1
|
Sunayama H, Takamiya K, Takano E, Horikawa R, Kitayama Y, Takeuchi T. Simultaneous Detection of Two Tumor Marker Proteins Using Dual-Colored Signaling Molecularly Imprinted Polymers Prepared via Multi-Step Post-Imprinting Modifications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200254] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hirobumi Sunayama
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Kazuhiro Takamiya
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Eri Takano
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Ryo Horikawa
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yukiya Kitayama
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Toshifumi Takeuchi
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
- Center for Advanced Medical Engineering Research & Development (CAMED), Kobe University, 1-5-1 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| |
Collapse
|
2
|
Mohammadinezhad R, Jalali SAH, Farahmand H. Evaluation of different direct and indirect SELEX monitoring methods and implementation of melt-curve analysis for rapid discrimination of variant aptamer sequences. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3823-3835. [PMID: 32676627 DOI: 10.1039/d0ay00491j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Systematic Evolution of Ligands by Exponential enrichment (SELEX) is an iterative method for in vitro selection of aptamers from a random synthetic oligonucleotide library. Successful retrieving of aptamers by SELEX relies on optimization of various steps including target immobilization, aptamer partitioning, amplification, and ssDNA generation, which all require spending considerable effort and cost. Furthermore, due to the random nature of the initial library, SELEX may redirect toward the selection of low-affinity aptamers that are over-represented in the ssDNA population due to PCR bias. Thus, precise monitoring of the SELEX process is crucial to ensure the selection of target-specific aptamers. In the present study, we investigated the reliability and simplicity of different direct and indirect monitoring methods including UV-Vis spectroscopy, real-time PCR quantification and melt-curve analysis, electrophoretic mobility shift assay (EMSA) and enzyme-linked oligonucleotide assay (ELONA) for selection of DNA aptamers for a protein target. All the examined methods were capable of illustrating the gradual evolution of specific aptamers by the progression of SELEX and showed almost similar results regarding the identification of the enriched round of selection. Moreover, we describe the use of melt-curve analysis in the colony real-time PCR method as a simple, robust, and repeatable tool for pre-sequencing separation of distinct aptamer clones.
Collapse
Affiliation(s)
- Rezvan Mohammadinezhad
- Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | | | | |
Collapse
|
3
|
Billinge ER, Platt M. Multiplexed, label-free detection of biomarkers using aptamers and Tunable Resistive Pulse Sensing (AptaTRPS). Biosens Bioelectron 2015; 68:741-748. [PMID: 25682502 DOI: 10.1016/j.bios.2015.02.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/06/2015] [Indexed: 12/26/2022]
Abstract
Diagnostics that are capable of detecting multiple biomarkers are improving the accuracy and efficiency of bioassays. In previous work we have demonstrated the potential of an aptamer-based sensor (aptasensor) utilising Tunable Resistive Pulse Sensing (TRPS). Here, we have advanced the technique identifying key experimental designs for potential POC assays. The assay utilised superparamagnetic beads, and using TRPS monitored their translocations through a pore. If the surfaces of the beads are modified with an aptamer, the frequency of beads (translocations/min) through the pore can be related to the concentration of specific proteins in the solution. Herein, we have demonstrated the successful use of TRPS to observe the binding of two proteins, to their specific aptamers simultaneously. We describe a series of experiments illustrating key factors which we believe are integral to bead-based assays and demonstrate a general method for a multiplexed assay. In summary, we have explored the effects of beads size, concentration, potential bias, pH and aptamer affinity to enhance the sensitivity and practically of a TRPS aptasensor. The method utilises the fact the binding of the aptamer to the protein results in a change in charge density on the bead surface, the isoelectric point of the protein then dominates the mobility of the beads, creating a multiplexed assay termed AptaTRPS. By alteration of the applied potential to the instrument it is possible to produce a positive signal in a simple multiplexed assay.
Collapse
Affiliation(s)
- Emily R Billinge
- Centre of Analytical Sciences, Department of Chemistry, School of Science, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
| | - Mark Platt
- Centre of Analytical Sciences, Department of Chemistry, School of Science, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom.
