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Sánchez Martín D, Oropesa-Nuñez R, Zardán Gómez de la Torre T. Formation of Visible Aggregates between Rolling Circle Amplification Products and Magnetic Nanoparticles as a Strategy for Point-of-Care Diagnostics. ACS Omega 2021; 6:32970-32976. [PMID: 34901648 PMCID: PMC8655940 DOI: 10.1021/acsomega.1c05047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
Visual detection of rolling circle amplification products (RCPs) has been achieved by specific aggregation with magnetic nanoparticles. The method presented here reliably generates aggregates in 1.5 h; these are visible to the naked eye in samples containing at least 0.4 fmol of RCPs. In addition, alternate current susceptometry and absorbance spectroscopy have also been used to quantify the amplified products. The specificity of the detection method was tested, and no non-specific aggregation was detected in samples containing up to 20 fmol of non-complementary amplified DNA. This method is a versatile tool for detecting pathogenic DNA in point-of-care diagnostics, with no readout equipment required. However, chips and automated assays can be used in conjugation with the developed method since detection and quantification can be achieved by commercially available readout instruments.
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Affiliation(s)
- Darío Sánchez Martín
- Department
of Material Sciences and Engineering, Division of Nanotechnology and
Functional Materials, Ångström Laboratory, Uppsala University, 751 21 Uppsala, Sweden
| | - Reinier Oropesa-Nuñez
- Department
of Material Sciences and Engineering, Division of Solid-State Physics,
Ångström Laboratory, Uppsala
University, 751 21 Uppsala, Sweden
| | - Teresa Zardán Gómez de la Torre
- Department
of Material Sciences and Engineering, Division of Nanotechnology and
Functional Materials, Ångström Laboratory, Uppsala University, 751 21 Uppsala, Sweden
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2
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Sánchez Martín D, Oropesa-Nuñez R, Zardán Gómez de la Torre T. Evaluating the Performance of a Magnetic Nanoparticle-Based Detection Method Using Circle-to-Circle Amplification. Biosensors 2021; 11:bios11060173. [PMID: 34071179 PMCID: PMC8226732 DOI: 10.3390/bios11060173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 01/22/2023]
Abstract
This work explores several issues of importance for the development of a diagnostic method based on circle-to-circle amplification (C2CA) and oligonucleotide-functionalized magnetic nanoparticles. Firstly, the performance of the detection method was evaluated in terms of sensitivity and speed. Synthetic target sequences for Newcastle disease virus and Salmonella were used as model sequences. The sensitivity of the C2CA assay resulted in detection of 1 amol of starting DNA target with a total amplification time of 40 min for both target sequences. Secondly, the functionalization of the nanoparticles was evaluated in terms of robustness and stability. The functionalization was shown to be very robust, and the stability test showed that 92% of the oligos were still attached on the particle surface after three months of storage at 4 °C. Altogether, the results obtained in this study provide a strong foundation for the development of a quick and sensitive diagnostic assay.
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Affiliation(s)
- Darío Sánchez Martín
- Division of Nanotechnology and Functional Materials, Department of Material Sciences and Engineering, Ångström Laboratory, Uppsala University, 751 03 Uppsala, Sweden;
| | - Reinier Oropesa-Nuñez
- Division of Solid-State Physics, Department of Material Sciences and Engineering, Ångström Laboratory, Uppsala University, 751 03 Uppsala, Sweden;
| | - Teresa Zardán Gómez de la Torre
- Division of Nanotechnology and Functional Materials, Department of Material Sciences and Engineering, Ångström Laboratory, Uppsala University, 751 03 Uppsala, Sweden;
- Correspondence: ; Tel.: +46-18-471-0000
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3
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Oropesa-Nuñez R, Zardán Gómez de la Torre T, Stopfel H, Svedlindh P, Strömberg M, Gunnarsson K. Insights into the Formation of DNA-Magnetic Nanoparticle Hybrid Structures: Correlations between Morphological Characterization and Output from Magnetic Biosensor Measurements. ACS Sens 2020; 5:3510-3519. [PMID: 33141554 PMCID: PMC7706118 DOI: 10.1021/acssensors.0c01623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Understanding
the binding mechanism between probe-functionalized
magnetic nanoparticles (MNPs) and DNA targets or amplification products
thereof is essential in the optimization of magnetic biosensors for
the detection of DNA. Herein, the molecular interaction forming hybrid
structures upon hybridization between DNA-functionalized magnetic
nanoparticles, exhibiting Brownian relaxation, and rolling circle
amplification products (DNA-coils) is investigated by the use of atomic
force microscopy in a liquid environment and magnetic biosensors measuring
the frequency-dependent magnetic response and the frequency-dependent
modulation of light transmission. This approach reveals the qualitative
and quantitative correlations between the morphological features of
the hybrid structures with their magnetic response. The suppression
of the high-frequency peak in the magnetic response and the appearance
of a new peak at lower frequencies match the formation of larger sized
assemblies upon increasing the concentration of DNA-coils. Furthermore,
an increase of the DNA-coil concentration induces an increase in the
number of MNPs per hybrid structure. This study provides new insights
into the DNA–MNP binding mechanism, and its versatility is
of considerable importance for the mechanistic characterization of
other DNA-nanoparticle biosensor systems.
