1
|
Naoumi N, Araya-Farias M, Megariti M, Alexandre L, Papadakis G, Descroix S, Gizeli E. Acoustic detection of a mutation-specific Ligase Chain Reaction based on liposome amplification. Analyst 2024; 149:3537-3546. [PMID: 38758167 DOI: 10.1039/d3an02142d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Single nucleotide variants (SNVs) play a crucial role in understanding genetic diseases, cancer development, and personalized medicine. However, existing ligase-based amplification and detection techniques, such as Rolling Circle Amplification and Ligase Detection Reaction, suffer from low efficiency and difficulties in product detection. To address these limitations, we propose a novel approach that combines Ligase Chain Reaction (LCR) with acoustic detection using highly dissipative liposomes. In our study, we are using LCR combined with biotin- and cholesterol-tagged primers to produce amplicons also modified at each end with a biotin and cholesterol molecule. We then apply the LCR mix without any purification directly on a neutravidin modified QCM device Au-surface, where the produced amplicons can bind specifically through the biotin end. To improve sensitivity, we finally introduce liposomes as signal enhancers. For demonstration, we used the detection of the BRAF V600E point mutation versus the wild-type allele, achieving an impressive detection limit of 220 aM of the mutant target in the presence of the same amount of the wild type. Finally, we combined the assay with a microfluidic fluidized bed DNA extraction technology, offering the potential for semi-automated detection of SNVs in patients' crude samples. Overall, our LCR/acoustic method outperforms other LCR-based approaches and surface ligation biosensing techniques in terms of detection efficiency and time. It effectively overcomes challenges related to DNA detection, making it applicable in diverse fields, including genetic disease and pathogen detection.
Collapse
Affiliation(s)
- Nikoletta Naoumi
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion, 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Monica Araya-Farias
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - Maria Megariti
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Lucile Alexandre
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Stephanie Descroix
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - Electra Gizeli
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion, 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| |
Collapse
|
2
|
Wang W, Gao Y, Wang W, Zhang J, Li Q, Wu ZS. Ultrasensitive Electrochemical Detection of cancer-Related Point Mutations Based on Surface-Initiated Three-Dimensionally Self-Assembled DNA Nanostructures from Only Two Palindromic Probes. Anal Chem 2021; 94:1029-1036. [PMID: 34932325 DOI: 10.1021/acs.analchem.1c03991] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sensitive and selective detection of proto-oncogenes, especially recognition of point mutation, is of great importance in cancer diagnosis. Here, a ligation-mediated technique is demonstrated for the construction of an intertwined three-dimensional DNA nanosheet (3D SDN) on an electrode surface from only two palindromic hairpin probes (HP1 and HP2), creating a powerful electrochemical biosensor (E-biosensor) for the detection of the p53 gene. First, a capturing probe (CP) is immobilized on an electrode surface via Au-S chemistry, forming an electrochemical sensing interface. In the presence of the target p53 (T), the triggering probe is covalently linked to CP by a ligase. Moreover, target hybridization/ligation/dehybridization process is repeated, amplifying the target hybridization event and increasing the content of surface-confined triggering fragments. As a result, HP1 is opened and in turn interacts with HP2, forming intertwined 3D SDN where HP1 and HP2 are alternately arranged in parallel. Common hybridization and interaction between palindromic fragments are responsible for the assembly in the horizontal and vertical directions, respectively. An electrochemical indicator, methylene blue (MB), can be inserted into 3D SDN, generating a strong electrochemical signal. Utilizing the 3D SDN-based E-biosensor, the target DNA is detected down to 3 fM with a linear response range from 10 fM to 10 nM. Single point mutations are reliably identified even in fetal bovine serum and cellular homogenate. Because of the several advantages of simple design, good universality, inexpensive instrumentation, high assay specificity, and sensitivity, the 3D SDN-based E-biosensor is expected to provide a potential platform for screening point mutation required by early clinical diagnostics and medical research.
