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Meftah M, Habel A, Baachaoui S, Yaacoubi-Loueslati B, Raouafi N. Sensitive electrochemical detection of polymorphisms in IL6 and TGFβ1 genes from ovarian cancer DNA patients using EcoRI and DNA hairpin-modified gold electrodes. Mikrochim Acta 2022; 190:15. [PMID: 36479645 DOI: 10.1007/s00604-022-05595-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022]
Abstract
Two electrochemical bioplatforms were prepared based on thiolated hairpin DNA probes tethered to AuNP-modified screen-printed electrodes to detect T > G and T > C polymorphisms, namely rs1880269 and rs1800469, present the interleukin-6 (IL6) and transforming growth factor β1 (TGFβ1) genes. The electrochemical readout was ensured by the detection of the double-stranded DNA using methylene blue as a redox probe after treatment by EcoRI restrictase. The main parameters influencing the analytical response such as the thiolated DNA probe concentration, incubation time with electrode, DNA hybridization time, EcoRI enzyme load, and its cleavage time were optimized based on the current intensity and signal-to-blank (S/B) ratio as selection criteria. Using spiked buffer solutions, the IL6 and TGFβ1 E-bioplatforms display wide ranges of linearity (1 × 102-1 × 108 fM and 5 × 101-1 × 105 fM, respectively) and limits of detection (47.9 fM and 16.6 fM, respectively). The two bioelectrodes have also good discrimination toward 1-mismatched, two mismatched, and non-complementary sequences, when they were used 30-fold higher than the target sequences. More importantly, the two bioplatforms successfully detected the single nucleotide polymorphisms (SNPs) in scarcely diluted genomic DNA, collected from 52 donors, and showed they can reliably distinguish between heterozygous (TG and TC genotypes) and homozygous (GG and CC genotypes) patients with respect to the control subjects (TT genotype), where the differences are statistically highly significant (p-value < 0.0001). Thus, the designed devices could be used to conduct large cohort studies targeting these mutations or extended to other SNPs.
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Affiliation(s)
- Maroua Meftah
- Sensors and Biosensors Group, Analytical Chemistry and Electrochemistry Lab (LR99ES15), Chemistry Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis El Manar, Tunisia
| | - Azza Habel
- Laboratory of Mycology, Pathologies and Biomarkers (LR16ES05), Biology Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis El Manar, Tunisia
| | - Sabrine Baachaoui
- Sensors and Biosensors Group, Analytical Chemistry and Electrochemistry Lab (LR99ES15), Chemistry Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis El Manar, Tunisia
| | - Basma Yaacoubi-Loueslati
- Laboratory of Mycology, Pathologies and Biomarkers (LR16ES05), Biology Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis El Manar, Tunisia
| | - Noureddine Raouafi
- Sensors and Biosensors Group, Analytical Chemistry and Electrochemistry Lab (LR99ES15), Chemistry Department, Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis El Manar, Tunisia.
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Restriction Endonuclease-Based Assays for DNA Detection and Isothermal Exponential Signal Amplification. SENSORS 2020; 20:s20143873. [PMID: 32664471 PMCID: PMC7411786 DOI: 10.3390/s20143873] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
Abstract
Application of restriction endonuclease (REase) enzymes for specific detection of nucleic acids provides for high assay specificity, convenience and low cost. A direct restriction assay format is based on the specific enzymatic cleavage of a target–probe hybrid that is accompanied with the release of a molecular marker into the solution, enabling target quantification. This format has the detection limit in nanomolar range. The assay sensitivity is improved drastically to the attomolar level by implementation of exponential signal amplification that is based on a cascade of self-perpetuating restriction endonuclease reactions. The cascade is started by action of an amplification “trigger”. The trigger is immobilized through a target-specific probe. Upon the target probe hybridization followed with specific cleavage, the trigger is released into the reaction solution. The solution is then added to the assay amplification stage, and the free trigger induces cleavage of amplification probes, thus starting the self-perpetuating cascade of REase-catalyzed events. Continuous cleavage of new amplification probes leads to the exponential release of new triggers and rapid exponential signal amplification. The proposed formats exemplify a valid isothermal alternative to qPCR with similar sensitivity achieved at a fraction of the associated costs, time and labor. Advantages and challenges of the approach are discussed.
