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Malofsky N, Nelson DJ, Pask ME, Haselton FR. L-DNA-Based Melt Analysis Enables Within-Sample Validation of PCR Products. Anal Chem 2024; 96:11897-11905. [PMID: 38975971 PMCID: PMC11270519 DOI: 10.1021/acs.analchem.4c01611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/09/2024]
Abstract
The melt analysis feature in most real-time polymerase chain reaction (PCR) instruments is a simple method for determining if expected or unexpected products are present. High-resolution melt (HRM) analysis seeks to improve the precision of melt temperature measurements for better PCR product sequence characterization. In the area of tuberculosis (TB) drug susceptibility screening, sequencing has shown that a single base change can be sufficient to make a first-line TB drug ineffective. In this study, a reagent-based calibration strategy based on synthetic left-handed (L)-DNA, designated LHRM, was developed to confirm validation of a PCR product with single base resolution. To test this approach, a constant amount of a double-stranded L-DNA melt comparator was added to each sample and used as a within-sample melt standard. The performance of LHRM and standard HRM was used to classify PCR products as drug-susceptible or not drug-susceptible with a test bed of nine synthetic katG variants, each containing single or multiple base mutations that are known to confer resistance to the first-line TB drug isoniazid (INH). LHRM achieved comparable classification to standard HRM relying only on within-sample melt differences between L-DNA and the unknown PCR product. Using a state-of-the-art calibrated instrument and multiple sample classification analysis, standard HRM was performed at 66.7% sensitivity and 98.8% specificity. Single sample analysis incorporating L-DNA for reagent-based calibration into every sample maintained high performance at 77.8% sensitivity and 98.7% specificity. LHRM shows promise as a high-resolution single sample method for validating PCR products in applications where the expected sequence is known.
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Affiliation(s)
- Nicole
A. Malofsky
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Dalton J. Nelson
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Megan E. Pask
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Frederick R. Haselton
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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2
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Spurlock N, Gabella WE, Nelson DJ, Evans DT, Pask ME, Schmitz JE, Haselton FR. Implementing L-DNA analogs as mirrors of PCR reactant hybridization state: theoretical and practical guidelines for PCR cycle control. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:2840-2849. [PMID: 38567817 PMCID: PMC11079981 DOI: 10.1039/d4ay00083h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/22/2024] [Indexed: 05/12/2024]
Abstract
In previous reports, we described a PCR cycle control approach in which the hybridization state of optically labeled L-DNA enantiomers of the D-DNA primers and targets determined when the thermal cycle was switched from cooling to heating and heating to cooling. A consequence of this approach is that it also "adapts" the cycling conditions to compensate for factors that affect the hybridization kinetics of primers and targets. It assumes, however, that the hybridization state of the labeled L-DNA analogs accurately reflects the hybridization state of the D-DNA primers and targets. In this report, the Van't Hoff equation is applied to determine the L-DNA concentration and ratio of L-DNA strands required by this assumption. Simultaneous fluorescence and temperature measurements were taken during L-DNA controlled cycling, and the optical and thermal switch points compared as a function of both total L-DNA concentration and ratio of strands. Based on the Van't Hoff relationship and these experimental results, L-DNA best mirrors the hybridization of PCR primers and targets when total L-DNA concentration is set equal to the initial concentration of the D-DNA primer of interest. In terms of strand ratios, L-DNA hybridization behavior most closely matches the behavior of their D-DNA counterparts throughout the reaction when one of the L-DNA strands is far in excess of the other. The L-DNA control algorithm was then applied to the practical case of the SARS-CoV-2 N2 reaction, which has been shown to fail or have a delayed Cq when PCR was performed without nucleic acid extraction. PCR Cq values for simulated "unextracted" PCR samples in a nasopharyngeal background and in an NaCl concentration similar to that of viral transport media were determined using either the L-DNA control algorithm (N = 6) or preset cycling conditions (N = 3) and compared to water background controls run in parallel. For preset cycling conditions, the presence of nasopharyngeal background or a high salt background concentration significantly increased Cq, but the L-DNA control algorithm had no significant delay. This suggests that a carefully designed L-DNA-based control algorithm "adapts" the cycling conditions to compensate for hybridization errors of the PCR D-DNA reactants that produce false negatives.