Collapse
Affiliation(s)
- Weijun Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Yansha Gao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Wenqing Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Jingjing Zhang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Qian Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| |
Collapse
|
3
|
Nicking-enhanced rolling circle amplification for sensitive fluorescent detection of cancer-related microRNAs. Anal Bioanal Chem 2018; 410:6819-6826. [PMID: 30066196 DOI: 10.1007/s00216-018-1277-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/02/2018] [Accepted: 07/16/2018] [Indexed: 01/23/2023]
Abstract
In this study, a biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) was proposed for the highly sensitive detection of cancer-related let-7a microRNA (miRNA). The sensing system consists of a padlock probe (PP), which contains a target recognition sequence and two binding sites for nicking endonuclease (NEase), and molecular beacon (MB) as reporting molecule. Upon hybridization with let-7a, the PP can be circularized by ligase. Then, the miRNA acted as polymerization primer to initiate rolling circle amplification (RCA). With the assistance of NEase, RCA products can be nicked on the cyclized PP and are displaced during the subsequent duplication process, generating numerous nicked fragments (NFs). These NFs not only induce another RCA reaction but also open the molecular beacons (MBs) via hybridization, leading to significantly amplified fluorescence signal. Under the optimized conditions, this method exhibits high sensitivity toward target miRNA let-7a with a detection limit of as low as 10 pM, a dynamic range of three orders of magnitude is achieved, and its family member is easily distinguished even with only one mismatched base. Meanwhile, it displays good recovery and satisfactory reproducibility in fetal bovine serum (FBS). Therefore, these merits endow the newly proposed N-RCA strategy with powerful implications for miRNA detection. Graphical abstract A biosensing system based on nicking-enhanced rolling circle amplification (N-RCA) for the highly sensitive detection of cancer-related let-7a microRNA.
Collapse
|
4
|
Computational Biosensors: Molecules, Algorithms, and Detection Platforms. MODELING, METHODOLOGIES AND TOOLS FOR MOLECULAR AND NANO-SCALE COMMUNICATIONS 2017. [PMCID: PMC7123247 DOI: 10.1007/978-3-319-50688-3_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Advanced nucleic acid-based sensor-applications require computationally intelligent biosensors that are able to concurrently perform complex detection and classification of samples within an in vitro platform. Realization of these cutting-edge computational biosensor systems necessitates innovation and integration of three key technologies: molecular probes with computational capabilities, algorithmic methods to enable in vitro computational post processing and classification, and immobilization and detection approaches that enable the realization of deployable computational biosensor platforms. We provide an overview of current technologies, including our contributions towards the development of computational biosensor systems.
Collapse
|
5
|
Pergolizzi G, Wagner GK, Bowater RP. Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea. Biosci Rep 2016; 36:00391. [PMID: 27582505 PMCID: PMC5052709 DOI: 10.1042/bsr20160003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 12/13/2022] Open
Abstract
DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterisation. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5'-phosphate of the DNA end that will ultimately be joined to the 3'-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use nicotinamide adenine dinucleotide ( β -NAD+) as their co-factor whereas those that are essential in other cells use adenosine-5'-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted by novel antibiotics and the complex molecular structure of β -NAD+ affords multiple opportunities for chemical modification. Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. Here, we review the recent advances that herald new opportunities to alter the biochemical activities of these important enzymes. The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes.
