1
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Beard JW, Hunt SL, Evans A, Goenner C, Miller BL. Mimicking an in cellulo environment for enzyme-free paper-based nucleic acid tests at the point of care. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582375. [PMID: 38464301 PMCID: PMC10925243 DOI: 10.1101/2024.02.27.582375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Point of care (PoC) nucleic acid amplification tests (NAATs) are a cornerstone of public health, providing the earliest and most accurate diagnostic method for many communicable diseases, such as HIV, in the same location the patient receives treatment. Communicable diseases disproportionately impact low-resource communities where NAATs are often unobtainable due to the resource intensive enzymes that drive the tests. Enzyme-free nucleic acid detection methods, such as hybridization chain reaction (HCR), use DNA secondary structures for self-driven amplification schemes producing large DNA nanostructures and capable of single molecule detection in cellulo. These thermodynamically driven DNA-based tests have struggled to penetrate the PoC diagnostic field due to their inadequate limits of detection or complex workflows. Here we present a proof-of-concept NAAT that combines HCR-based amplification of a target nucleic acid sequence with paper-based nucleic acid filtration and enrichment capable of detecting sub pM levels of synthetic DNA. We reconstruct the favorable hybridization conditions of an in cellulo reaction in vitro by incubating HCR in an evaporating, microvolume environment containing poly(ethylene glycol) as a crowding agent. We demonstrate that the kinetics and thermodynamics of DNA-DNA and DNA-RNA hybridization is enhanced by the dynamic evaporating environment and inclusion of crowding agents, bringing HCR closer to meeting PoC NAAT needs.
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Affiliation(s)
- Jeffrey W. Beard
- Department of Dermatology, University of Rochester, Rochester, NY 14627, USA
| | - Samuel L. Hunt
- Department of Dermatology, University of Rochester, Rochester, NY 14627, USA
| | - Alexander Evans
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, USA
| | - Coleman Goenner
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14627, USA
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester, Rochester, NY 14627, USA
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14627, USA
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14627, USA
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2
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Huang Y, Gao Z, Ma C, Sun Y, Huang Y, Jia C, Zhao J, Feng S. An integrated microfluidic chip for nucleic acid extraction and continued cdPCR detection of pathogens. Analyst 2023. [PMID: 37194305 DOI: 10.1039/d3an00271c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This paper introduces an enclosed microfluidic chip that integrates sample preparation and the chamber-based digital polymerase chain reaction (cdPCR). The sample preparation of the chip includes nucleic acid extraction and purification based on magnetic beads, which adsorb nucleic acids by moving around the reaction chambers to complete the reactions including lysis, washing, and elution. The cdPCR area of the chip consists of tens of thousands of regularly arranged microchambers. After the sample preparation processes are completed, the purified nucleic acid can be directly introduced into the microchambers for amplification and detection on the chip. The nucleic acid extraction performance and digital quantification performance of the system were examined using synthetic SARS-CoV-2 plasmid templates at concentrations ranging from 101-105 copies per μL. Further on, a simulated clinical sample was used to test the system, and the integrated chip was able to accurately detect SARS-CoV-2 virus particle samples doped with interference (saliva) with a detection limit of 10 copies per μL. This integrated system could provide a promising tool for point-of-care testing of pathogenic infections.
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Affiliation(s)
- Yaru Huang
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, China.
- School of Life Sciences, Shanghai Normal University, China
| | - Zehang Gao
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, China.
| | - Cong Ma
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, China.
- School of Information Science and Technology, ShanghaiTech University, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, China
| | - Yimeng Sun
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, China
| | - Yuhang Huang
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, China.