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Affiliation(s)
- Nicholas Spurlock
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - William E Gabella
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, USA
| | - Dalton J Nelson
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - David T Evans
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - Megan E Pask
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
| | - Jonathan E Schmitz
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, PMB 351631, Nashville, TN, USA.
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3
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方 楚, 唐 田, 周 琛, 张 婧, 林 华, 朱 娅, 杨 加, 汪 川. [Development of a Catalytic Hairpin Assembly-Based Fluorescent Assay for the Rapid Detection of SARS-CoV-2 Target RNA]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:183-189. [PMID: 38322527 PMCID: PMC10839497 DOI: 10.12182/20240160601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Indexed: 02/08/2024]
Abstract
Objective To develop a catalytic hairpin assembly (CHA)-based fluorescent assay for the detection of the target RNA of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), so as to realize the rapid nucleic acid testing of SARS-CoV-2. Methods A 24-nt segment of the SARS-CoV-2 nucleocapsid protein gene (N gene, NC_045512.2) was chosen as the target RNA and the hairpin motif 1 (H1) and hairpin motif 2 (H2) were designed based on the principle of CHA reaction. The H1 motif was labelled with a fluorophore group as well as a quencher group. When the target RNA was added to the hairpin motifs, CHA reaction was triggered at room temperature (25 ℃), which led to the amplification of fluorescence signal, thereby enabling the rapid detection of the target RNA. After the optimization of the hairpin motifs and the experimental conditions, the sensitivity and the specificity of the testing method were measured to evaluate its performance. Results We successfully constructed a CHA-based fluorescent assay specifically for the target RNA of SARS-CoV-2. With this method, testing could be completed at room temperature within 30 min. This testing method exhibited excellent specificity and could be used to accurately distinguish the perfectly-matched target RNA from the target RNA with single-base mutations. In addition, the testing method demonstrated good sensitivity, with a detection limit of 50 pmol/L. Conclusion The proposed assay enables the simple and rapid detection of the SARS-CoV-2 target RNA with excellent sensitivity and specificity, showing great promise for further optimization and subsequent clinical application for the rapid detection of SARS-CoV-2 nucleic acid.
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Affiliation(s)
- 楚斌 方
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 田 唐
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 琛 周
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 婧 张
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 华 林
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 娅岚 朱
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 加雪 杨
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - 川 汪
- 四川大学华西公共卫生学院/四川大学华西第四医院 (成都 610041)West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
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4
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Ang YS, Yung LYL. Design strategies for countering the effect of fluorophore-quencher labelling on DNA hairpin thermodynamics. Chem Commun (Camb) 2023; 59:13167-13170. [PMID: 37849331 DOI: 10.1039/d3cc02427j] [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: 10/19/2023]
Abstract
We report the impact of fluorophore-quencher labelling on the thermodynamics of hairpin opening by testing five fluorophores and two quenchers labelled at the end and/or internal positions. Two counter strategies were introduced, i.e. label the hairpin probe at an internal position or append an external hairpin stem on the trigger strand to promote coaxial stacking hybridization. The observations remained valid for complex hairpin opening operations such as hybridization chain reaction.
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Affiliation(s)
- Yan Shan Ang
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore.
| | - Lin-Yue Lanry Yung
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore.
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5
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Limanskaya OY, Limanskii OP. Intramolecular Interactions in the Fluorophore–Quencher System in Linear and Hairpin Probes for Real-Time PCR. CYTOL GENET+ 2023. [DOI: 10.3103/s009545272302007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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6
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Idili A, Parolo C, Alvarez-Diduk R, Merkoçi A. Rapid and Efficient Detection of the SARS-CoV-2 Spike Protein Using an Electrochemical Aptamer-Based Sensor. ACS Sens 2021; 6:3093-3101. [PMID: 34375076 PMCID: PMC8370117 DOI: 10.1021/acssensors.1c01222] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
The
availability of sensors able to rapidly detect SARS-CoV-2 directly
in biological fluids in a single step would allow performing massive
diagnostic testing to track in real time and contain the spread of
COVID-19. Motivated by this, here, we developed an electrochemical
aptamer-based (EAB) sensor able to achieve the rapid, reagentless,
and quantitative measurement of the SARS-CoV-2 spike (S) protein.