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Ghindilis AL, Chesnokov O, Ngasala B, Smith MW, Smith K, Mårtensson A, Oleinikov AV. Detection of sub-microscopic blood levels of Plasmodium falciparum using Tandem Oligonucleotide Repeat Cascade Amplification (TORCA) assay with an attomolar detection limit. Sci Rep 2019; 9:2901. [PMID: 30814636 PMCID: PMC6393570 DOI: 10.1038/s41598-019-39921-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/05/2019] [Indexed: 11/09/2022] Open
Abstract
Tandem Oligonucleotide Repeat Cascade Amplification (TORCA) based on signal rather than target amplification under isothermal conditions was developed for nucleic acid assays. The initial signal was generated by hybridization of single stranded DNA targets to immobilized recognition probes followed by hybrid cleavage with specific restriction endonuclease (REase), and release of trigger oligonucleotides (Tr1). The signal amplification chamber contained two bead types carrying single-stranded amplification probes and two amplification REases. The probes consisted of multiple tandem repeats of either Tr1 or another trigger Tr2, with the tandem-Tr1 anchored to the beads through the antisense Tr2 linker and vice versa. Addition of the recognition reaction solution and Tr1 hybridization to the anti-Tr1 linkers started cleavage and release of additional Tr1 and Tr2, resulting in exponential signal amplification. The cleavage cascade also released horseradish peroxidase (HRP) pre-attached to the amplification probes, and the resultant signal was measured colorimetrically. A TORCA assay was developed for detection of Plasmodium falciparum parasites in blood. It had the detection limit in the attomolar concentration range, successfully detecting sub-microscopic P. falciparum infections at less than 0.75 infected erythrocytes per microliter. Further TORCA optimization will likely produce the quantitative isothermal alternative to PCR at a fraction of its cost.
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Affiliation(s)
| | - Olga Chesnokov
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33428, USA
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Akademiska sjukhuset, 751 85, Uppsala, Sweden
| | - Maria W Smith
- TORCATECH, LLC, 5210 104th Street SW, Mukilteo, WA, 98275, USA
| | - Kenneth Smith
- TORCATECH, LLC, 5210 104th Street SW, Mukilteo, WA, 98275, USA
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Akademiska sjukhuset, 751 85, Uppsala, Sweden
| | - Andrew V Oleinikov
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33428, USA
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Ghindilis AL, Smith MW, Simon HM, Seoudi IA, Yazvenko NS, Murray IA, Fu X, Smith K, Jen-Jacobson L, Xu SY. Restriction Cascade Exponential Amplification (RCEA) assay with an attomolar detection limit: a novel, highly specific, isothermal alternative to qPCR. Sci Rep 2015; 5:7737. [PMID: 25583452 PMCID: PMC4291554 DOI: 10.1038/srep07737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 12/10/2014] [Indexed: 11/24/2022] Open
Abstract
An alternative to qPCR was developed for nucleic acid assays, involving signal rather than target amplification. The new technology, Restriction Cascade Exponential Amplification (RCEA), relies on specific cleavage of probe-target hybrids by restriction endonucleases (REase). Two mutant REases for amplification (Ramp), S17C BamHI and K249C EcoRI, were conjugated to oligonucleotides, and immobilized on a solid surface. The signal generation was based on: (i) hybridization of a target DNA to a Ramp-oligonucleotide probe conjugate, followed by (ii) specific cleavage of the probe-target hybrid using a non-immobilized recognition REase. The amount of Ramp released into solution upon cleavage was proportionate to the DNA target amount. Signal amplification was achieved through catalysis, by the free Ramp, of a restriction cascade containing additional oligonucleotide-conjugated Ramp and horseradish peroxidase (HRP). Colorimetric quantification of free HRP indicated that the RCEA achieved a detection limit of 10 aM (10−17 M) target concentration, or approximately 200 molecules, comparable to the sensitivity of qPCR-based assays. The RCEA assay had high specificity, it was insensitive to non-specific binding, and detected target sequences in the presence of foreign DNA. RCEA is an inexpensive isothermal assay that allows coupling of the restriction cascade signal amplification with any DNA target of interest.
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Affiliation(s)
| | - Maria W Smith
- 1] Cascade Biosystems, Inc., E7279 State Road 170, Colfax, WI 54730, USA [2] Center for Coastal Margin Observation and Prediction, and Institute of Environmental Health, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Holly M Simon
- Center for Coastal Margin Observation and Prediction, and Institute of Environmental Health, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Ihab A Seoudi
- Hamad Medical Corporation, P.O. Box 3050 Doha, Qatar
| | - Nina S Yazvenko
- Cascade Biosystems, Inc., E7279 State Road 170, Colfax, WI 54730, USA
| | - Iain A Murray
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Xiaoqing Fu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Kenneth Smith
- Cascade Biosystems, Inc., E7279 State Road 170, Colfax, WI 54730, USA
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, 320 Clapp Hall, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Shuang-Yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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