- School of Life Sciences, Shanghai Normal University, China
| | - Chunping Jia
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, China
| | - Jianlong Zhao
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, China
- Xiangfu Laboratory, Jiaxing, Zhejiang 314102, China
| | - Shilun Feng
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, China
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3
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Sritong N, Sala de Medeiros M, Basing LA, Linnes JC. Promise and perils of paper-based point-of-care nucleic acid detection for endemic and pandemic pathogens. LAB ON A CHIP 2023; 23:888-912. [PMID: 36688463 PMCID: PMC10028599 DOI: 10.1039/d2lc00554a] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
From HIV and influenza to emerging pathogens like COVID-19, each new infectious disease outbreak has highlighted the need for massively-scalable testing that can be performed outside centralized laboratory settings at the point-of-care (POC) in order to prevent, track, and monitor endemic and pandemic threats. Nucleic acid amplification tests (NAATs) are highly sensitive and can be developed and scaled within weeks while protein-based rapid tests require months for production. Combining NAATs with paper-based detection platforms are promising due to the manufacturability, scalability, and simplicity of each of these components. Typically, paper-based NAATs consist of three sequential steps: sample collection and preparation, amplification of DNA or RNA from pathogens of interest, and detection. However, these exist within a larger ecosystem of sample collection and interpretation workflow, usability, and manufacturability which can be vastly perturbed during a pandemic emergence. This review aims to explore the challenges of paper-based NAATs covering sample-to-answer procedures along with three main types of clinical samples; blood, urine, and saliva, as well as broader operational, scale up, and regulatory aspects of device development and implementation. To fill the technological gaps in paper-based NAATs, a sample-in-result-out system that incorporates the integrated sample collection, sample preparation, and integrated internal amplification control while also balancing needs of users and manufacturability upfront in the early design process is required.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | | | - Laud Anthony Basing
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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4
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Kumar S, Kharb A, Vazirani A, Chauhan RS, Pramanik G, Sengupta M, Ghosh S. Nucleic acid extraction from complex biofluid using toothpick-actuated over-the-counter medical-grade cotton. Bioorg Med Chem 2022; 73:117009. [PMID: 36126446 DOI: 10.1016/j.bmc.2022.117009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022]
Abstract
Nucleic acid amplification technique (NAAT)-assisted detection is the primary intervention for pathogen molecular diagnostics. However, NAATs such as quantitative real-time polymerase chain reaction (qPCR) require prior purification or extraction of target nucleic acid from the sample of interest since the latter often contains polymerase inhibitors. Similarly, genetic disease screening is also reliant on the successful extraction of pure patient genomic DNA from the clinical sample. However, such extraction techniques traditionally utilize spin-column techniques that in turn require centralized high-speed centrifuges. This hinders any potential deployment of qPCR- or PCR-like NAAT methods in resource-constrained settings. The development of instrument-free nucleic acid extraction methods, especially those utilizing readily available materials would be of great interest and benefit to NAAT-mediated molecular diagnosis workflows in resource-constrained settings. In this report, we screened medical-grade cotton, a readily available over-the-counter biomaterial to extract genomic DNA (gDNA) spiked in 30 %, 45 %, and 60 % serum or cell lysate. The extraction was carried out in a completely instrument-free manner using cotton and a sterilized toothpick and was completed in 30 min (with using chaotropic salt) or 10 min (without using chaotropic salt). The quality of the extracted DNA was then probed using PCR followed by agarose gel analysis for preliminary validation of the study. The qPCR experiments then quantitatively established the extraction efficiency (0.3-27 %, depending on serum composition). Besides, percent similarity score obtained from the Sanger sequencing experiments probed the feasibility of extracted DNA towards polymerase amplification with fluorescent nucleotide incorporation. Overall, our method demonstrated that DNA extraction could be performed utilizing toothpick-mounted cotton both with or without using a chaotropic salt, albeit with a difference in the quality of the extracted DNA.
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Affiliation(s)
- Shrawan Kumar
- Department of Chemistry, Bennett University, India; Department of Biotechnology, Bennett University, India; Center of Excellence for Nanosensors and Nanomedicine, Bennett University, India
| | - Anjali Kharb
- Department of Biotechnology, Bennett University, India
| | - Aman Vazirani
- Department of Biotechnology, Bennett University, India
| | | | - Goutam Pramanik
- UGC-DAE CSR, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata 700 106, India
| | - Mrittika Sengupta
- Department of Biotechnology, Bennett University, India; Center of Excellence for Nanosensors and Nanomedicine, Bennett University, India
| | - Souradyuti Ghosh
- Department of Chemistry, Bennett University, India; Department of Biotechnology, Bennett University, India; Center of Excellence for Nanosensors and Nanomedicine, Bennett University, India; UGC-DAE CSR, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata 700 106, India.