| |
Collapse
|
4
|
Herbáth M, Papp K, Balogh A, Matkó J, Prechl J. Exploiting fluorescence for multiplex immunoassays on protein microarrays. Methods Appl Fluoresc 2014; 2:032001. [PMID: 29148470 DOI: 10.1088/2050-6120/2/3/032001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein microarray technology is becoming the method of choice for identifying protein interaction partners, detecting specific proteins, carbohydrates and lipids, or for characterizing protein interactions and serum antibodies in a massively parallel manner. Availability of the well-established instrumentation of DNA arrays and development of new fluorescent detection instruments promoted the spread of this technique. Fluorescent detection has the advantage of high sensitivity, specificity, simplicity and wide dynamic range required by most measurements. Fluorescence through specifically designed probes and an increasing variety of detection modes offers an excellent tool for such microarray platforms. Measuring for example the level of antibodies, their isotypes and/or antigen specificity simultaneously can offer more complex and comprehensive information about the investigated biological phenomenon, especially if we take into consideration that hundreds of samples can be measured in a single assay. Not only body fluids, but also cell lysates, extracted cellular components, and intact living cells can be analyzed on protein arrays for monitoring functional responses to printed samples on the surface. As a rapidly evolving area, protein microarray technology offers a great bulk of information and new depth of knowledge. These are the features that endow protein arrays with wide applicability and robust sample analyzing capability. On the whole, protein arrays are emerging new tools not just in proteomics, but glycomics, lipidomics, and are also important for immunological research. In this review we attempt to summarize the technical aspects of planar fluorescent microarray technology along with the description of its main immunological applications.
Collapse
Affiliation(s)
- Melinda Herbáth
- Department of Immunology, Eötvös Loránd University, Budapest, 1117 Hungary
| | | | | | | | | |
Collapse
|
5
|
Vanbrabant J, Leirs K, Vanschoenbeek K, Lammertyn J, Michiels L. reMelting curve analysis as a tool for enrichment monitoring in the SELEX process. Analyst 2014; 139:589-95. [PMID: 24325000 DOI: 10.1039/c3an01884a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Current aptamer selection procedures enable limited control and transparency on how the DNA selection pool is evolving. Affinity tests and binding analyses are not always informative. Here we show that real-time PCR provides a valuable tool for the follow-up of aptamer selection. Limited time, work and amount of amplified ssDNA make this an interesting instrument to set-up a SELEX design and monitor the enrichment of oligonucleotides. reMelting Curve Analysis (rMCA) after reannealing under stringent conditions provides information about enrichment, compared to a random library. Monitoring the SELEX process and optimising conditions by means of the proposed methods can increase the selection efficiency in a controlled way. rMCA is applied in enrichment simulations and three different selection procedures. Our results imply that rMCA can be used for different SELEX designs and different targets. SELEX pool diversity analysis by rMCA has been proven to be a useful, reproducible tool to detect and evaluate enrichment of specific binding aptamers while the selection procedure is being performed.
Collapse
|
6
|
Ayoglu B, Häggmark A, Neiman M, Igel U, Uhlén M, Schwenk JM, Nilsson P. Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev Mol Diagn 2014; 11:219-34. [DOI: 10.1586/erm.10.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
7
|
Billinge ER, Broom M, Platt M. Monitoring aptamer-protein interactions using tunable resistive pulse sensing. Anal Chem 2013; 86:1030-7. [PMID: 24380606 DOI: 10.1021/ac401764c] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aptamers are short single-stranded pieces of DNA or RNA capable of binding to analytes with specificity and high affinity. Due to their comparable selectivity, stability, and cost, over the last two decades, aptamers have started to challenge antibodies in their use on many technology platforms. The binding event often leads to changes in the aptamer's secondary and tertiary structure; monitoring such changes has led to the creation of many new analytical sensors. Here, we demonstrate the use of a tunable resistive pulse sensing (TRPS) technology to monitor the interaction between several DNA aptamers and their target, thrombin. We immobilized the aptamers onto the surface of superparamagnetic beads, prior to their incubation with the thrombin protein. The protein binding to the aptamer caused a conformational change resulting in the shielding of the polyanion backbone; this was monitored by a change in the translocation time and pulse frequency of the particles traversing the pore. This signal was sensitive enough to allow the tagless detection of thrombin down to nanomolar levels. We further demonstrate the power of TRPS by performing real time detection and characterization of the aptamer-target interaction and measuring the association rates of the thrombin protein to the aptamer sequences.
Collapse
Affiliation(s)
- Emily R Billinge
- Department of Chemistry, Centre for Analytical Science, Loughborough University , Loughborough, Leicestershire LE11 3TU, United Kingdom
| | | | | |
Collapse
|
8
|
Loo AH, Bonanni A, Pumera M. Biorecognition on graphene: physical, covalent, and affinity immobilization methods exhibiting dramatic differences. Chem Asian J 2012; 8:198-203. [PMID: 23090869 DOI: 10.1002/asia.201200756] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Indexed: 01/09/2023]
Abstract
The preparation of biorecognition layers on the surface of a sensing platform is a very crucial step for the development of sensitive and selective biosensors. Different protocols have been used thus far for the immobilization of biomolecules onto various electrode surfaces. In this work, we investigate how the protocol followed for the immobilization of a DNA aptamer affects the performance of the fabricated thrombin aptasensor. Specifically, the differences in selectivity and optimum amount of immobilized aptamer of the fabricated aptasensors adopting either physical, covalent, or affinity immobilization were compared. It was discovered that while all three methods of immobilization uniformly show a similar optimum amount of immobilized aptamer, physical, and covalent immobilization methods exhibit higher selectivity than affinity immobilization. Hence, it is believed that our findings are very important in order to optimize and improve the performance of graphene-based aptasensors.
