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Afzal M, Park J, Jeon JS, Akmal M, Yoon TS, Sung HJ. Acoustofluidic Separation of Proteins Using Aptamer-Functionalized Microparticles. Anal Chem 2021; 93:8309-8317. [PMID: 34075739 DOI: 10.1021/acs.analchem.1c01198] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We propose an acoustofluidic method for the triseparation of proteins conjugated with aptamer-coated microparticles inside a microchannel. Traveling surface acoustic waves (TSAWs) produced from a slanted-finger interdigital transducer (SFIT) are used to separate the protein-loaded microparticles of different sizes via the TSAW-driven acoustic radiation force (ARF). The acoustofluidic device consists of an SFIT deposited onto a piezoelectric lithium niobate substrate and a polydimethylsiloxane (PDMS) microfluidic channel on top of the substrate. The TSAWs propagating on the substrate penetrate into the sample fluid flow, where the human protein-conjugated microparticles are suspended, inside the PDMS microchannel. The microparticles are subjected to the TSAW-driven ARF with varying magnitude depending on their size and thus flow along different streamlines, leading to triseparation of the proteins. In this work, we used two different-sized streptavidin-functionalized polystyrene (PS) microparticles to capture two kinds of aptamers (apt15 and aptD17.4), which were labeled with a respective biotin molecule at one end. The biotin ends of the aptamers were attached to the microparticles through streptavidin-biotin linkage, whereas the free ends of the aptamers were used to capture their target proteins of thrombin (th) and immunoglobulin E (IgE). The resultant PS-apt15-th and PS-aptD17.4-IgE complexes, as well as mCardinal2, were used for experimental demonstration of acoustofluidic triseparation of the human proteins. We achieved simultaneous separation of proteins of three kinds (th, IgE, and mCardinal2) for the first time via the TSAW-driven ARF in the proposed acoustofluidic device.
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Affiliation(s)
- Muhammad Afzal
- Department of Mechanical Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Jinsoo Park
- School of Mechanical Engineering, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Korea
| | - Jessie S Jeon
- Department of Mechanical Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Muhammad Akmal
- Department of Materials Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Tae-Sung Yoon
- Department of Proteome Structural Biology, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Hyung Jin Sung
- Department of Mechanical Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
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Yan SR, Foroughi MM, Safaei M, Jahani S, Ebrahimpour N, Borhani F, Rezaei Zade Baravati N, Aramesh-Boroujeni Z, Foong LK. A review: Recent advances in ultrasensitive and highly specific recognition aptasensors with various detection strategies. Int J Biol Macromol 2020; 155:184-207. [PMID: 32217120 DOI: 10.1016/j.ijbiomac.2020.03.173] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/03/2020] [Accepted: 03/19/2020] [Indexed: 12/17/2022]
Abstract
One of the most studied topics in analytical chemistry and physics is to develop bio-sensors. Aptamers are small single-stranded RNA or DNA oligonucleotides (5-25 kDa), which have advantages in comparison to their antibodies such as physicochemical stability and high binding specificity. They are able to integrate with proteins or small molecules, including intact viral particles, plant lectins, gene-regulation factor, growth factors, antibodies and enzymes. The aptamers have reportedly shown some unique characteristics, including long shelf-life, simple modification to provide covalent bonds to material surfaces, minor batch variation, cost-effectiveness and slight denaturation susceptibility. These features led important efforts toward the development of aptamer-based sensors, known as apta-sensors classified into optical, electrical and mass-sensitive based on the signal transduction mode. This review provided a number of current advancements in selecting, development criteria, and aptamers application with the focus on the effect of apta-sensors, specifically for disease-associated analyses. The review concentrated on the current reports of apta-sensors that are used for evaluating different food and environmental pollutants.
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Affiliation(s)
- Shu-Rong Yan
- Institute of Smart Finance, Yango University, Fuzhou 350015, China
| | | | - Mohadeseh Safaei
- Student Research Committee, School of Public Health, Bam University of Medical Sciences, Bam, Iran
| | - Shohreh Jahani
- Student Research Committee, School of Public Health, Bam University of Medical Sciences, Bam, Iran; Bam University of Medical Sciences, Bam, Iran
| | - Nasser Ebrahimpour
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Fariba Borhani
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Zahra Aramesh-Boroujeni
- Department of Clinical Laboratory, AlZahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Loke Kok Foong
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Viet Nam.