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Affiliation(s)
- Reinier Oropesa-Nuñez
- Department of Materials Science and Engineering, Uppsala University, Ångströmlaboratoriet, Box 35, SE-751 03 Uppsala, Sweden
| | - Teresa Zardán Gómez de la Torre
- Department of Materials Science and Engineering, Uppsala University, Ångströmlaboratoriet, Box 35, SE-751 03 Uppsala, Sweden
| | - Henry Stopfel
- Department of Materials Science and Engineering, Uppsala University, Ångströmlaboratoriet, Box 35, SE-751 03 Uppsala, Sweden
| | - Peter Svedlindh
- Department of Materials Science and Engineering, Uppsala University, Ångströmlaboratoriet, Box 35, SE-751 03 Uppsala, Sweden
| | - Mattias Strömberg
- Department of Materials Science and Engineering, Uppsala University, Ångströmlaboratoriet, Box 35, SE-751 03 Uppsala, Sweden
| | - Klas Gunnarsson
- Department of Materials Science and Engineering, Uppsala University, Ångströmlaboratoriet, Box 35, SE-751 03 Uppsala, Sweden
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Minero GAS, Cangiano V, Fock J, Garbarino F, Hansen MF. Optomagnetic Detection of Rolling Circle Amplification Products. Methods Mol Biol 2020; 2063:3-15. [PMID: 31667758 DOI: 10.1007/978-1-0716-0138-9_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Rolling circle amplification (RCA) of a synthetic nucleic acid target is detected using magnetic nanoparticles (MNPs) combined with an optomagnetic (OM) readout. Two RCA assays are developed with on-chip detection of rolling circle products (RCPs) either at end-point where MNPs are mixed with the sample after completion of RCA or in real time where MNPs are mixed with the sample during RCA. The plastic chip acts as a cuvette, which is positioned in a setup integrated with temperature control and simultaneous detection of four parallel DNA hybridization reactions between functionalized MNPs and products of DNA amplification. The OM technique probes the small-angle rotation of MNPs bearing oligonucleotide probes complementary to the repeated nucleotide sequence of the RCPs. This rotation is restricted when MNPs bind to RCPs, which can be observed as a turn-off of the signal from MNPs that are free to rotate. The amount of MNPs bound to RCPs is found to increase in response to the amplification time as well as in response to the synthetic DNA target concentration (2-40 pM dynamic range). We report OM real-time results obtained with MNPs present during RCA and compare to relevant end-point OM results for RCPs generated for different RCA times. The real-time approach avoids opening of tubes post-RCA and thus reduces risk of lab contamination with amplification products without compromising the sensitivity and dynamic range of the assay.