Collapse
Affiliation(s)
- Giulia Pergolizzi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, N/A, United Kingdom
| | - Gerd K Wagner
- Department of Chemistry, King's College London, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London, N/A, United Kingdom
| | - Richard Peter Bowater
- School of Biological Sciences, University of East Anglia, Norwich, N/A, NR4 7TJ, United Kingdom
| |
Collapse
|
6
|
Kong LX, Perebikovsky A, Moebius J, Kulinsky L, Madou M. Lab-on-a-CD. ACTA ACUST UNITED AC 2016; 21:323-55. [DOI: 10.1177/2211068215588456] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Indexed: 12/14/2022]
|
7
|
Smith S, Mager D, Perebikovsky A, Shamloo E, Kinahan D, Mishra R, Torres Delgado SM, Kido H, Saha S, Ducrée J, Madou M, Land K, Korvink JG. CD-Based Microfluidics for Primary Care in Extreme Point-of-Care Settings. MICROMACHINES 2016; 7:mi7020022. [PMID: 30407395 PMCID: PMC6190444 DOI: 10.3390/mi7020022] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/08/2016] [Accepted: 01/19/2016] [Indexed: 02/02/2023]
Abstract
We review the utility of centrifugal microfluidic technologies applied to point-of-care diagnosis in extremely under-resourced environments. The various challenges faced in these settings are showcased, using areas in India and Africa as examples. Measures for the ability of integrated devices to effectively address point-of-care challenges are highlighted, and centrifugal, often termed CD-based microfluidic technologies, technologies are presented as a promising platform to address these challenges. We describe the advantages of centrifugal liquid handling, as well as the ability of a standard CD player to perform a number of common laboratory tests, fulfilling the role of an integrated lab-on-a-CD. Innovative centrifugal approaches for point-of-care in extremely resource-poor settings are highlighted, including sensing and detection strategies, smart power sources and biomimetic inspiration for environmental control. The evolution of centrifugal microfluidics, along with examples of commercial and advanced prototype centrifugal microfluidic systems, is presented, illustrating the success of deployment at the point-of-care. A close fit of emerging centrifugal systems to address a critical panel of tests for under-resourced clinic settings, formulated by medical experts, is demonstrated. This emphasizes the potential of centrifugal microfluidic technologies to be applied effectively to extremely challenging point-of-care scenarios and in playing a role in improving primary care in resource-limited settings across the developing world.
Collapse
Affiliation(s)
- Suzanne Smith
- Council for Scientific and Industrial Research, Meiring Naude Road, Brummeria, Pretoria 0001, South Africa.
| | - Dario Mager
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany.
| | - Alexandra Perebikovsky
- School of Engineering and School of Physical Sciences, University of California, Irvine, 4200 Engineering Gateway, Irvine, CA 92697-3975, USA.
| | - Ehsan Shamloo
- School of Engineering and School of Physical Sciences, University of California, Irvine, 4200 Engineering Gateway, Irvine, CA 92697-3975, USA.
| | - David Kinahan
- School of Physical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Rohit Mishra
- School of Physical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Saraí M Torres Delgado
- Simulation Laboratory, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg im Breisgau 79085, Germany.
| | - Horacio Kido
- School of Engineering and School of Physical Sciences, University of California, Irvine, 4200 Engineering Gateway, Irvine, CA 92697-3975, USA.
| | - Satadal Saha
- Foundation for Innovations in Health and JSV Innovations Private Limited, 44A S P Mukherjee Road, Kolkata 700026, India.
| | - Jens Ducrée
- School of Physical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Marc Madou
- School of Engineering and School of Physical Sciences, University of California, Irvine, 4200 Engineering Gateway, Irvine, CA 92697-3975, USA.
| | - Kevin Land
- Council for Scientific and Industrial Research, Meiring Naude Road, Brummeria, Pretoria 0001, South Africa.
| | - Jan G Korvink
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany.
| |
Collapse
|
8
|
Bowater RP, Cobb AM, Pivonkova H, Havran L, Fojta M. Biophysical and electrochemical studies of protein–nucleic acid interactions. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-014-1405-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
9
|
Zhao B, Tong Z, Zhao G, Mu R, Shang H, Guan Y. Effects of 2'-O-methyl nucleotide on ligation capability of T4 DNA ligase. Acta Biochim Biophys Sin (Shanghai) 2014; 46:727-37. [PMID: 25022752 DOI: 10.1093/abbs/gmu058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To further understand the ligation mechanism, effects of 2'-O-methyl nucleotide (2'-OMeN) on the T4 DNA ligation efficiency were investigated. Fluorescence resonance energy transfer assay was used to monitor the nick-joining process by T4 DNA ligase. Results showed that substitutions at 5'- and 3'-ends of the nick decreased the ligation efficiency by 48.7% ± 6.7% and 70.6% ± 4.0%, respectively. Substitutions at both 5'- and 3'-ends decreased the ligation efficiency by 76.6% ± 1.3%. Corresponding kinetic parameters, Vmax, Km, and kcat, have been determined in each case by using the Michaelis-Menten equation. The kinetic data showed that the 2'-OMeN substitutions reduced the maximal initial velocity and increased the Michaelis constant of T4 DNA ligase. Mismatches at 5'- and 3'-ends of the nick have also shown different influences on the ligation. Results here showed that the sugar pucker conformation at 3'-end impairs the ligation efficiency more profoundly than that at 5'-end. Different concentrations of Mg(2+), Ca(2+), K(+), Na(+), and ATP were also demonstrated to affect the T4 DNA ligase activity. These results enriched our knowledge about the effects of 2'-OMeN substitutions on the T4 DNA ligase.