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5
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Lee K, Tripathi A. An investigation into simplifying total RNA extraction with minimal equipment using a low volume, electrokinetically driven microfluidic protocol. BIOMICROFLUIDICS 2022; 16:044107. [PMID: 35992642 PMCID: PMC9385220 DOI: 10.1063/5.0096684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Current methods for total RNA extraction are time-consuming and require several hands-on steps and specialized equipment. Microfluidic devices can offer the opportunity to reduce the number of hands-on steps, decrease the volumes of reagents required for purification, and make extraction high throughput. Here, we investigated the translation of a high volume magnetic bead-based total RNA extraction method (from human whole blood) onto a low input volume microfluidic device. Our results first show that RNA integrity is maintained when the reagent volumes are scaled down by a factor of 22 and the wash buffers are combined 1:1. With our microfluidic method, the number of wash steps can be reduced from four to one. Thus, the time to complete RNA extraction can be reduced from 2 h to 40 min. These manipulations to the conventional protocol yielded RNA amplifiable within 40 cycles of reverse transcription quantitative PCR (RT-qPCR) when using the microfluidic device to simplify the wash steps. To improve the purification of the RNA during the bead transport through the microchannel, we also investigated the effect of a synergetic application of the electrokinetic flow. Our results show that DNase I and other contaminants surrounding the beads get washed away more effectively via electrophoretic transport. Most notably, RNA adsorption on the beads is strong enough to counter electrophoretically-driven desorption. In all, our work opens new ways to extract high-quality total RNA rapidly and simply from a small quantity of blood, making the process of RNA extraction more accessible.
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Affiliation(s)
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island 02912, USA
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6
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Zamani M, Furst AL, Klapperich CM. Strategies for Engineering Affordable Technologies for Point-of-Care Diagnostics of Infectious Diseases. Acc Chem Res 2021; 54:3772-3779. [PMID: 34612619 PMCID: PMC8996141 DOI: 10.1021/acs.accounts.1c00434] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Disease prevalence is highest in low-resource settings (LRS) due to the lack of funds, infrastructure, and personnel required to carry out laboratory-based molecular tests. In high-resource settings, gold-standard molecular tests for diseases consist of nucleic acid amplification tests (NAATs) due to their excellent sensitivity and specificity. These tests require the extraction, amplification, and detection of nucleic acids from clinical samples. In high-resource settings, all three of these steps require highly specialized, costly, and onerous equipment that cannot be used in LRS. Nucleic acid extraction involves multiple centrifugation steps. Amplification consists of the polymerase chain reaction (PCR), which requires thermal cyclers. The detection of amplified DNA is typically done with specialized thermal cyclers that are capable of fluorescence detection. Traditional methods used to extract, amplify, and detect nucleic acids cannot be used outside of a laboratory in LRS. Thus, there is a need for affordable point-of-care devices to ease the high burden of disease in LRS.The past decade of work on paper-based fluidic devices has resulted in the invention of many paper-based biosensors for disease detection as well as isothermal amplification techniques that replace PCR. However, a challenge still remains in detecting pathogenic biomarkers from complex human samples without specialized laboratory equipment. Our research has focused on the development of affordable technologies to extract and detect nucleic acids in clinical samples with minimal equipment. Here we describe methods for the paper-based extraction, amplification, and detection of nucleic acids. This Account provides an overview of our latest technologies developed to detect an array of diseases in low-resource settings. We focus on detecting nucleic acids of H1N1, human papillomavirus (HPV), Neisseria gonorrheae (NG), Chlamydia trachomatis (CT), Trichomonas vaginalis (TV), and malaria from a variety of clinical sample types. H1N1 RNA was extracted from nasopharyngeal swabs; HPV, NG, and CT DNA were extracted from either cervical, urethral, or vaginal swabs; TV DNA was extracted from urine; and malaria DNA was extracted from whole blood. Different sample types necessitate different nucleic extraction protocols; we provide guidelines for assay design based on the clinical sample type used. We compare the pros and cons of different isothermal amplification techniques, namely, helicase-dependent amplification (HDA), loop-mediated isothermal amplification (LAMP), and a novel isothermal amplification technique that we developed: isothermal-identical multirepeat sequences (iso-IMRS). Finally, we compare various detection mechanisms, including lateral-flow and electrochemical readouts. Electrochemical readouts frequently employ gold electrodes due to strong gold-thiol coupling. However, the high cost of gold precludes their use in LRS. We discuss our development of novel gold leaf electrodes that can be made without specialized equipment for a fraction of the cost of commercially available gold electrodes.