First, we demonstrated the ability of the selected aptamer to undergo
a binding-induced conformational change in the presence of its target
using fluorescence spectroscopy. Then, we engineered the aptamer to
work as a bioreceptor in the EAB platform and we demonstrated its
sensitivity and specificity. Finally, to demonstrate the clinical
potential of the sensor, we tested it directly in biological fluids
(serum and artificial saliva), achieving the rapid (minutes) and single-step
detection of the S protein in its clinical range.
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Affiliation(s)
- Andrea Idili
- Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Bellaterra 08193 Barcelona, Spain
| | - Claudio Parolo
- Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Bellaterra 08193 Barcelona, Spain
- Barcelona Institute for Global Health, 08036 Barcelona, Spain
| | - Ruslán Alvarez-Diduk
- Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Bellaterra 08193 Barcelona, Spain
| | - Arben Merkoçi
- Institut Català de Nanociència i Nanotecnologia (ICN2), Campus UAB, Bellaterra 08193 Barcelona, Spain
- CSIC and the Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
- Institucio′ Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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7
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Through the looking glass: milestones on the road towards mirroring life. Trends Biochem Sci 2021; 46:931-943. [PMID: 34294544 DOI: 10.1016/j.tibs.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/05/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022]
Abstract
Naturally occurring DNA, RNA, and proteins predominantly exist in only one enantiomeric form (homochirality). Advances in biotechnology and chemical synthesis allow the production of the respective alternate enantiomeric form, enabling access to mirror-image versions of these natural biopolymers. Exploiting the unique properties of such mirror molecules has already led to many applications, such as biostable and nonimmunogenic therapeutics or sensors. However, a 'roadblock' for unlocking the mirror world is the lack of biological systems capable of synthesizing critical building blocks including mirror oligonucleotides and oligopeptides to reducing cost and improve purity. Here, we provide an overview of the current progress, applications, and challenges of the molecular mirror world by identifying milestones towards mirroring life.
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8
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Zimmers ZA, Adams NM, Haselton FR. Addition of mirror-image L-DNA elements to DNA amplification circuits to distinguish leakage from target signal. Biosens Bioelectron 2021; 188:113354. [PMID: 34034212 DOI: 10.1016/j.bios.2021.113354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
DNA amplification circuits that rely on thermodynamically-driven hybridization events triggered by a target nucleic acid are becoming increasingly utilized due to their relative simplicity. A drawback of these circuits is that non-specific amplification, or circuit leakage, must be estimated using a separate "no-target" control reaction to eliminate false positives. Aside from requiring an additional reaction, the problem with this approach is the difficulty of creating a no-target control for biological specimens. To overcome this limitation, we propose a strategy that combines both reactions into the same tube using naturally-occurring right-handed D-DNA circuit elements for the target detection reaction and identical synthetic mirror-image left-handed L-DNA circuit elements for the no-target control reaction. We illustrate this approach using catalyzed hairpin assembly (CHA), one of the most studied DNA amplification circuits. In a dual-chirality CHA design, the right-handed circuit signal is produced by target-specific amplification and circuit leakage, whereas the left-handed circuit signal is produced only by circuit leakage. The target-specific amplification is calculated as the difference between the two signals. The limit of detection of this dual-chirality CHA reaction was found to be similar to that of traditional CHA (81 vs 92 pM, respectively). Furthermore, the left-handed no-target signal matched the right-handed leakage across a wide range of sample conditions including background DNA, increased salt concentration, increased temperature, and urine. These results demonstrate the robustness of a dual-chirality design and the potential utility of left-handed DNA in the development of new DNA amplification circuits better-suited for target detection applications in biological samples.
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Affiliation(s)
- Zackary A Zimmers
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA.