Collapse
Affiliation(s)
- Bin Zhao
- Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China Department of Human Movement Science, Shenyang Sport University, Shenyang 110102, China
| | - Zhaoxue Tong
- Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China
| | - Guojie Zhao
- Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China
| | - Runqing Mu
- Department of Clinical Diagnosis, First Hospital of China Medical University, Shenyang 110001, China
| | - Hong Shang
- Department of Clinical Diagnosis, First Hospital of China Medical University, Shenyang 110001, China
| | - Yifu Guan
- Key Laboratory of Medical Cell Biology, Ministry of Education, Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China
| |
Collapse
|
10
|
DNA fluorescence shift sensor: a rapid method for the detection of DNA hybridization using silver nanoclusters. J Colloid Interface Sci 2014; 433:183-188. [PMID: 25129336 DOI: 10.1016/j.jcis.2014.07.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/22/2014] [Accepted: 07/23/2014] [Indexed: 12/25/2022]
Abstract
DNA-templated silver nanoclusters (AgNC) are a class of subnanometer sized fluorophores with good photostability and brightness. It has been applied as a diagnostic tool mainly for deoxyribonucleic acid (DNA) detection. Integration of DNA oligomers to generate AgNCs is interesting as varying DNA sequences can result in different fluorescence spectra. This allows a simple fluorescence shifting effect to occur upon DNA hybridization with the hybridization efficiency being a pronominal factor for successful shifting. The ability to shift the fluorescence spectra as a result of hybridization overcomes the issue of background intensities in most fluorescent based assays. Here we describe an optimized method for the detection of single-stranded and double-stranded synthetic forkhead box P3 (FOXP3) target by hybridization with the DNA fluorescence shift sensor. The system forms a three-way junction by successful hybridization of AgNC, G-rich strand (G-rich) to the target DNA, which generated a shift in fluorescence spectra with a marked increase in fluorescence intensity. The DNA fluorescence shift sensor presents a rapid and specific alternative to conventional DNA detection.
Collapse
|
11
|
Qiu L, Qiu L, Zhou H, Wu Z, Shen G, Yu R. Sensitive and selective electrochemical DNA sensor for the analysis of cancer-related single nucleotide polymorphism. NEW J CHEM 2014. [DOI: 10.1039/c4nj00549j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
12
|
Stejskalová E, Horáková P, Vacek J, Bowater RP, Fojta M. Enzyme-linked electrochemical DNA ligation assay using magnetic beads. Anal Bioanal Chem 2014; 406:4129-36. [PMID: 24820061 DOI: 10.1007/s00216-014-7811-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/23/2014] [Accepted: 04/03/2014] [Indexed: 01/19/2023]
Abstract
DNA ligases are essential enzymes in all cells and have been proposed as targets for novel antibiotics. Efficient DNA ligase activity assays are thus required for applications in biomedical research. Here we present an enzyme-linked electrochemical assay based on two terminally tagged probes forming a nicked junction upon hybridization with a template DNA. Nicked DNA bearing a 5' biotin tag is immobilized on the surface of streptavidin-coated magnetic beads, and ligated product is detected via a 3' digoxigenin tag recognized by monoclonal antibody-alkaline phosphatase conjugate. Enzymatic conversion of napht-1-yl phosphate to napht-1-ol enables sensitive detection of the voltammetric signal on a pyrolytic graphite electrode. The technique was tested under optimal conditions and various situations limiting or precluding the ligation reaction (such as DNA substrates lacking 5'-phosphate or containing a base mismatch at the nick junction, or application of incompatible cofactor), and utilized for the analysis of the nick-joining activity of a range of recombinant Escherichia coli DNA ligase constructs. The novel technique provides a fast, versatile, specific, and sensitive electrochemical assay of DNA ligase activity.