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Sepehri S, Agnarsson B, Torre TZG, Schneiderman JF, Blomgren J, Jesorka A, Johansson C, Nilsson M, Albert J, Strømme M, Winkler D, Kalaboukhov A. Characterization of Binding of Magnetic Nanoparticles to Rolling Circle Amplification Products by Turn-On Magnetic Assay. Biosensors (Basel) 2019; 9:E109. [PMID: 31533330 DOI: 10.3390/bios9030109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/30/2019] [Accepted: 09/04/2019] [Indexed: 01/23/2023]
Abstract
The specific binding of oligonucleotide-tagged 100 nm magnetic nanoparticles (MNPs) to rolling circle products (RCPs) is investigated using our newly developed differential homogenous magnetic assay (DHMA). The DHMA measures ac magnetic susceptibility from a test and a control samples simultaneously and eliminates magnetic background signal. Therefore, the DHMA can reveal details of binding kinetics of magnetic nanoparticles at very low concentrations of RCPs. From the analysis of the imaginary part of the DHMA signal, we find that smaller MNPs in the particle ensemble bind first to the RCPs. When the RCP concentration increases, we observe the formation of agglomerates, which leads to lower number of MNPs per RCP at higher concentrations of RCPs. The results thus indicate that a full frequency range of ac susceptibility observation is necessary to detect low concentrations of target RCPs and a long amplification time is not required as it does not significantly increase the number of MNPs per RCP. The findings are critical for understanding the underlying microscopic binding process for improving the assay performance. They furthermore suggest DHMA is a powerful technique for dynamically characterizing the binding interactions between MNPs and biomolecules in fluid volumes.
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Minero GAS, Cangiano V, Garbarino F, Fock J, Hansen MF. Integration of microbead DNA handling with optomagnetic detection in rolling circle amplification assays. Mikrochim Acta 2019; 186:528. [DOI: 10.1007/s00604-019-3636-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/25/2019] [Indexed: 01/14/2023]
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Yu H, Xu X, Liang P, Loh KY, Guntupalli B, Roncancio D, Xiao Y. A Broadly Applicable Assay for Rapidly and Accurately Quantifying DNA Surface Coverage on Diverse Particles. Bioconjug Chem 2017; 28:933-943. [PMID: 28156100 DOI: 10.1021/acs.bioconjchem.6b00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA-modified particles are used extensively for applications in sensing, material science, and molecular biology. The performance of such DNA-modified particles is greatly dependent on the degree of surface coverage, but existing methods for quantitation can only be employed for certain particle compositions and/or conjugation chemistries. We have developed a simple and broadly applicable exonuclease III (Exo III) digestion assay based on the cleavage of phosphodiester bonds-a universal feature of DNA-modified particles-to accurately quantify DNA probe surface coverage on diverse, commonly used particles of different compositions, conjugation chemistries, and sizes. Our assay utilizes particle-conjugated, fluorophore-labeled probes that incorporate two abasic sites; these probes are hybridized to a complementary DNA (cDNA) strand, and quantitation is achieved via cleavage and digestion of surface-bound probe DNA via Exo III's apurinic endonucleolytic and exonucleolytic activities. The presence of the two abasic sites in the probe greatly speeds up the enzymatic reaction without altering the packing density of the probes on the particles. Probe digestion releases a signal-generating fluorophore and liberates the intact cDNA strand to start a new cycle of hybridization and digestion, until all fluorophore tags have been released. Since the molar ratio of fluorophore to immobilized DNA is 1:1, DNA surface coverage can be determined accurately based on the complete release of fluorophores. Our method delivers accurate, rapid, and reproducible quantitation of thiolated DNA on the surface of gold nanoparticles, and also performs equally well with other conjugation chemistries, substrates, and particle sizes, and thus offers a broadly useful assay for quantitation of DNA surface coverage.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Xiaowen Xu
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Pingping Liang
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Kang Yong Loh
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Bhargav Guntupalli
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Daniel Roncancio
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
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8
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Donolato M, Antunes P, de la Torre TZG, Hwu E, Chen C, Burger R, Rizzi G, Bosco FG, Strømme M, Boisen A, Hansen MF. Quantification of rolling circle amplified DNA using magnetic nanobeads and a Blu-ray optical pick-up unit. Biosens Bioelectron 2015; 67:649-55. [DOI: 10.1016/j.bios.2014.09.097] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/10/2014] [Accepted: 09/29/2014] [Indexed: 11/20/2022]