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Poturnayová A, Dzubinová Ľ, Buríková M, Bízik J, Hianik T. Detection of Breast Cancer Cells Using Acoustics Aptasensor Specific to HER2 Receptors. BIOSENSORS 2019; 9:E72. [PMID: 31137893 PMCID: PMC6627288 DOI: 10.3390/bios9020072] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/17/2019] [Accepted: 05/23/2019] [Indexed: 12/02/2022]
Abstract
Detection of the breast cancer cells is important for early diagnosis of the cancer. We applied thickness shear mode acoustics method (TSM) for detection of SK-BR-3 breast cancer cells using DNA aptamers specific to HER2 positive membrane receptors. The biotinylated aptamers were immobilized at the neutravidin layer chemisorbed at gold surface of TSM transducer. Addition of the cells resulted in decrease of resonant frequency, fs, and in increase of motional resistance, Rm. Using gold nanoparticles (AuNPs), modified by aptamers it was possible improving the limit of detection (LOD) that reached 550 cells/mL, while without amplification the sensitivity of the detection of SK-BR-3 cells was 1574 cells/mL. HER2 negative cell line MDA-MB-231 did not resulted in significant changes of fs. The viability studies demonstrated that cells are stable at experimental conditions used during at least 8 h. AuNPs were not toxic on the cells up to concentration of 1 μg/mL.
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Affiliation(s)
- Alexandra Poturnayová
- Institute of Animal Biochemistry and Genetics, Center of Biosciences SAS, Dúbravská cesta 9, 840 05 Bratislava, Slovakia.
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48 Bratislava, Slovakia.
| | - Ľudmila Dzubinová
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48 Bratislava, Slovakia.
| | - Monika Buríková
- Cancer Research Institute, Biomedical Research Center SAS, Dúbravská cesta 9, 840 05 Bratislava, Slovakia.
| | - Jozef Bízik
- Cancer Research Institute, Biomedical Research Center SAS, Dúbravská cesta 9, 840 05 Bratislava, Slovakia.
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48 Bratislava, Slovakia.
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Poturnayová A, Buríková M, Bízik J, Hianik T. DNA Aptamers in the Detection of Leukemia Cells by the Thickness Shear Mode Acoustics Method. Chemphyschem 2019; 20:545-554. [PMID: 30552789 DOI: 10.1002/cphc.201801126] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/13/2018] [Indexed: 12/11/2022]
Abstract
By using the thickness shear mode acoustics method (TSM) and single-molecule force spectroscopy (SMFS) we studied the interactions between DNA aptamers (sgc8c) specific to the protein tyrosine kinase 7 (PTK7), which is localized in the membranes of leukemia lymphoblastics (MOLT-4), and lymphocyte (Jurkat) cell lines, as well with PTK7-negative U266 myeloid leukemia cells. The TSM method allowed the development of a highly sensitive, label-free biosensor for the detection leukemia cells with a limit of detection of (195±20) cells/mL. SMFS approved the high selectivity of the sgc8c aptamers to the PTK7 receptors at the cell surface and allowed determining the binding probability of the aptamers to the PTK7 receptors at different cell lines.
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Affiliation(s)
- Alexandra Poturnayová
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University Mlynská dolina F1, 842 48, Bratislava, Slovakia.,Institute of Animal Biochemistry and Genetics, Center of Biosciences SAS Dúbravská cesta 9, 840 05, Bratislava, Slovakia
| | - Monika Buríková
- Cancer Research Institute, Biomedical Research Center SAS, Dúbravská cesta 9, 840 05, Bratislava, Slovakia
| | - Jozef Bízik
- Cancer Research Institute, Biomedical Research Center SAS, Dúbravská cesta 9, 840 05, Bratislava, Slovakia
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics Faculty of Mathematics, Physics and Informatics, Comenius University Mlynská dolina F1, 842 48, Bratislava, Slovakia
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Karapetis S, Nikolelis D, Hianik T. Label-Free and Redox Markers-Based Electrochemical Aptasensors for Aflatoxin M1 Detection. SENSORS (BASEL, SWITZERLAND) 2018; 18:E4218. [PMID: 30513767 PMCID: PMC6308435 DOI: 10.3390/s18124218] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 11/25/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022]
Abstract
We performed a comparative analysis of the sensitivity of aptamer-based biosensors for detection mycotoxin aflatoxin M₁ (AFM1) depending on the method of immobilization of DNA aptamers and method of the detection. Label-free electrochemical impedance spectroscopy (EIS) and differential pulse voltammetry (DPV) for ferrocene labeled neutravidin layers were used for this purpose. Amino-modified DNA aptamers have been immobilized at the surface of polyamidoamine dendrimers (PAMAM) of fourth generation (G4) or biotin-modified aptamers were immobilized at the neutravidin layer chemisorbed at gold surface. In the first case the limit of detection (LOD) has been determined as 8.47 ng/L. In the second approach the LOD was similar 8.62 ng/L, which is below of allowable limits of AFM1 in milk and milk products. The aptasensors were validated in a spiked milk samples with good recovery better than 78%. Comparative analysis of the sensitivity of immuno- and aptasensors was also performed and showed comparable sensitivity.