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Affiliation(s)
- Marjon Zamani
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ariel L Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Catherine M Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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7
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Nichols ZE, Geddes CD. Sample Preparation and Diagnostic Methods for a Variety of Settings: A Comprehensive Review. Molecules 2021; 26:5666. [PMID: 34577137 PMCID: PMC8470389 DOI: 10.3390/molecules26185666] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Sample preparation is an essential step for nearly every type of biochemical analysis in use today. Among the most important of these analyses is the diagnosis of diseases, since their treatment may rely greatly on time and, in the case of infectious diseases, containing their spread within a population to prevent outbreaks. To address this, many different methods have been developed for use in the wide variety of settings for which they are needed. In this work, we have reviewed the literature and report on a broad range of methods that have been developed in recent years and their applications to point-of-care (POC), high-throughput screening, and low-resource and traditional clinical settings for diagnosis, including some of those that were developed in response to the coronavirus disease 2019 (COVID-19) pandemic. In addition to covering alternative approaches and improvements to traditional sample preparation techniques such as extractions and separations, techniques that have been developed with focuses on integration with smart devices, laboratory automation, and biosensors are also discussed.
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Affiliation(s)
- Zach E. Nichols
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD 21250, USA;
- Institute of Fluorescence, University of Maryland, Baltimore County, 701 E Pratt Street, Baltimore, MD 21270, USA
| | - Chris D. Geddes
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD 21250, USA;
- Institute of Fluorescence, University of Maryland, Baltimore County, 701 E Pratt Street, Baltimore, MD 21270, USA
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8
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Tai WC, Chang YC, Chou D, Fu LM. Lab-on-Paper Devices for Diagnosis of Human Diseases Using Urine Samples-A Review. BIOSENSORS 2021; 11:260. [PMID: 34436062 PMCID: PMC8393526 DOI: 10.3390/bios11080260] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 12/23/2022]
Abstract
In recent years, microfluidic lab-on-paper devices have emerged as a rapid and low-cost alternative to traditional laboratory tests. Additionally, they were widely considered as a promising solution for point-of-care testing (POCT) at home or regions that lack medical infrastructure and resources. This review describes important advances in microfluidic lab-on-paper diagnostics for human health monitoring and disease diagnosis over the past five years. The review commenced by explaining the choice of paper, fabrication methods, and detection techniques to realize microfluidic lab-on-paper devices. Then, the sample pretreatment procedure used to improve the detection performance of lab-on-paper devices was introduced. Furthermore, an in-depth review of lab-on-paper devices for disease measurement based on an analysis of urine samples was presented. The review concludes with the potential challenges that the future development of commercial microfluidic lab-on-paper platforms for human disease detection would face.