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Donolato M, Antunes P, Bejhed RS, Zardán Gómez de la Torre T, Østerberg FW, Strömberg M, Nilsson M, Strømme M, Svedlindh P, Hansen MF, Vavassori P. Novel Readout Method for Molecular Diagnostic Assays Based on Optical Measurements of Magnetic Nanobead Dynamics. Anal Chem 2015; 87:1622-9. [DOI: 10.1021/ac503191v] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marco Donolato
- CIC nanoGUNE Consolider, Tolosa Hiribidea 76, 20018 San Sebastian, Spain
- Department
of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
| | - Paula Antunes
- Department
of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
| | - Rebecca S. Bejhed
- The
Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box
534, SE-751 21 Uppsala, Sweden
| | | | - Frederik W. Østerberg
- Department
of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
| | - Mattias Strömberg
- The
Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box
534, SE-751 21 Uppsala, Sweden
| | - Mats Nilsson
- Science
for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University,
Box 1031, 17121 Solna, Sweden
| | - Maria Strømme
- The
Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box
534, SE-751 21 Uppsala, Sweden
| | - Peter Svedlindh
- The
Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box
534, SE-751 21 Uppsala, Sweden
| | - Mikkel F. Hansen
- Department
of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800 Kongens Lyngby, Denmark
| | - Paolo Vavassori
- CIC nanoGUNE Consolider, Tolosa Hiribidea 76, 20018 San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
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10
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Østerberg FW, Rizzi G, Donolato M, Bejhed RS, Mezger A, Strömberg M, Nilsson M, Strømme M, Svedlindh P, Hansen MF. On-chip detection of rolling circle amplified DNA molecules from Bacillus globigii spores and Vibrio cholerae. Small 2014; 10:2877-2882. [PMID: 24616417 DOI: 10.1002/smll.201303325] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 01/10/2014] [Indexed: 06/03/2023]
Abstract
For the first time DNA coils formed by rolling circle amplification are quantified on-chip by Brownian relaxation measurements on magnetic nanobeads using a magnetoresistive sensor. No external magnetic fields are required besides the magnetic field arising from the current through the sensor, which makes the setup very compact. Limits of detection down to 500 Bacillus globigii spores and 2 pM of Vibrio cholerae are demonstrated, which are on the same order of magnitude or lower than those achieved previously using a commercial macro-scale AC susceptometer. The chip-based readout is an important step towards the realization of field tests based on rolling circle amplification molecular analyses.
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Affiliation(s)
- Frederik W Østerberg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Building 345 East, DK-2800, Kongens Lyngby, Denmark
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Strömberg M, Zardán Gómez de la Torre T, Nilsson M, Svedlindh P, Strømme M. A magnetic nanobead-based bioassay provides sensitive detection of single- and biplex bacterial DNA using a portable AC susceptometer. Biotechnol J 2013; 9:137-45. [PMID: 24174315 PMCID: PMC3910167 DOI: 10.1002/biot.201300348] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/27/2013] [Accepted: 10/29/2013] [Indexed: 11/06/2022]
Abstract
Bioassays relying on magnetic read-out using probe-tagged magnetic nanobeads are potential platforms for low-cost biodiagnostic devices for pathogen detection. For optimal assay performance it is crucial to apply an easy, efficient and robust bead-probe conjugation protocol. In this paper, sensitive (1.5 pM) singleplex detection of bacterial DNA sequences is demonstrated in a portable AC susceptometer by a magnetic nanobead-based bioassay principle; the volume-amplified magnetic nanobead detection assay (VAM-NDA). Two bead sizes, 100 and 250 nm, are investigated along with a highly efficient, rapid, robust, and stable conjugation chemistry relying on the avidin–biotin interaction for bead-probe attachment. Avidin-biotin conjugation gives easy control of the number of detection probes per bead; thus allowing for systematic investigation of the impact of varying the detection probe surface coverage upon bead immobilization in rolling circle amplified DNA-coils. The existence of an optimal surface coverage is discussed. Biplex VAM-NDA detection is for the first time demonstrated in the susceptometer: Semi-quantitative results are obtained and it is concluded that the concentration of DNA-coils in the incubation volume is of crucial importance for target quantification. The present findings bring the development of commercial biodiagnostic devices relying on the VAM–NDA further towards implementation in point-of-care and outpatient settings.