Collapse
Affiliation(s)
- Eva Stejskalová
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
| | | | | | | | | |
Collapse
|
13
|
|
14
|
Ermini ML, Mariani S, Scarano S, Campa D, Barale R, Minunni M. Single nucleotide polymorphism detection by optical DNA-based sensing coupled with whole genomic amplification. Anal Bioanal Chem 2012; 405:985-93. [PMID: 22955671 DOI: 10.1007/s00216-012-6345-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/01/2012] [Accepted: 08/08/2012] [Indexed: 12/11/2022]
Abstract
The work presented here deals with the optimization of a strategy for detection of single nucleotide polymorphisms based on surface plasmon resonance imaging. First, a sandwich-like assay was designed, and oligonucleotide sequences were computationally selected in order to study optimized conditions for the detection of the rs1045642 single nucleotide polymorphism in the gene ABCB1. Then the strategy was optimized on a surface plasmon resonance imaging biosensor using synthetic DNA sequences in order to evaluate the best conditions for the detection of a single mismatching base. Finally, the assay was tested on DNA extracted from human blood which was subsequently amplified using a whole genome amplification kit. The direct detection of the polymorphism was successfully achieved. The biochip was highly regenerable and reusable for up to 20 measurements. Furthermore, coupling these promising results with the multiarray assay, we can foresee applying this biosensor in clinical research extended to concurrent analysis of different polymorphisms.
Collapse
Affiliation(s)
- M L Ermini
- Dipartimento di Chimica, Università di Firenze, Sesto Fiorentino, Italy
| | | | | | | | | | | |
Collapse
|
15
|
Highly sensitive and selective colorimetric genotyping of single-nucleotide polymorphisms based on enzyme-amplified ligation on magnetic beads. Biosens Bioelectron 2012; 36:89-94. [DOI: 10.1016/j.bios.2012.03.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 03/26/2012] [Accepted: 03/29/2012] [Indexed: 11/22/2022]
|
16
|
Saha K, Agasti SS, Kim C, Li X, Rotello VM. Gold nanoparticles in chemical and biological sensing. Chem Rev 2012; 112:2739-79. [PMID: 22295941 PMCID: PMC4102386 DOI: 10.1021/cr2001178] [Citation(s) in RCA: 2769] [Impact Index Per Article: 230.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Krishnendu Saha
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Sarit S. Agasti
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Chaekyu Kim
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Xiaoning Li
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| |
Collapse
|
17
|
Huang K, Martí AA. Recent trends in molecular beacon design and applications. Anal Bioanal Chem 2011; 402:3091-102. [PMID: 22159461 DOI: 10.1007/s00216-011-5570-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 12/26/2022]
Abstract
A molecular beacon (MB) is a hairpin-structured oligonucleotide probe containing a photoluminescent species (PLS) and a quencher at different ends of the strand. In a recognition and detection process, the hybridization of MBs with target DNA sequences restores the strong photoluminescence, which is quenched before hybridization. Making better MBs involves reducing the background photoluminescence and increasing the brightness of the PLS, which therefore involves the development of new PLS and quenchers, as well as innovative PLS-quencher systems. Heavy-metal complexes, nanocrystals, pyrene compounds, and other materials with excellent photophysical properties have been applied as PLS of MBs. Nanoparticles, nanowires, graphene, metal films, and many other media have also been introduced to quench photoluminescence. On the basis of their high specificity, selectivity, and sensitivity, MBs are developed as a general platform for sensing, producing, and carrying molecules other than oligonucleotides.