Collapse
Affiliation(s)
- Adeline Huiling Loo
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | | | | |
Collapse
|
9
|
Chen Y, Nakamoto K, Niwa O, Corn RM. On-chip synthesis of RNA aptamer microarrays for multiplexed protein biosensing with SPR imaging measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8281-8285. [PMID: 22458258 PMCID: PMC3368080 DOI: 10.1021/la300656c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Microarrays of RNA aptamers are fabricated in a one-step, multiplexed enzymatic synthesis on gold thin films in a microfluidic format and then employed in the detection of protein biomarkers with surface plasmon resonance imaging (SPRI) measurements. Single-stranded RNA (ssRNA) oligonucleotides are transcribed on-chip from double-stranded DNA (dsDNA) templates attached to microarray elements (denoted as generator elements) by the surface transcription reaction of T7 RNA polymerase. As they are synthesized, the ssRNA oligonucleotides diffuse in the microfluidic channel and are quickly captured by hybridization adsorption onto adjacent single-stranded DNA (ssDNA) microarray elements (denoted as detector elements) that contain a sequence complementary to 5'-end of the ssRNA. The RNA aptamers attached to these detector elements are subsequently used in SPRI measurements for the bioaffinity detection of protein biomarkers. The microfluidic generator-detector element format permits the simultaneous fabrication of multiple ssRNA oligonucleotides with different capture sequences that can hybridize simultaneously to distinct detector elements and thus create a multiplexed aptamer microarray. In an initial set of demonstration experiments, SPRI measurements are used to monitor the bioaffinity adsorption of human thrombin (hTh) and vascular endothelial growth factor (VEGF) proteins onto RNA aptamer microarrays fabricated in situ with this on-chip RNA polymerase synthesis methodology. Additional SPRI measurements of the hydrolysis and desorption of the surface-bound ssRNA aptamers with a surface RNase H are used to verify the capture of ssRNA with RNA-DNA surface hybridization onto the detector elements. The on-chip RNA synthesis described here is an elegant, one-step multiplexed methodology for the rapid and contamination-free fabrication of RNA aptamer microarrays for protein biosensing with SPRI.
Collapse
Affiliation(s)
- Yulin Chen
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Kohei Nakamoto
- National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
- Institute of Material Science, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan
| | - Osamu Niwa
- National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
- Institute of Material Science, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8573, Japan
| | - Robert M. Corn
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| |
Collapse
|
10
|
Urban PL, Amantonico A, Zenobi R. Lab-on-a-plate: extending the functionality of MALDI-MS and LDI-MS targets. MASS SPECTROMETRY REVIEWS 2011; 30:435-478. [PMID: 21254192 DOI: 10.1002/mas.20288] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We review the literature that describes how (matrix-assisted) laser desorption/ionization (MA)LDI target plates can be used not only as sample supports, but beyond that: as functional parts of analytical protocols that incorporate detection by MALDI-MS or matrix-free LDI-MS. Numerous steps of analytical procedures can be performed directly on the (MA)LDI target plates prior to the ionization of analytes in the ion source of a mass spectrometer. These include homogenization, preconcentration, amplification, purification, extraction, digestion, derivatization, synthesis, separation, detection with complementary techniques, data storage, or other steps. Therefore, we consider it helpful to define the "lab-on-a-plate" as a format for carrying out extensive sample treatment as well as bioassays directly on (MA)LDI target plates. This review introduces the lab-on-plate approach and illustrates it with the aid of relevant examples from the scientific and patent literature.
Collapse
Affiliation(s)
- Pawel L Urban
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | | | | |
Collapse
|
11
|
Bogomolova A, Aldissi M. Real-time aptamer quantum dot fluorescent flow sensor. Biosens Bioelectron 2011; 26:4099-103. [PMID: 21515039 DOI: 10.1016/j.bios.2011.04.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 03/21/2011] [Accepted: 04/01/2011] [Indexed: 11/30/2022]
Abstract
The goal of this work was to develop and test a novel real-time biosensing approach which can be adapted to either environmental or clinical monitoring of biological pathogens. We have developed a working prototype of a real-time aptamer-based fluorescent flow sensor. The sensor utilizes a competitive displacement approach to measure the binding of the analyte, which keeps the nonspecific binding below detectable levels. The complex of surface-immobilized DNA aptamer with fluorescent complementary oligonucleotide releases the oligonucleotide upon binding with a specific target, which is translated by a decrease in fluorescence. Bright and stable fluorescence of quantum dots is utilized for prolonged detection of the analyte in flow conditions. The real-time sensor prototype is developed with previously characterized ATP-specific aptamer and is capable of specifically detecting 0.1 mM of ATP in biological buffer, with a quantitative response up to 5 mM. The developed prototype is portable and easy to use and its design allows further miniaturization and multiplexing. The developed real-time sensing approach can be adapted to a variety of targets of environmental and clinical significance.