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Affiliation(s)
- Mattias Strömberg
- Department of Engineering Sciences, Division of Solid State Physics, Uppsala University, Uppsala, Sweden.
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Engström A, Zardán Gómez de la Torre T, Strømme M, Nilsson M, Herthnek D. Detection of rifampicin resistance in Mycobacterium tuberculosis by padlock probes and magnetic nanobead-based readout. PLoS One 2013; 8:e62015. [PMID: 23630621 PMCID: PMC3632517 DOI: 10.1371/journal.pone.0062015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/17/2013] [Indexed: 01/29/2023] Open
Abstract
Control of the global epidemic tuberculosis is severely hampered by the emergence of drug-resistant Mycobacterium tuberculosis strains. Molecular methods offer a more rapid means of characterizing resistant strains than phenotypic drug susceptibility testing. We have developed a molecular method for detection of rifampicin-resistant M. tuberculosis based on padlock probes and magnetic nanobeads. Padlock probes were designed to target the most common mutations associated with rifampicin resistance in M. tuberculosis, i.e. at codons 516, 526 and 531 in the gene rpoB. For detection of the wild type sequence at all three codons simultaneously, a padlock probe and two gap-fill oligonucleotides were used in a novel assay configuration, requiring three ligation events for circularization. The assay also includes a probe for identification of the M. tuberculosis complex. Circularized probes were amplified by rolling circle amplification. Amplification products were coupled to oligonucleotide-conjugated magnetic nanobeads and detected by measuring the frequency-dependent magnetic response of the beads using a portable AC susceptometer.
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Affiliation(s)
- Anna Engström
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Preparedness, Swedish Institute for Communicable Disease Control, Solna, Sweden
| | - Teresa Zardán Gómez de la Torre
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Uppsala, Sweden
| | - Maria Strømme
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Uppsala, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - David Herthnek
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Rudbeck Laboratory, Uppsala, Sweden
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Abstract
As food safety management further develops, microbiological testing will continue to play an important role in assessing whether Food Safety Objectives are achieved. However, traditional microbiological culture-based methods are limited, particularly in their ability to provide timely data. The present review discusses the reasons for the increasing interest in rapid methods, current developments in the field, the research needs, and the future trends. The advent of biotechnology has introduced new technologies that led to the emergence of rapid diagnostic methods and altered food testing practices. Rapid methods are comprised of many different detection technologies, including specialized enzyme substrates, antibodies and DNA, ranging from simple differential plating media to the use of sophisticated instruments. The use of non-invasive sampling techniques for live animals especially came into focus with the 1990s outbreak of bovine spongiform encephalopathy that was linked to the human outbreak of Creutzfeldt Jakob's Disease. Serology is still an important tool in preventing foodborne pathogens to enter the human food supply through meat and milk from animals. One of the primary uses of rapid methods is for fast screening of large number of samples, where most of them are expected to be test-negative, leading to faster product release for sale. This has been the main strength of rapid methods such as real-time Polymerase Chain Reaction (PCR). Enrichment PCR, where a primary culture broth is tested in PCR, is the most common approach in rapid testing. Recent reports show that it is possible both to enrich a sample and enumerate by pathogen-specific real-time PCR, if the enrichment time is short. This can be especially useful in situations where food producers ask for the level of pathogen in a contaminated product. Another key issue is automation, where the key drivers are miniaturization and multiple testing, which mean that not only one instrument is flexible enough to test for many pathogens but also many pathogens can be detected with one test. The review is mainly based on the author's scientific work that has contributed with the following new developments to this field: (i) serologic tests for large-scale screening, surveillance, or eradication programs, (ii) same-day detection of Salmonella that otherwise was considered as difficult to achieve, (iii) pathogen enumeration following a short log-phase enrichment, (iv) detection of foodborne pathogens in air samples, and finally (v) biotracing of pathogens based on mathematical modeling, even in the absence of isolate. Rapid methods are discussed in a broad global health perspective, international food supply, and for improvement of quantitative microbial risk assessments. The need for quantitative sample preparation techniques, culture-independent, metagenomic-based detection, online monitoring, a global validation infrastructure has been emphasized. The cost and ease of use of rapid assays remain challenging obstacles to surmount.