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9
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DNA hybridisation kinetics using single-molecule fluorescence imaging. Essays Biochem 2021; 65:27-36. [PMID: 33491734 PMCID: PMC8056036 DOI: 10.1042/ebc20200040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023]
Abstract
Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about the process which are still unknown. Prior to the invention of single-molecule microscopy, DNA hybridisation experiments were conducted at the ensemble level, and thus it was impossible to directly observe individual hybridisation events and understand fully the kinetics of DNA hybridisation. In this mini-review, recent single-molecule fluorescence-based studies of DNA hybridisation are discussed, particularly for short nucleic acids, to gain more insight into the kinetics of DNA hybridisation. As well as looking at single-molecule studies of intrinsic and extrinsic factors affecting DNA hybridisation kinetics, the influence of the methods used to detect hybridisation of single DNAs is considered. Understanding the kinetics of DNA hybridisation not only gives insight into an important biological process but also allows for further advancements in the growing field of nucleic acid biotechnology.
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10
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Helicase-like functions in phosphate loop containing beta-alpha polypeptides. Proc Natl Acad Sci U S A 2021; 118:2016131118. [PMID: 33846247 DOI: 10.1073/pnas.2016131118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The P-loop Walker A motif underlies hundreds of essential enzyme families that bind nucleotide triphosphates (NTPs) and mediate phosphoryl transfer (P-loop NTPases), including the earliest DNA/RNA helicases, translocases, and recombinases. What were the primordial precursors of these enzymes? Could these large and complex proteins emerge from simple polypeptides? Previously, we showed that P-loops embedded in simple βα repeat proteins bind NTPs but also, unexpectedly so, ssDNA and RNA. Here, we extend beyond the purely biophysical function of ligand binding to demonstrate rudimentary helicase-like activities. We further constructed simple 40-residue polypeptides comprising just one β-(P-loop)-α element. Despite their simplicity, these P-loop prototypes confer functions such as strand separation and exchange. Foremost, these polypeptides unwind dsDNA, and upon addition of NTPs, or inorganic polyphosphates, release the bound ssDNA strands to allow reformation of dsDNA. Binding kinetics and low-resolution structural analyses indicate that activity is mediated by oligomeric forms spanning from dimers to high-order assemblies. The latter are reminiscent of extant P-loop recombinases such as RecA. Overall, these P-loop prototypes compose a plausible description of the sequence, structure, and function of the earliest P-loop NTPases. They also indicate that multifunctionality and dynamic assembly were key in endowing short polypeptides with elaborate, evolutionarily relevant functions.
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11
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Euliano EM, Hardcastle AN, Victoriano CM, Gabella WE, Haselton FR, Adams NM. Multiplexed Adaptive RT-PCR Based on L-DNA Hybridization Monitoring for the Detection of Zika, Dengue, and Chikungunya RNA. Sci Rep 2019; 9:11372. [PMID: 31388071 PMCID: PMC6684530 DOI: 10.1038/s41598-019-47862-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/25/2019] [Indexed: 02/06/2023] Open
Abstract
Reverse transcription polymerase chain reaction (RT-PCR) is the gold standard for the molecular diagnosis of many infectious diseases, including RNA viruses, but is generally limited to settings with access to trained personnel and laboratory resources. We have previously reported a fundamentally simpler thermal cycling platform called Adaptive PCR, which dynamically controls thermal cycling conditions during each cycle by optically monitoring the annealing and melting of mirror-image L-DNA surrogates of the PCR primers and targets. In this report, we integrate optically-controlled reverse transcription and single-channel monitoring of L-DNAs to develop a multiplexed Adaptive RT-PCR instrument and assay for the detection of Zika, dengue, and chikungunya virus RNA with high target specific and low limits of detection. The assay is demonstrated to detect as low as 5 copies/reaction of Zika or chikungunya RNA and 50 copies/reaction of dengue RNA. The multiplexed Adaptive RT-PCR instrument is robust and has many of the features required to implement diagnostic assays for RNA viruses in settings that lack traditional laboratory resources.
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Affiliation(s)
- Erin M Euliano
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Austin N Hardcastle
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Christia M Victoriano
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - William E Gabella
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, 37235, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA.
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