Collapse
Affiliation(s)
- Anastasia Bogomolova
- Smart Polymers Research Corporation, 108 4th Street, Belleair Beach, FL 33786, USA
| | | |
Collapse
|
12
|
Protein microarrays and biomarkers of infectious disease. Int J Mol Sci 2010; 11:5165-83. [PMID: 21614200 PMCID: PMC3100839 DOI: 10.3390/ijms11125165] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 12/11/2010] [Accepted: 12/15/2010] [Indexed: 01/11/2023] Open
Abstract
Protein microarrays are powerful tools that are widely used in systems biology research. For infectious diseases, proteome microarrays assembled from proteins of pathogens will play an increasingly important role in discovery of diagnostic markers, vaccines, and therapeutics. Distinct formats of protein microarrays have been developed for different applications, including abundance-based and function-based methods. Depending on the application, design issues should be considered, such as the need for multiplexing and label or label free detection methods. New developments, challenges, and future demands in infectious disease research will impact the application of protein microarrays for discovery and validation of biomarkers.
Collapse
|
13
|
Yang X, Bing T, Mei H, Fang C, Cao Z, Shangguan D. Characterization and application of a DNA aptamer binding to L-tryptophan. Analyst 2010; 136:577-85. [PMID: 21076782 DOI: 10.1039/c0an00550a] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA aptamers for specific recognition of L-tryptophan have been evolved by a SELEX (systematic evolution of ligands by exponential enrichment) technique. Truncation-mutation experiments suggest that a 34-mer sequence, Trp3a-1, possesses the strongest binding ability to L-tryptophan. Trp3a-1 is predicted to adopt a loop-stem secondary structure, in which the loop may further fold into a binding pocket for L-tryptophan with the help of the stem. The specificity investigation shows that Trp3a-1 strongly binds to L-tryptophan, has almost no binding to other amino acids, and weakly binds to some tryptophan analogs and peptides containing the L-tryptophan residue. The binding of Trp3a-1 to L-tryptophan is mainly contributed to by hydrogen bonds and precise stacking formed between the binding pocket of Trp3a-1 and all groups on L-tryptophan. This aptamer has also been proved to be an effective ligand for the chiral separation of D/L-tryptophan. L-tryptophan and its derivatives are known to play important biological roles; this aptamer ligand could be used as a tool for the analysis of tryptophan and other related studies.
Collapse
Affiliation(s)
- Xiaojuan Yang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | | | | | | | | | | |
Collapse
|
14
|
Rowe W, Platt M, Wedge DC, Day PJR, Kell DB, Knowles JD. Convergent evolution to an aptamer observed in small populations on DNA microarrays. Phys Biol 2010; 7:036007. [PMID: 20811084 DOI: 10.1088/1478-3975/7/3/036007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The development of aptamers on custom synthesized DNA microarrays, which has been demonstrated in recent publications, can facilitate detailed analyses of sequence and fitness relationships. Here we use the technique to observe the paths taken through sequence-fitness space by three different evolutionary regimes: asexual reproduction, recombination and model-based evolution. The different evolutionary runs are made on the same array chip in triplicate, each one starting from a small population initialized independently at random. When evolving to a common target protein, glucose-6-phosphate dehydrogenase (G6PD), these nine distinct evolutionary runs are observed to develop aptamers with high affinity and to converge on the same motif not present in any of the starting populations. Regime specific differences in the evolutions, such as speed of convergence, could also be observed.
Collapse
Affiliation(s)
- W Rowe
- Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK.
| | | | | | | | | | | |
Collapse
|
15
|
Fabris L, Schierhorn M, Moskovits M, Bazan GC. Aptatag-based multiplexed assay for protein detection by surface-enhanced Raman spectroscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:1550-1557. [PMID: 20623739 DOI: 10.1002/smll.201000262] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Silver-nanoparticle dimers held together by a Raman reporter, capped with DNA aptamers and stabilized by polyethylene glycol chains, can be used to develop a multiplexed heterogeneous bioassay for protein detection with high sensitivity and selectivity.
Collapse
Affiliation(s)
- Laura Fabris
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA.
| | | | | | | |
Collapse
|
16
|
|