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Affiliation(s)
- J Hoorfar
- National Food Institute, Technical University ofDenmark, Mørkhøj Bygade 19, Søborg, Denmark.
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14
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de la Torre TZG, Mezger A, Herthnek D, Johansson C, Svedlindh P, Nilsson M, Strømme M. Detection of rolling circle amplified DNA molecules using probe-tagged magnetic nanobeads in a portable AC susceptometer. Biosens Bioelectron 2011; 29:195-9. [PMID: 21907556 DOI: 10.1016/j.bios.2011.08.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/10/2011] [Accepted: 08/14/2011] [Indexed: 01/16/2023]
Abstract
Here, the volume-amplified magnetic nanobead detection assay (VAM-NDA) is for the first time applied for detection of rolling circle amplified (RCA) DNA molecules in a portable, commercial AC susceptometer that operates at ambient temperatures and with an analysis time of about 20 min. The performance of the assay is investigated using three different magnetic nanobead sizes: 50, 130 and 250nm. The performance of the assay using the AC susceptometer is compared to the performance achieved using a superconducting quantum interference device (SQUID). It is found that the performance of the assay is comparable in the two setups with a quantitative detection limit of ∼4pM for all bead sizes under study. The findings show that the VAM-NDA holds promise for future wide-spread implementation in commercial AC susceptometer setups thus opening up for the possibility to perform magnetic bead-based DNA detection in point-of-care and outpatient settings.
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Affiliation(s)
- Teresa Zardán Gómez de la Torre
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden
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15
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Stougaard M, Juul S, Andersen FF, Knudsen BR. Strategies for highly sensitive biomarker detection by Rolling Circle Amplification of signals from nucleic acid composed sensors. Integr Biol (Camb) 2011; 3:982-92. [DOI: 10.1039/c1ib00049g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Göransson J, Zardán Gómez De La Torre T, Strömberg M, Russell C, Svedlindh P, Strømme M, Nilsson M. Sensitive Detection of Bacterial DNA by Magnetic Nanoparticles. Anal Chem 2010; 82:9138-40. [DOI: 10.1021/ac102133e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jenny Göransson
- Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Teresa Zardán Gómez De La Torre
- Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Mattias Strömberg
- Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Camilla Russell
- Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Peter Svedlindh
- Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Maria Strømme
- Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Mats Nilsson
- Ångström Laboratory, Department of Engineering Sciences, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
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17
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Hu J, Zhang CY. Sensitive Detection of Nucleic Acids with Rolling Circle Amplification and Surface-Enhanced Raman Scattering Spectroscopy. Anal Chem 2010; 82:8991-7. [DOI: 10.1021/ac1019599] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Juan Hu
- Institute of Biomedical Engineering and Health Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Chun-yang Zhang
- Institute of Biomedical Engineering and Health Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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18
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Akhtar S, Strömberg M, Zardán Gómez de la Torre T, Russell C, Gunnarsson K, Nilsson M, Svedlindh P, Strømme M, Leifer K. Real-Space Transmission Electron Microscopy Investigations of Attachment of Functionalized Magnetic Nanoparticles to DNA-Coils Acting as a Biosensor. J Phys Chem B 2010; 114:13255-62. [DOI: 10.1021/jp105756b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sultan Akhtar
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Mattias Strömberg
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Teresa Zardán Gómez de la Torre
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Camilla Russell
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Klas Gunnarsson
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Mats Nilsson
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Peter Svedlindh
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Maria Strømme
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Klaus Leifer
- Department of Engineering Sciences, Division of Electron Microscopy and Nanoengineering, Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, and Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
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19
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Ohrmalm C, Jobs M, Eriksson R, Golbob S, Elfaitouri A, Benachenhou F, Strømme M, Blomberg J. Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm. Nucleic Acids Res 2010; 38:e195. [PMID: 20864443 PMCID: PMC2995084 DOI: 10.1093/nar/gkq777] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes.
