that the intensity during the extension cycle increases while the template is being extended. Results obtained for different lengths are used to estimate an in vitro polymerase activity rate of Thermus aquaticus and Thermus brockianus. An important practical consequence of this result is that the extension time of each PCR cycle can be individually optimized while the reaction is in progress. We demonstrate this idea of adaptive feedback control and show that the total number of cycles and total time required to reach maximum fluorescence is reduced as compared to conventional PCR.
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Affiliation(s)
- Sudip Mondal
- Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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45
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Ando Y. Liver transplantation and new therapeutic approaches for familial amyloidotic polyneuropathy (FAP). Med Mol Morphol 2005; 38:142-54. [PMID: 16170462 DOI: 10.1007/s00795-005-0288-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Accepted: 04/11/2005] [Indexed: 11/30/2022]
Abstract
Liver transplantation has been considered as a promising therapy to halt the progression of clinical symptoms in familial amyloidotic polyneuropathy (FAP) because most transthyretin (TTR) is produced by the liver. In addition, domino liver transplantation using an FAP patient's liver has been performed because of a shortage of donor livers. However, because the use of liver transplantation as therapy for FAP has given rise to several problems, an alternative treatment is needed. We have tried several other approaches. Recent studies suggested that certain metal ions affect amyloidogenesis. Among metal ions tested in an in vitro amyloid formation study, Cr3+ increased stability of both normal and mutant TTR tetramers and suppressed TTR amyloidogenesis induced by low pH. Our findings indicate that Cr3+ acts to suppress TTR amyloidogenesis. BSB, a Congo red derivative that binds to amyloid fibrils in FAP as well as to those in senile plaques in Alzheimer's disease, effectively suppressed TTR amyloid formation in vitro. BSB may thus be useful for preventing amyloid formation. Free radical scavenger therapy was also tried in FAP patients but yielded no conclusive results. Immunization for transgenic mice having the ATTR V30M gene using ATTR Y78P resulted in suppression of amyloid deposits. Finally, an RNA/DNA chimera and single-stranded oligonucleotides (SSOs) were tested in vitro and in vivo in an attempt to repair the amyloidogenic TTR gene in the liver and retina. On the basis of results achieved so far, SSO is a promising tool for gene therapy.
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Affiliation(s)
- Yukio Ando
- Department of Diagnostic Medicine, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto, 860-0811, Japan.
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46
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Matsuno H, Furusawa H, Okahata Y. Kinetic studies of DNA cleavage reactions catalyzed by an ATP-dependent deoxyribonuclease on a 27-MHz quartz-crystal microbalance. Biochemistry 2005; 44:2262-70. [PMID: 15709738 DOI: 10.1021/bi048486+] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Catalytic DNA cleavage reactions by an ATP-dependent deoxyribonuclease (DNase) from Micrococcus luteus were monitored directly with a DNA-immobilized 27-MHz quartz-crystal microbalance (QCM). The 27-MHz QCM is a very sensitive mass-measuring device in aqueous solution, as the frequency decreases linearly with increasing mass on the electrode at a nanogram level. Three steps in ATP-dependent DNA hydrolysis reactions, including (1) binding of DNase to the end of double-stranded DNA (dsDNA) on the QCM electrode (mass increase), (2) degradation of one strand of dsDNA in the 3' --> 5' direction depending on ATP (mass decrease), and (3) release of the enzyme from the nonhydrolyzed 5'-free-ssDNA (mass decrease), could be monitored stepwise from the time dependencies of QCM frequency changes. Kinetic parameters for each step were obtained as follows. The binding constant (K(a)) of DNase to the dsDNA was determined as (28 +/- 2) x 10(6) M(-)(1) (k(on) = (8.0 +/- 0.3) x 10(3) M (-)(1) s(-)(1) and k(off) = (0.29 +/-0.01) x 10(-)(3) s(-)(1)), and it decreased to (0.79 +/- 0.16) x 10(6) M(-)(1) (k'(on) = (2.3 +/- 0.2) x 10(3) M (-)(1) s(-)(1) and k'(off) = (2.9 +/- 0.1) x 10(-)(3) s(-)(1)) for the completely nonhydrolyzed 5'-free ssDNA. This is the reason the DNase bound to the dsDNA substrate can easily release from the nonhydrolyzed 5'-free-ssDNA after the complete hydrolysis of the 3' --> 5' direction of the complementary ssDNA. K(a) values depended on the DNA structures on the QCM, and the order of these values was as follows: the dsDNA having a 4-base-mismatched base-pair end (3) > the dsDNA having a 5' 15-base overhanging end (2) > the dsDNA having a blunt end (1) > the ssDNA having a 3'-free end (4) >> the ssDNA having a 5'-free end (5). Thus, DNase hardly recognized the free 5' end of ssDNA. Michaelis-Menten parameters (K(m) for ATP and k(cat)) of the hydrolysis process also could be obtained, and the order of k(cat)/K(m) was as follows: the dsDNA having a blunt end (1) approximately the dsDNA having a 4-base-mismatched base-pair end (3) > the ssDNA having a free 3' end (4) >> the ssDNA having a free 5' end (5). Thus, DNase could not recognize and not hydrolyze the free 5' end of ssDNA. The DNA hydrolysis reaction could be driven by dATP and GTP (purine base) as well as ATP, whereas the cleavage efficiency was very low driven with UTP, CTP (pyrimidine base), ADP, and AMP.