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Affiliation(s)
- Wei-Chun Tai
- Department of Oral and Maxillofacial Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan;
| | - Yu-Chi Chang
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan;
| | - Dean Chou
- Department of Biomedical Engineering, National Cheng Kung University, Tainan 701, Taiwan;
| | - Lung-Ming Fu
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan;
- Graduate Institute of Materials Engineering, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
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9
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Mancuso CP, Lu ZX, Qian J, Boswell SA, Springer M. A Semi-Quantitative Isothermal Diagnostic Assay Utilizing Competitive Amplification. Anal Chem 2021; 93:9541-9548. [PMID: 34180655 PMCID: PMC9837715 DOI: 10.1021/acs.analchem.1c01576] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Quantitative diagnostics that are rapid, inexpensive, sensitive, robust, and field-deployable are needed to contain the spread of infectious diseases and inform treatment strategies. While current gold-standard techniques are highly sensitive and quantitative, they are slow and require expensive equipment. Conversely, current rapid field-deployable assays available provide essentially binary information about the presence of the target analyte, not a quantitative measure of concentration. Here, we report the development of a molecular diagnostic test [quantitative recombinase polymerase amplification (qRPA)] that utilizes competitive amplification during a recombinase polymerase amplification (RPA) assay to provide semi-quantitative information on a target nucleic acid. We demonstrate that qRPA can quantify DNA, RNA, and viral titers in HIV and COVID-19 patient samples and that it is more robust to environmental perturbations than traditional RPA. These features make qRPA potentially useful for at-home testing to monitor the progress of viral infections or other diseases.
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Affiliation(s)
| | | | | | - Sarah A. Boswell
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States,Massachusetts Consortium on Pathogen Readiness, Boston, Massachusetts 20115, United States
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10
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Newsham E, Richards-Kortum R. CRISPR-Based Electrochemical Sensor Permits Sensitive and Specific Viral Detection in Low-Resource Settings. ACS CENTRAL SCIENCE 2021; 7:926-928. [PMID: 34235253 PMCID: PMC8227593 DOI: 10.1021/acscentsci.1c00555] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Emilie Newsham
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Rebecca Richards-Kortum
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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11
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Zamani M, Robson JM, Fan A, Bono MS, Furst AL, Klapperich CM. Electrochemical Strategy for Low-Cost Viral Detection. ACS CENTRAL SCIENCE 2021; 7:963-972. [PMID: 34235257 PMCID: PMC8227598 DOI: 10.1021/acscentsci.1c00186] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 05/08/2023]
Abstract
Sexually transmitted infections, including the human immunodeficiency virus (HIV) and the human papillomavirus (HPV), disproportionally impact those in low-resource settings. Early diagnosis is essential for managing HIV. Similarly, HPV causes nearly all cases of cervical cancer, the majority (90%) of which occur in low-resource settings. Importantly, infection with HPV is six times more likely to progress to cervical cancer in women who are HIV-positive. An inexpensive, adaptable point-of-care test for viral infections would make screening for these viruses more accessible to a broader set of the population. Here, we report a novel, cost-effective electrochemical platform using gold leaf electrodes to detect clinically relevant viral loads. We have combined this platform with loop-mediated isothermal amplification and a CRISPR-based recognition assay to detect HPV. Lower limits of detection were demonstrated down to 104 total copies of input nucleic acids, which is a clinically relevant viral load for HPV DNA. Further, proof-of-concept experiments with cervical swab samples, extracted using standard extraction protocols, demonstrated that the strategy is extendable to complex human samples. This adaptable technology could be applied to detect any viral infection rapidly and cost-effectively.
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Affiliation(s)
- Marjon Zamani
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - James M. Robson
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Andy Fan
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Michael S. Bono
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Ariel L. Furst
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- (A.L.F.)
| | - Catherine M. Klapperich
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- (C.M.K.)
