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Biosensors
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Application of CRISPR Cas Systems for Biosensing
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Application of CRISPR Cas Systems for Biosensing

A special issue of Biosensors (ISSN 2079-6374). This special issue belongs to the section "Biosensor and Bioelectronic Devices".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 34374

Special Issue Editors

Prof. Dr. Chung-Chiun Liu

E-Mail Website
Guest Editor
Department of Chemical and Biomolecular Engineering and Electronics Design Center, Case Western Reserve University, Cleveland, OH 44106, USA
Interests: electrochemical-based chemical and bio-sensors; microfabrication technology; nano-catalysts and sensing meterials; CRISPR-related biosensing strategy; bio-conjugation technology
Special Issues, Collections and Topics in MDPI journals
Dr. Yifan Dai

E-Mail Website
Guest Editor
Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
Interests: DNA biotechnology; electrochemical biosensing strategies

Special Issue Information

Dear Colleagues,

We are announcing a Special Issue on “Application of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Cas Systems for Biosensing”. CRISPR, a powerful gene-editing tool, has demonstrated its capability as a powerful recognition element in biosensing. Owing to the high specificity and modularity of CRISPR Cas systems, CRISPR-based biosensing systems have shown promising accuracy and sensitivity for the detection of nucleic acids. The utilization of CRISPR for both electrochemical biosensors and optical biosensors highlights the importance of multi-disciplinary contributions to sensing science as an imminent biosensing area. For this Special Issue, we invite research with different modalities to describe different perspectives on CRISPR-based biosensing systems. Specifically, the following issues are of scientific interest to this Special Issue: the methods of integrating CRISPR into various biosensing systems; the role of CRISPR Cas systems in the design of biosensing strategies; and the difference between conventional nucleic acid probe-based recognition elements and CRISPR-based recognition elements. Contributed manuscripts will be peer-reviewed by well-qualified reviewers, and a rapid decision on the status of the manuscript will be made by the Editorial Board of Biosensors based on the results of the review.

We invite you to submit your manuscript(s) to this Special Issue on the Application of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Cas Systems for Biosensing. The deadline for submission to this Special Issue is December 31, 2020.

Prof. Dr. Chung Chiun Liu
Dr. Yifan Dai
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biosensors is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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Published Papers (7 papers)

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Editorial

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2 pages, 184 KiB  
Editorial
Application of CRISPR Cas Systems for Biosensing
by Chung Chiun Liu and Yifan Dai
Biosensors 2023, 13(7), 672; https://doi.org/10.3390/bios13070672 - 23 Jun 2023
Viewed by 1487
Abstract
The essential properties of a biosensor are its sensitivity and selectivity to detect, monitor and quantify the biomarker(s) for the interests of medicine [...] Full article
(This article belongs to the Special Issue Application of CRISPR Cas Systems for Biosensing)