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Affiliation(s)
- Hisao Matsuno
- Department of Biomolecular Engineering, Frontier Collaborative Research Center, Tokyo Institute of Technology and CREST, Japan Science and Technology Corporation (JST), 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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47
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Stengel G, Knoll W. Surface plasmon field-enhanced fluorescence spectroscopy studies of primer extension reactions. Nucleic Acids Res 2005; 33:e69. [PMID: 15849312 PMCID: PMC1084329 DOI: 10.1093/nar/gni067] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Surface plasmon field-enhanced fluorescence spectroscopy (SPFS) utilizes the evanescent electromagnetic field of a surface plasmon to excite chromophors in close proximity to the surface. While conventional surface plasmon resonance spectroscopy allows the observation of surface reactions by means of refractive index changes, SPFS additionally provides a channel for the read-out of fluorescence changes. Thus, the detection limit for low mass compounds, whose adsorption is only accompanied by small refractive index changes, can be substantially improved by fluorescent labeling. In this study, we present the first example that utilizes SPFS to follow the dynamics of an enzymatic reaction. The elongation of surface-tethered DNA has been observed by the incorporation of Cy5-labeled nucleotides into the nascent strand by the action of DNA polymerase I (Klenow fragment). The technique offers a rapid way to determine the binding constant and the catalytic activity of a DNA processing enzyme, here exemplified by the Klenow fragment. Furthermore, the effect of mispaired bases in the primer/template duplex and the influence of different label densities have been studied. The resulting sensitivity for nucleotide incorporation, being in the femtomolar regime, combined with the specificity of the enzyme for fully complementary DNA duplexes suggest the application of this assay as a powerful tool for DNA detection.
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Affiliation(s)
- Gudrun Stengel
- Max-Planck-Institute for Polymer Research Ackermannweg 10, D-55128 Mainz, Germany.
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48
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Christ K, Rüttinger HH, Höpfner M, Rothe U, Bendas G. The Detection of UV-induced Membrane Damages by a Combination of Two Biosensor Techniques. Photochem Photobiol 2005; 81:1417-23. [PMID: 16354115 DOI: 10.1562/2005-04-19-ra-493] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Ketoprofen is an important anti-inflammatory drug, but its dermal application is limited because of the photosensitizing properties causing phototoxic reactions of the skin when exposed to UV light. We have recently investigated the peroxide formation of ketoprofen in solutions of linoleic acid during UV irradiation. To continue these studies and focus on UV-induced changes in membrane integrity and barrier function we established an in vitro model using two biosensor techniques simultaneously. Support-fixed bilayers were irradiated with different doses of UV-B up to damaging intensities with or without ketoprofen. Cyclic voltammetry was carried out to detect alterations in membrane permeability; quartz crystal microbalance (QCM) measurements were helpful in analyzing whether a permeability increase was caused by depletion of membrane components. In absence of ketoprofen, increasing UV-B doses induce membrane permeabilities of both unsaturated and saturated bilayers. QCM measurements could not reveal a significant loss of membrane components as a reason for the permeability. In contrast, 0.3 mM ketoprofen induced a dose-dependent increase in membrane permeability. QCM results indicated a mass loss. Although this model does not explain all molecular mechanisms of membrane damage by ketoprofen, the combined application of both QCM and CV is a novel and powerful tool to investigate functional mechanisms of UV-induced membrane damages.
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Affiliation(s)
- Katrin Christ
- University of Bonn, Department of Pharmacy, An der Immenburg 4, 53121 Bonn, Germany.
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49
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Nishino H, Murakawa A, Mori T, Okahata Y. Kinetic studies of AMP-dependent phosphorolysis of amylopectin catalyzed by phosphorylase b on a 27 MHz quartz-crystal microbalance. J Am Chem Soc 2004; 126:14752-7. [PMID: 15535699 DOI: 10.1021/ja046583k] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Catalytic cleavage reactions of phosphorylase b were monitored directly on an amylopectin-immobilized 27 MHz quartz-crystal microbalance (QCM). When the inactivated phosphorylase b was injected into a phosphate buffer solution of amylopectin-immobilized QCM (method A), the binding of the enzyme to amylopectin was observed as a frequency decrease (mass increase). Then, when AMP (adenosine monophosphate) was added to activate the enzyme, the frequency gradually increased (mass decreased) due to the phosphorolysis of amylopectin in the presence of phosphates as buffers. When the AMP-activated phosphorylase b was employed (method B), the continuous reaction was observed which includes both the mass increase due to the enzyme binding to amylopectin at first and then the following mass decrease due to the phosphorolysis by the AMP-activated enzyme. All kinetic parameters for the enzyme binding to the substrate (binding and dissociation rate constants, k(on) and k(off), and dissociation constant, K(d)), the AMP binding to the enzyme as activator (K(AMP)), the catalytic rate constant (k(cat)) were obtained from curve fittings of time-courses of frequency (mass) changes. The obtained kinetic parameters were compared with those from Michaelis-Menten kinetics.
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Affiliation(s)
- Hidekazu Nishino
- Contribution from the Department of Biomolecular Engineering, Frontier Collaborative Research Center, Tokyo Institute of Technology and CREST, Japan Science and Technology Corporation (JST), 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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50
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Nishino H, Nihira T, Mori T, Okahata Y. Direct Monitoring of Enzymatic Glucan Hydrolysis on a 27-MHz Quartz-Crystal Microbalance. J Am Chem Soc 2004; 126:2264-5. [PMID: 14982404 DOI: 10.1021/ja0361805] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By using a highly sensitive 27-MHz glucan-immobilized quartz-crystal microbalance, we could follow kinetically all processes (enzyme binding and release, kon and koff, and intramolecular hydrolysis rates, kcat) of glucan hydrolysis by glucoamylase by detecting directly the formation and decay of the enzyme-substrate complex as mass changes.
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Affiliation(s)
- Hidekazu Nishino
- Department of Biomolecular Engineering, Tokyo Institute of Technology and CREST, JST, Nagatsuda, Midori-ku, Yokohama 226-8501, Japan
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