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Affiliation(s)
- Stefanos Karapetis
- Department of Nuclear Physics and Biophysics, Comenius University, Mlynska dolina F1, 842 48 Bratislava, Slovakia.
- Laboratory of Inorganic & Analytical Chemistry, School of Chemical Engineering, Department of Chemical Sciences, National Technical University of Athens, 9 Iroon Polytechniou St., 157 80 Athens, Greece.
| | - Dimitrios Nikolelis
- Laboratory of Environmental Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis-Kouponia, 157 71 Athens, Greece.
| | - Tibor Hianik
- Department of Nuclear Physics and Biophysics, Comenius University, Mlynska dolina F1, 842 48 Bratislava, Slovakia.
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Hianik T. Affinity Biosensors for Detection Immunoglobulin E and Cellular Prions. Antibodies vs. DNA Aptamers. ELECTROANAL 2016. [DOI: 10.1002/elan.201600153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Tibor Hianik
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics and Informatics; Comenius University; Mlynska dolina F1 842 48 Bratislava Slovakia
- OpenLab “DNA-Sensors” of Kazan Federal University; 18 Kremlevskaya Street Kazan 420008 Russian Federation
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Peculiarities of the interaction of the restriction endonuclease BspD6I with DNA containing its recognition site. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1072-1082. [PMID: 27216152 DOI: 10.1016/j.bbapap.2016.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 04/08/2016] [Accepted: 05/19/2016] [Indexed: 11/20/2022]
Abstract
BACKGROUND Nicking endonucleases are enzymes that recognize specific sites in double-stranded DNA and cleave only one strand at a predetermined position. These enzymes are involved in DNA replication and repair; they can also function as subunits of bacterial heterodimeric restriction endonucleases. One example of such a proteins is the restriction endonuclease BspD6I (R.BspD6I) from Bacillus species strain D6, which consists of the large subunit - nicking endonuclease BspD6I (Nt.BspD6I), and the small subunit (ss.BspD6I). Nt.BspD6I can function independently. Similar enzymes are now widely used in numerous biotechnological applications. The aim of this study was to investigate the fundamental properties of two subunits of R.BspD6I and their interdependence in the course of R.BspD6I activity. METHODS The binding and hydrolysis of DNA duplexes by R.BspD6I are primary analyzed by gel electrophoresis. To elucidate the difference between Nt.BspD6I interaction with the substrate and product of hydrolysis, the thickness shear mode acoustic method is used. RESULTS AND CONCLUSIONS The thermodynamic and kinetic parameters of the Nt.BspD6I interaction with DNA are determined. For the first time we demonstrated that Nt.BspD6I bends the DNA during complex formation. Nt.BspD6I is able to form complexes with the product nicked in the top strand and ss.BspD6I cleaves the bottom strand of the DNA consecutively. Furthermore, the influence of dA methylation in the R.BspD6I recognition site on ss.BspD6I activity is analyzed. GENERAL SIGNIFICANCE The obtained results provide evidence that Nt.BspD6I coordinates the activity of R.BspD6I by strictly coupling of the bottom strand cleavage by ss.BspD6I to the top strand cleavage.
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Use of aptamers in immunoassays. Mol Immunol 2016; 70:149-54. [PMID: 26774749 DOI: 10.1016/j.molimm.2015.12.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/02/2015] [Accepted: 12/15/2015] [Indexed: 12/19/2022]
Abstract
Aptamers, short single-chain DNA or RNA oligonucleotides, react specifically with small molecules, as well as with proteins. Unlike antibodies, they may be obtained relatively easily. Aptamers are now widely employed in immunological studies and could replace antibodies in immunoassays. In this short review, methods for immobilizing aptamers on various insoluble materials (so-called apta-sorbents) are described. Recent findings on their use in the detection and isolation of immunoglobulins and their application in various immunoassays are also discussed.