Collapse
Affiliation(s)
- Kewei Huang
- Department of Chemistry, Rice University, 6100 South Main Street, Houston, TX 77005, USA
| | | |
Collapse
|
18
|
Ahangar LE, Mehrgardi MA. 3,4-Diaminobenzoic acid (DABA) as a redox label for electrochemical detection of single base mismatches. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
19
|
Shi C, Ge Y, Gu H, Ma C. Highly sensitive chemiluminescent point mutation detection by circular strand-displacement amplification reaction. Biosens Bioelectron 2011; 26:4697-701. [DOI: 10.1016/j.bios.2011.05.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 05/14/2011] [Indexed: 11/30/2022]
|
20
|
Deoxyribonucleic Acid Molecular Design for Electrochemical Biosensors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1016/s1872-2040(10)60449-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
21
|
Zhang Y, Wang Y, Wang H, Jiang JH, Shen GL, Yu RQ, Li J. Electrochemical DNA biosensor based on the proximity-dependent surface hybridization assay. Anal Chem 2010; 81:1982-7. [PMID: 19173619 DOI: 10.1021/ac802512d] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper describes a novel electrochemical DNA (E-DNA) biosensor for simple, rapid, and specific detection of nucleic acids based on the proximity-dependent surface hybridization assay. This E-DNA biosensor was constructed by self-assembly of a 3' short thiolated capture probe on the gold electrode. DNA detection was realized by outputting a remarkable redox current of the 5' ferrocene (Fc) tail labeled probe. When the target DNA was introduced into the system, it was complementary to the 5' Fc labeled probe at the one-half-segment and complementary to the 3' short thiolated capture probe at the other half-segment, resulting in forming a stable duplex complex. As a result, the Fc probe was proximate to the electrode surface, and the Faradaic current was observed. This E-DNA biosensor was proved to have a low detection limit (1 fM) and a wide dynamic range (from 1 fM to 1 nM) due to the stable hybridization mode. In addition, the sensing system could discriminate the complementary sequence from mismatch sequences, with high sensitivity, stability, and reusability.
Collapse
Affiliation(s)
- Yanli Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | | | | | | | | | | | | |
Collapse
|
22
|
Wan Y, Lao R, Liu G, Song S, Wang L, Li D, Fan C. Multiplexed Electrochemical DNA Sensor for Single-Nucleotide Polymorphism Typing by Using Oligonucleotide-Incorporated Nonfouling Surfaces. J Phys Chem B 2010; 114:6703-6. [DOI: 10.1021/jp100871u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ying Wan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Ruojun Lao
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Gang Liu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Shiping Song
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Lihua Wang
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Di Li
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| | - Chunhai Fan
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China, and Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, P.R. China
| |
Collapse
|
23
|
Jin X, Fei Y, Zhang L, Liu X, Shen G, Yu R. An electrochemical molecular switch for one-step, reusable detection of a single-base mutation of DNA. Analyst 2009; 135:121-6. [PMID: 20024191 DOI: 10.1039/b911672a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new strategy for one-step, reusable and sensitive detection of a single-base mutation based on an electrochemical molecular switch is developed in the present work. When the hybridization reaction takes place in the presence of target DNA, the Fc-labeled terminal of the open switch molecule can be captured by the probe through the predesigned complementary bases of both sequences. By this method, a signal-on sensor featuring both generalizability and simplicity towards reagentless detection of DNA with sensitivity and selectivity electrochemical system is built on. The approach had been demonstrated with the identification of a single-base mutation of alpha-thalassemia point mutation in Hb Constant Spring codon 142 (TAA --> CAA). The wild-type and mutant-type of the synthetic 16 mer DNA sequences as the model targets were successfully discriminated. The results showed that the response signal was linear to the logarithm of the target concentration in the range from 0.01 to 100 pM with a detection limit of 0.01 pM. The regeneration experiment demonstrated that the sensor interface can be easily and successfully regenerated. All these revealed that the present system is a promising candidate for single-base mutation discrimination.