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12
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Jeong S, González-Grandío E, Navarro N, Pinals RL, Ledesma F, Yang D, Landry MP. Extraction of Viral Nucleic Acids with Carbon Nanotubes Increases SARS-CoV-2 Quantitative Reverse Transcription Polymerase Chain Reaction Detection Sensitivity. ACS NANO 2021; 15:10309-10317. [PMID: 34105936 PMCID: PMC8204751 DOI: 10.1021/acsnano.1c02494] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/04/2021] [Indexed: 05/25/2023]
Abstract
The global SARS-CoV-2 coronavirus pandemic has led to a surging demand for rapid and efficient viral infection diagnostic tests, generating a supply shortage in diagnostic test consumables including nucleic acid extraction kits. Here, we develop a modular method for high-yield extraction of viral single-stranded nucleic acids by using "capture" ssDNA sequences attached to carbon nanotubes. Target SARS-CoV-2 viral RNA can be captured by ssDNA-nanotube constructs via hybridization and separated from the liquid phase in a single-tube system with minimal chemical reagents, for downstream quantitative reverse transcription polymerase chain reaction (RT-qPCR) detection. This nanotube-based extraction method enables 100% extraction yield of target SARS-CoV-2 RNA from phosphate-buffered saline in comparison to ∼20% extraction yield when using a commercial silica-column kit. Notably, carbon nanotubes enable extraction of nucleic acids directly from 50% human saliva with a similar efficiency as achieved with commercial DNA/RNA extraction kits, thereby bypassing the need for further biofluid purification and avoiding the use of commercial extraction kits. Carbon nanotube-based extraction of viral nucleic acids facilitates high-yield and high-sensitivity identification of viral nucleic acids such as the SARS-CoV-2 viral genome with a reduced reliance on reagents affected by supply chain obstacles.
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Affiliation(s)
- Sanghwa Jeong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Eduardo González-Grandío
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Nicole Navarro
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Rebecca L Pinals
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Francis Ledesma
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Darwin Yang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute (IGI), Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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13
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Obino D, Vassalli M, Franceschi A, Alessandrini A, Facci P, Viti F. An Overview on Microfluidic Systems for Nucleic Acids Extraction from Human Raw Samples. SENSORS 2021; 21:s21093058. [PMID: 33925730 PMCID: PMC8125272 DOI: 10.3390/s21093058] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 02/08/2023]
Abstract
Nucleic acid (NA) extraction is a basic step for genetic analysis, from scientific research to diagnostic and forensic applications. It aims at preparing samples for its application with biomolecular technologies such as isothermal and non-isothermal amplification, hybridization, electrophoresis, Sanger sequencing and next-generation sequencing. Multiple steps are involved in NA collection from raw samples, including cell separation from the rest of the specimen, cell lysis, NA isolation and release. Typically, this process needs molecular biology facilities, specialized instrumentation and labor-intensive operations. Microfluidic devices have been developed to analyze NA samples with high efficacy and sensitivity. In this context, the integration within the chip of the sample preparation phase is crucial to leverage the promise of portable, fast, user-friendly and economic point-of-care solutions. This review presents an overview of existing lab-on-a-chip (LOC) solutions designed to provide automated NA extraction from human raw biological fluids, such as whole blood, excreta (urine and feces), saliva. It mainly focuses on LOC implementation aspects, aiming to describe a detailed panorama of strategies implemented for different human raw sample preparations.
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Affiliation(s)
- Daniele Obino
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
| | - Massimo Vassalli
- Centre for the Cellular Microenvironment, James Watt School of Engineering, University of Glasgow, James Watt South Building, Glasgow G128LT, UK;
| | | | - Andrea Alessandrini
- Nanoscience Institute, National Research Council, 41125 Modena, Italy;
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Paolo Facci
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
- Correspondence:
| | - Federica Viti
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
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14
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Lee WC, Ng HY, Hou CY, Lee CT, Fu LM. Recent advances in lab-on-paper diagnostic devices using blood samples. LAB ON A CHIP 2021; 21:1433-1453. [PMID: 33881033 DOI: 10.1039/d0lc01304h] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lab-on-paper, or microfluidic paper-based analytical devices (μPADs), use paper as a substrate material, and are patterned with a system of microchannels, reaction zones and sensing elements to perform analysis and detection. The sample transfer in such devices is performed by capillary action. As a result, external driving forces are not required, and hence the size and cost of the device are significantly reduced. Lab-on-paper devices have thus attracted significant attention for point-of-care medical diagnostic purposes in recent years, particularly in less-developed regions of the world lacking medical resources and infrastructures. This review discusses the major advances in lab-on-paper technology for blood analysis and diagnosis in the past five years. The review focuses particularly on the many clinical applications of lab-on-paper devices, including diabetes diagnosis, acute myocardial infarction (AMI) detection, kidney function diagnosis, liver function diagnosis, cholesterol and triglyceride (TG) analysis, sickle-cell disease (SCD) and phenylketonuria (PKU) analysis, virus analysis, C-reactive protein (CRP) analysis, blood ion analysis, cancer factor analysis, and drug analysis. The review commences by introducing the basic transmission principles, fabrication methods, structural characteristics, detection techniques, and sample pretreatment process of modern lab-on-paper devices. A comprehensive review of the most recent applications of lab-on-paper devices to the diagnosis of common human diseases using blood samples is then presented. The review concludes with a brief summary of the main challenges and opportunities facing the lab-on-paper technology field in the coming years.