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Affiliation(s)
- Christina Ohrmalm
- Clinical Virology, Department of Medical Sciences, Uppsala University and Academic Hospital, 751 85 Uppsala, Sweden
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20
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Zardán Gómez de la Torre T, Strömberg M, Russell C, Göransson J, Nilsson M, Svedlindh P, Strømme M. Investigation of immobilization of functionalized magnetic nanobeads in rolling circle amplified DNA coils. J Phys Chem B 2010; 114:3707-13. [PMID: 20175549 DOI: 10.1021/jp911251k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Immobilization characteristics for single-stranded oligonucleotide-functionalized magnetic beads with nominal sizes of 40, 80, 130, and 250 nm in rolling circle amplified (RCA) DNA coils is investigated by employing complex magnetization measurements, dynamic light scattering and fluorescence microscopy. It was found that larger beads in a polydisperse bead size distribution more easily immobilize in the RCA DNA coils than do smaller beads. This may be related to a higher oligonucleotide surface coverage for the larger beads. Furthermore, it was concluded that both bead size and oligonucleotide surface coverage determine whether beads immobilize to give isolated coils with beads or larger clusters of beads and coils. A small bead size and a low oligonucleotide surface coverage favor the first kind of immobilization behavior, whereas a large bead size and a high oligonucleotide surface coverage favor the other. The present findings could be used to optimize both size and surface functionalization of beads employed in substrate-free magnetic biosensors.
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Affiliation(s)
- Teresa Zardán Gómez de la Torre
- Division of Nanotechnology and Functional Materials, Department of Engineering Sciences, Uppsala University, The Angstrom Laboratory, Box 534, SE-751 21 Uppsala, Sweden
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21
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Strömberg M, Zardán Gómez de la Torre T, Göransson J, Gunnarsson K, Nilsson M, Svedlindh P, Strømme M. Multiplex Detection of DNA Sequences Using the Volume-Amplified Magnetic Nanobead Detection Assay. Anal Chem 2009; 81:3398-406. [DOI: 10.1021/ac900561r] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mattias Strömberg
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, Department of Engineering Sciences, Division of Solid State Physics, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden
| | - Teresa Zardán Gómez de la Torre
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, Department of Engineering Sciences, Division of Solid State Physics, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden
| | - Jenny Göransson
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, Department of Engineering Sciences, Division of Solid State Physics, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden
| | - Klas Gunnarsson
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, Department of Engineering Sciences, Division of Solid State Physics, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden
| | - Mats Nilsson
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, Department of Engineering Sciences, Division of Solid State Physics, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden
| | - Peter Svedlindh
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, Department of Engineering Sciences, Division of Solid State Physics, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden
| | - Maria Strømme
- Department of Engineering Sciences, Division of Nanotechnology and Functional Materials, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, Department of Engineering Sciences, Division of Solid State Physics, Uppsala University, The Ångström Laboratory, Box 534, SE-751 21 Uppsala, Sweden, and Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden
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22
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Conze T, Shetye A, Tanaka Y, Gu J, Larsson C, Göransson J, Tavoosidana G, Söderberg O, Nilsson M, Landegren U. Analysis of genes, transcripts, and proteins via DNA ligation. Annu Rev Anal Chem (Palo Alto Calif) 2009; 2:215-239. [PMID: 20636060 DOI: 10.1146/annurev-anchem-060908-155239] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Analytical reactions in which short DNA strands are used in combination with DNA ligases have proven useful for measuring, decoding, and locating most classes of macromolecules. Given the need to accumulate large amounts of precise molecular information from biological systems in research and in diagnostics, ligation reactions will continue to offer valuable strategies for advanced analytical reactions. Here, we provide a basis for further development of methods by reviewing the history of analytical ligation reactions, discussing the properties of ligation reactions that render them suitable for engineering novel assays, describing a wide range of successful ligase-based assays, and briefly considering future directions.
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Affiliation(s)
- Tim Conze
- Department of Genetics and Pathology, The Rudbeck Lab, Uppsala University, Uppsala, Sweden
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