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Vorobyeva M, Timoshenko V, Vorobjev P, Venyaminova A. Aptamers Against Immunologic Targets: Diagnostic and Therapeutic Prospects. Nucleic Acid Ther 2015; 26:52-65. [PMID: 26643948 DOI: 10.1089/nat.2015.0568] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The concept of in vitro selection of nucleic acid aptamers emerged 25 years ago, and since then tremendous progress has been achieved in the development of different aptamers and their applications for various bioanalytical and therapeutic purposes. Among other protein targets of aptamers, immune system proteins are of particular interest both as diagnostic markers and therapeutic targets. The present review summarizes up-to-date articles concerning the selection and design of DNA and RNA aptamers against immunologic targets such as antibodies, cytokines, and T-cell and B-cell receptors. We also discuss the prospects of employing aptamers as recognizing modules of diagnostic aptasensors, potential therapeutic candidates for the treatment of autoimmune diseases and cancer, and specific tools for functional studies of immune system proteins.
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Affiliation(s)
- Mariya Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine , Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentina Timoshenko
- Institute of Chemical Biology and Fundamental Medicine , Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel Vorobjev
- Institute of Chemical Biology and Fundamental Medicine , Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
| | - Alya Venyaminova
- Institute of Chemical Biology and Fundamental Medicine , Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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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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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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DNA aptamer configuration affects the sensitivity and binding kinetics of thrombin. ACTA CHIMICA SLOVACA 2012. [DOI: 10.2478/v10188-012-0009-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA aptamer configuration affects the sensitivity and binding kinetics of thrombinThrombin is serine protease involved in the coagulation cascade, which converts soluble fibrinogen into insoluble strands of fibrin - a matrix of the blood clot formation. Development of the sensitive method of the thrombin detection in nanomolar level is important for clinical practice. In this work we applied acoustic thickness shear mode method (TSM) for study the binding of human thrombin depending on DNA aptamer configuration. We compared sensitivity of detection and binding kinetics of the thrombin to the conventional DNA aptamers and aptamer dimers immobilized at the surface of quartz crystal transducer. We have shown that aptasensors based on aptamer dimers more sensitively detect thrombin. The aptamer-thrombin complexes were also more stable as revealed from equilibrium dissociation constant,KD, that was 4 times lower for aptamer dimers in comparison with conventional aptamers. Determination of motional resistance,Rm, from acoustic impedance analysis allowed us to find important differences in physico-chemical properties of layers formed by conventional aptamers and aptamer dimers.
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Ryazanova AY, Kubareva EA, Grman I, Lavrova NV, Ryazanova EM, Oretskaya TS, Hianik T. The study of the interaction of (cytosine-5)-DNA methyltransferase SsoII with DNA by acoustic method. Analyst 2011; 136:1227-33. [PMID: 21274469 DOI: 10.1039/c0an00545b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of (cytosine-5)-DNA methyltransferase SsoII (M.SsoII) with double-stranded DNA was studied by means of thickness shear mode acoustic method (TSM) and gel electrophoresis. M.SsoII recognizes in double-stranded DNA the methylation site 5'-CCNGG-3' (N=A, C, G, T) and methylates the inner cytosine residue. M.SsoII also acts as a transcription factor via binding to the regulatory site 5'-AGGACAAATTGTCCT-3' in the promoter region of SsoII restriction-modification system. We designed three 60-mer biotinylated DNA duplexes: with the methylation site (60met), with the regulatory site (60reg), and without a specific binding site (60oct). A strong binding of M.SsoII with each one of the studied DNA immobilized on the TSM transducer has been shown. The equilibrium dissociation constants, K(D), of the M.SsoII-DNA complexes decreased in the order 60oct>60reg>60met, suggesting a higher stability of M.SsoII-60met complex in comparison with the others. The association rate constant, k(a), was also higher for 60met, while similar values were obtained for 60reg and 60oct. The difference in the kinetic parameters for 60met and 60reg suggested a possible way of coordination between the two M.SsoII functions in a cell.