Collapse
Affiliation(s)
- Xiaoyong Jin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Chemistry and Chemical Engineering College, Hunan University, Changsha 410082, PR China.
| | | | | | | | | | | |
Collapse
|
24
|
Miranda-Castro R, de-los-Santos-Álvarez N, Lobo-Castañón M, Miranda-Ordieres A, Tuñón-Blanco P. Structured Nucleic Acid Probes for Electrochemical Devices. ELECTROANAL 2009. [DOI: 10.1002/elan.200904653] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
25
|
Huang Y, Zhang YL, Xu X, Jiang JH, Shen GL, Yu RQ. Highly Specific and Sensitive Electrochemical Genotyping via Gap Ligation Reaction and Surface Hybridization Detection. J Am Chem Soc 2009; 131:2478-80. [DOI: 10.1021/ja808700d] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yong Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Yan-Li Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Xiangmin Xu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Guo-Li Shen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| |
Collapse
|
26
|
Won BY, Shin SC, Chung WY, Shin S, Cho DY, Park HG. Mismatch DNA-specific enzymatic cleavage employed in a new method for the electrochemical detection of genetic mutations. Chem Commun (Camb) 2009:4230-2. [DOI: 10.1039/b907268c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
27
|
Han K, Chen L, Lin Z, Li G. Target induced dissociation (TID) strategy for the development of electrochemical aptamer-based biosensor. Electrochem commun 2009. [DOI: 10.1016/j.elecom.2008.10.054] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
|
28
|
|
29
|
Lucarelli F, Capponcelli S, Marrazza G, Sangiorgi L, Mascini M. Split hybridisation probes for electrochemical typing of single-nucleotide polymorphisms. Analyst 2008; 134:52-9. [PMID: 19082174 DOI: 10.1039/b806514d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes the development of a highly selective single-nucleotide polymorphisms (SNPs) typing method based on the use of split hybridisation probes and demonstrates the concept through the electrochemical analysis of single-base mutations in actual patient samples. The requirement that two probes hybridised adjacent to one another to allow for stabilisation (via base-stacking) and binding of the allele-specific oligonucleotide (ASO), imparted highly stringent selectivity criteria to the assay. Simple rules for tuning the characteristics of such stacking/ASO probe pairs and achieve full mismatch discrimination at ambient conditions (with no need to strictly control the temperature) are provided. All genotyping experiments were indeed performed at room temperature, using the planar surface of disposable probe-modified gold electrodes as the genosensing platform. The ability to detect nanomolar amounts of a synthetic target even within a vast excess of single-base substituted sequences gave strong evidence of the specificity of the split probes assay. Proving the general validity of this genotyping approach, application of the analytical pathway was further demonstrated for clinical targets (amplified from the human TP53 gene) whose mutational site was poorly accessible, being part of a thermodynamically stable hairpin. In combination with use of auxiliary oligonucleotides (which restored the availability of each pre-defined hybridisation site), the assay demonstrated the ability to fully discriminate single-base mutations with detection limits in the high picomolar range (total analysis time: 60 min). Our specific probe design, hybridisation and signal transduction paths make the analytical process remarkably simple, relatively low cost and, thus, well suited for low throughput analysis of clinically relevant samples.
Collapse
Affiliation(s)
- Fausto Lucarelli
- Department of Chemistry, University of Florence, via della Lastruccia 3, 50019 Sesto F.no, Florence, Italy
| | | | | | | | | |
Collapse
|
30
|
Innovative integrated system for real-time measurement of hybridization and melting on standard format microarrays. Biotechniques 2008; 44:913-20. [PMID: 18533901 DOI: 10.2144/000112758] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Despite the great popularity and potential of microarrays, their use for research and clinical applications is still hampered by lengthy and costly design and optimization processes, mainly because the technology relies on the end point measurement of hybridization. Thus, the ability to monitor many hybridization events on a standard microarray slide in real time would greatly expand the use and benefit of this technology, as it would give access to better prediction of probe performance and improved optimization of hybridization parameters. Although real-time hybridization and thermal denaturation measurements have been reported, a complete walk-away system compatible with the standard format of microarrays is still unavailable. To address this issue, we have designed a biochip tool that combines a hybridization station with active mixing capability and temperature control together with a fluorescence reader in a single compact benchtop instrument. This integrated live hybridization machine (LHM) allows measuring in real time the hybridization of target DNA to thousands of probes simultaneously and provides excellent levels of detection and superior sequence discrimination. Here we show on an environmental single nucleotide polymorphism (SNP) model system that the LHM enables a variety of experiments unachievable with conventional biochip tools.