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Affiliation(s)
- Wen-Chin Lee
- Division of Nephrology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, 833, Taiwan.
| | - Hwee-Yeong Ng
- Division of Nephrology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, 833, Taiwan.
| | - Chih-Yao Hou
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung 811, Taiwan
| | - Chien-Te Lee
- Division of Nephrology, Kaohsiung Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, 833, Taiwan.
| | - Lung-Ming Fu
- Department of Engineering Science, National Cheng Kung University, Tainan, 701, Taiwan.
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15
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Kolluri N, Kamath S, Lally P, Zanna M, Galagan J, Gitaka J, Kamita M, Cabodi M, Lolabattu SR, Klapperich CM. Development and Clinical Validation of Iso-IMRS: A Novel Diagnostic Assay for P. falciparum Malaria. Anal Chem 2021; 93:2097-2105. [PMID: 33464825 PMCID: PMC7859932 DOI: 10.1021/acs.analchem.0c03847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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In many countries
targeting malaria elimination, persistent malaria
infections can have parasite loads significantly below the lower limit
of detection (LLOD) of standard diagnostic techniques, making them
difficult to identify and treat. The most sensitive diagnostic methods
involve amplification and detection of Plasmodium DNA by polymerase chain reaction (PCR), which requires expensive
thermal cycling equipment and is difficult to deploy in resource-limited
settings. Isothermal DNA amplification assays have been developed,
but they require
complex primer design, resulting in high nonspecific amplification,
and show a decrease in sensitivity than PCR methods. Here, we have
used a computational approach to design a novel isothermal amplification
assay with a simple primer design to amplify P. falciparum DNA with analytical sensitivity comparable to PCR. We have identified
short DNA sequences repeated throughout the parasite genome to be
used as primers for DNA amplification and demonstrated that these
primers can be used, without modification, to isothermally amplify P. falciparum parasite DNA via strand displacement
amplification. Our novel assay shows a LLOD of ∼1 parasite/μL
within a 30 min amplification time. The assay was demonstrated with
clinical samples using patient blood and saliva. We further characterized
the assay using direct amplicon next-generation sequencing and modified
the assay to work with a visual readout. The technique developed here
achieves similar analytical sensitivity to current gold standard PCR
assays requiring a fraction of time and resources for PCR. This highly
sensitive isothermal assay can be more easily adapted to field settings,
making it a potentially useful tool for malaria elimination.
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Affiliation(s)
- Nikunja Kolluri
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Shwetha Kamath
- Division of Research and Development, Jigsaw Bio Solutions Private Limited, No. 87, 4th Floor, Mundhra Chambers, 22nd Main, Banashankari 2nd Stage, Bangalore 560070, Karnataka, India
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Mina Zanna
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - James Galagan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, General Kago Road, P.O. Box 342, Thika 01000, Kenya
| | - Moses Kamita
- Directorate of Research and Innovation, Mount Kenya University, General Kago Road, P.O. Box 342, Thika 01000, Kenya
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
| | - Srinivasa Raju Lolabattu
- Division of Research and Development, Jigsaw Bio Solutions Private Limited, No. 87, 4th Floor, Mundhra Chambers, 22nd Main, Banashankari 2nd Stage, Bangalore 560070, Karnataka, India
| | - Catherine M Klapperich
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Room 702, Boston, Massachusetts 02215, United States
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