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Affiliation(s)
- A Yu Ryazanova
- Faculty of Bioengineering and Bioinformatics, Chemistry Department, and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
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Šnejdárková M, Poturnayová A, Rybár P, Lhoták P, Himl M, Flídrová K, Hianik T. High sensitive calixarene-based sensor for detection of dopamine by electrochemical and acoustic methods. Bioelectrochemistry 2010; 80:55-61. [DOI: 10.1016/j.bioelechem.2010.03.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2010] [Revised: 03/05/2010] [Accepted: 03/14/2010] [Indexed: 10/19/2022]
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Uludağ Y, Hammond R, Cooper MA. A signal amplification assay for HSV type 1 viral DNA detection using nanoparticles and direct acoustic profiling. J Nanobiotechnology 2010. [PMCID: PMC2836275 DOI: 10.1186/1477-3155-8-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Nucleic acid based recognition of viral sequences can be used together with label-free biosensors to provide rapid, accurate confirmation of viral infection. To enhance detection sensitivity, gold nanoparticles can be employed with mass-sensitive acoustic biosensors (such as a quartz crystal microbalance) by either hybridising nanoparticle-oligonucleotide conjugates to complimentary surface-immobilised ssDNA probes on the sensor, or by using biotin-tagged target oligonucleotides bound to avidin-modified nanoparticles on the sensor. We have evaluated and refined these signal amplification assays for the detection from specific DNA sequences of Herpes Simplex Virus (HSV) type 1 and defined detection limits with a 16.5 MHz fundamental frequency thickness shear mode acoustic biosensor. Results In the study the performance of semi-homogeneous and homogeneous assay formats (suited to rapid, single step tests) were evaluated utilising different diameter gold nanoparticles at varying DNA concentrations. Mathematical models were built to understand the effects of mass transport in the flow cell, the binding kinetics of targets to nanoparticles in solution, the packing geometries of targets on the nanoparticle, the packing of nanoparticles on the sensor surface and the effect of surface shear stiffness on the response of the acoustic sensor. This lead to the selection of optimised 15 nm nanoparticles that could be used with a 6 minute total assay time to achieve a limit of detection sensitivity of 5.2 × 10-12 M. Larger diameter nanoparticles gave poorer limits of detection than smaller particles. The limit of detection was three orders of magnitude lower than that observed using a hybridisation assay without nanoparticle signal amplification. Conclusions An analytical model was developed to determine optimal nanoparticle diameter, concentration and probe density, which allowed efficient and rapid optimisation of assay parameters. Numerical analysis and subsequent associated experimental data suggests that the response of the mass sensitive biosensor system used in conjunction with captured particles was affected by i) the coupled mass of the particle, ii) the proximal contact area between the particle and the sensor surface and iii) the available capture area on the particle and binding dynamics to this capture area. The latter two effects had more impact on the detection limit of the system than any potential enhancement due to added mass from a larger nanoparticle.
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Hianik T, Grman I, Karpisova I. The effect of DNA aptamer configuration on the sensitivity of detection thrombin at surface by acoustic method. Chem Commun (Camb) 2009:6303-5. [PMID: 19826702 DOI: 10.1039/b910981a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using an acoustic method we showed that the aptamer configuration, especially those comprised of dimers with binding exosites sensitive to heparin and fibrinogen at thrombin, substantially increases the aptasensor sensitivity.
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Affiliation(s)
- Tibor Hianik
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska dolina F1, 84248 Bratislava, Slovakia.
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Bartošík M, Gajdoš V, Kostečka P, Fojta M, Paleček E, Volkov E, Oretskaya T, Hianik T. Detection of Abasic Sites in DNA by Electrochemical, Immunoelectrochemical and Acoustic Methods Using OsO4, 2,2′-bipyridine as a Probe for Unpaired Thymine Residues. ELECTROANAL 2009. [DOI: 10.1002/elan.200804380] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Evtugyn G, Porfireva A, Ryabova M, Hianik T. Aptasensor for Thrombin Based on Carbon Nanotubes-Methylene Blue Composites. ELECTROANAL 2008. [DOI: 10.1002/elan.200804345] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ostatná V, Vaisocherová H, Homola J, Hianik T. Effect of the immobilisation of DNA aptamers on the detection of thrombin by means of surface plasmon resonance. Anal Bioanal Chem 2008; 391:1861-9. [PMID: 18481050 DOI: 10.1007/s00216-008-2133-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 04/07/2008] [Accepted: 04/11/2008] [Indexed: 11/26/2022]
Abstract
We report a multichannel surface plasmon resonance (SPR) sensor for detection of thrombin via DNA aptamers immobilized on the SPR sensor surface. A detailed investigation of the effect of the immobilisation method on the interaction between thrombin and DNA aptamers is presented. Three basic approaches to the immobilisation of aptamers on the surface of the SPR sensor are examined: (i) immobilisation based on chemisorption of aptamers modified with SH groups, (ii) immobilisation of biotin-tagged aptamers via previously immobilized avidin, neutravidin or streptavidin molecular linkers, and (iii) immobilisation employing dendrimers as a support layer for subsequent immobilisation of aptamers. A level of nonspecific binding of thrombin to immobilized human serum albumin (HSA) for each of the immobilisation methods is determined. Immobilisation of aptamers by means of the streptavidin-biotin system yields the best results both in terms of sensor specificity and sensitivity.
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Affiliation(s)
- Veronika Ostatná
- Department of Nuclear Physics and Biophysics, Comenius University, Mlynská dolina F1, 842 48, Bratislava, Slovak Republic
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