Collapse
|
31
|
Li X, Qi H, Shen L, Gao Q, Zhang C. Electrochemical Aptasensor for the Determination of Cocaine Incorporating Gold Nanoparticles Modification. ELECTROANAL 2008. [DOI: 10.1002/elan.200704193] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
32
|
Liu G, Wan Y, Gau V, Zhang J, Wang L, Song S, Fan C. An enzyme-based E-DNA sensor for sequence-specific detection of femtomolar DNA targets. J Am Chem Soc 2008; 130:6820-5. [PMID: 18459781 DOI: 10.1021/ja800554t] [Citation(s) in RCA: 370] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we report an enzyme-based E-DNA sensor for the sequence-specific detection of nucleic acids. This DNA sensor employs a "stem-loop" DNA probe dually labeled with biotin and digoxigenin (DIG). The probe is immobilized at an avidin-modified electrode surface via the biotin-avidin bridge, and the DIG serves as an affinity tag for the enzyme binding. In the initial state of the sensor, the probe adopts the stem-loop structure, which shields DIG from being approached by a bulky horseradish peroxidase-linked-anti-DIG antibody (anti-DIG-HRP) due to the steric effect. After hybridization, the probe undergoes a significant conformational change, forcing DIG away from the electrode. As a result, the DIG label becomes accessible by the anti-DIG-HRP, and the target hybridization event can be sensitively transduced via the enzymatically amplified electrochemical current signal. By using this new strategy, we demonstrate that the prototype E-DNA sensor has been able to detect as low as femtomolar DNA targets with excellent differentiation ability for even single mismatches.
Collapse
Affiliation(s)
- Gang Liu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | | | | | | | | | | | | |
Collapse
|
33
|
Electrochemical and piezoelectric DNA biosensors for hybridisation detection. Anal Chim Acta 2008; 609:139-59. [DOI: 10.1016/j.aca.2007.12.035] [Citation(s) in RCA: 199] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 12/19/2007] [Accepted: 12/21/2007] [Indexed: 11/21/2022]
|
34
|
Affiliation(s)
- Audrey Sassolas
- Laboratoire de Génie Enzymatique et Biomoléculaire, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 43 Boulevard du 11 Novembre 1918, Villeurbanne F-69622, France, UMR5246, Centre National de La Recherche Scientifque, Villeurbanne F-69622, France, Université de Lyon, Lyon F-69622, France, Université Lyon 1, Lyon F-69622, France, Institut National des Sciences Appliquées de Lyon, École d'Ingénieurs, Villeurbanne F-69621, France, and École Supérieure Chimie Physique Électronique de Lyon,
| | - Béatrice D. Leca-Bouvier
- Laboratoire de Génie Enzymatique et Biomoléculaire, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 43 Boulevard du 11 Novembre 1918, Villeurbanne F-69622, France, UMR5246, Centre National de La Recherche Scientifque, Villeurbanne F-69622, France, Université de Lyon, Lyon F-69622, France, Université Lyon 1, Lyon F-69622, France, Institut National des Sciences Appliquées de Lyon, École d'Ingénieurs, Villeurbanne F-69621, France, and École Supérieure Chimie Physique Électronique de Lyon,
| | - Loïc J. Blum
- Laboratoire de Génie Enzymatique et Biomoléculaire, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 43 Boulevard du 11 Novembre 1918, Villeurbanne F-69622, France, UMR5246, Centre National de La Recherche Scientifque, Villeurbanne F-69622, France, Université de Lyon, Lyon F-69622, France, Université Lyon 1, Lyon F-69622, France, Institut National des Sciences Appliquées de Lyon, École d'Ingénieurs, Villeurbanne F-69621, France, and École Supérieure Chimie Physique Électronique de Lyon,
| |
Collapse
|