Research

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13 pages, 2399 KiB  
Article
A Gene Circuit Combining the Endogenous I-E Type CRISPR-Cas System and a Light Sensor to Produce Poly-β-Hydroxybutyric Acid Efficiently
by Xiaomeng Li, Wei Jiang, Qingsheng Qi and Quanfeng Liang
Biosensors 2022, 12(8), 642; https://doi.org/10.3390/bios12080642 - 15 Aug 2022
Cited by 5 | Viewed by 2357
Abstract
‘Metabolic burden,’ which arises when introducing exogenic synthesizing pathways into a host strain, remains a challenging issue in metabolic engineering. Redirecting metabolic flux from cell growth to product synthesis at an appropriate culture timepoint is ideal for resolving this issue. In this report, [...] Read more.
‘Metabolic burden,’ which arises when introducing exogenic synthesizing pathways into a host strain, remains a challenging issue in metabolic engineering. Redirecting metabolic flux from cell growth to product synthesis at an appropriate culture timepoint is ideal for resolving this issue. In this report, we introduce optogenetics—which is capable of precise temporal and spatial control—as a genetic switch, accompanied by the endogenous type I-E CRISPRi system in Escherichia coli (E. coli) to generate a metabolic platform that redirects metabolic flux. Poly-β-hydroxybutyric acid (PHB) production was taken as an example to demonstrate the performance of this platform. A two-to-three-fold increase in PHB content was observed under green light when compared with the production of PHB under red light, confirming the regulatory activity of this platform and its potential to redirect metabolic flux to synthesize target products. Full article
(This article belongs to the Special Issue Application of CRISPR Cas Systems for Biosensing)
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10 pages, 1776 KiB  
Article
Cas14a1-Mediated Nucleic Acid Diagnostics for Spinal Muscular Atrophy
by Zhiqing Hu, Miaomiao Chen, Chunhua Zhang, Zhuo Li, Mai Feng, Lingqian Wu, Miaojin Zhou and Desheng Liang
Biosensors 2022, 12(5), 268; https://doi.org/10.3390/bios12050268 - 23 Apr 2022
Cited by 3 | Viewed by 3258
Abstract
Spinal muscular atrophy (SMA) is the main genetic cause of infant death. In >95% of the patients with SMA, the disease is caused by a single hotspot pathogenic mutation: homozygous deletion of exon 7 of the survival motor neuron 1 gene (SMN1 [...] Read more.
Spinal muscular atrophy (SMA) is the main genetic cause of infant death. In >95% of the patients with SMA, the disease is caused by a single hotspot pathogenic mutation: homozygous deletion of exon 7 of the survival motor neuron 1 gene (SMN1). Recently, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein (Cas)-based assays have been developed as a promising new option for nucleic acid detection. Here, we developed a Cas14a1-based assay combined with asymmetric PCR to establish a method for detection of the homozygous deletion of SMN1 exon 7 in SMA patients. The minimum detectable concentration of genomic DNA reached 5.26 aM with our method, and the assessment of its detection performance in 33 clinical samples revealed that the results were completely consistent with those of multiple ligation-dependent probe amplification and quantitative PCR. Thus, our novel nucleic acid diagnostics combining CRISPR/Cas14a1 and asymmetric PCR not only provides specific and sensitive testing of the deletion of SMN1 exon 7, but also holds promise for an accurate detection platform of genetic diseases and pathogens in multiple sample types. Full article
(This article belongs to the Special Issue Application of CRISPR Cas Systems for Biosensing)
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13 pages, 2587 KiB  
Article
CRISPR/Cas12a-Based Ultrasensitive and Rapid Detection of JAK2 V617F Somatic Mutation in Myeloproliferative Neoplasms
by Miaomiao Chen, Chunhua Zhang, Zhiqing Hu, Zhuo Li, Menglin Li, Lingqian Wu, Miaojin Zhou and Desheng Liang
Biosensors 2021, 11(8), 247; https://doi.org/10.3390/bios11080247 - 24 Jul 2021
Cited by 11 | Viewed by 7472
Abstract
The JAK2 V617F mutation is a major diagnostic, therapeutic, and monitoring molecular target of Philadelphia-negative myeloproliferative neoplasms (MPNs). To date, numerous methods of detecting the JAK2 V617F mutation have been reported, but there is no gold-standard diagnostic method for clinical applications. Here, [...] Read more.
The JAK2 V617F mutation is a major diagnostic, therapeutic, and monitoring molecular target of Philadelphia-negative myeloproliferative neoplasms (MPNs). To date, numerous methods of detecting the JAK2 V617F mutation have been reported, but there is no gold-standard diagnostic method for clinical applications. Here, we developed and validated an efficient Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR associated protein 12a (Cas12a)-based assay to detect the JAK2 V617F mutation. Our results showed that the sensitivity of the JAK2 V617F/Cas12a fluorescence detection system was as high as 0.01%, and the JAK2 V617F/Cas12a lateral flow strip assay could unambiguously detect as low as 0.5% of the JAK2 V617F mutation, which was much higher than the sensitivity required for clinical application. The minimum detectable concentration of genomic DNA achieved was 0.01 ng/μL (~5 aM, ~3 copies/μL). In addition, the whole process only took about 1.5 h, and the cost of an individual test was much lower than that of the current assays. Thus, our methods can be applied to detect the JAK2 V617F mutation, and they are highly sensitive, rapid, cost-effective, and convenient. Full article
(This article belongs to the Special Issue Application of CRISPR Cas Systems for Biosensing)
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11 pages, 2166 KiB  
Article
Cas12a and Lateral Flow Strip-Based Test for Rapid and Ultrasensitive Detection of Spinal Muscular Atrophy
by Chunhua Zhang, Zhuo Li, Miaomiao Chen, Zhiqing Hu, Lingqian Wu, Miaojin Zhou and Desheng Liang
Biosensors 2021, 11(5), 154; https://doi.org/10.3390/bios11050154 - 14 May 2021
Cited by 9 | Viewed by 6340
Abstract
Spinal muscular atrophy (SMA) is characterized by severe lethality and irreversible progression. Early diagnosis of SMA is of more practical significance with the emergence of effective therapy. However, existing techniques to identify SMA patients rely on cumbersome instruments, hindering their accessibility and application. [...] Read more.
Spinal muscular atrophy (SMA) is characterized by severe lethality and irreversible progression. Early diagnosis of SMA is of more practical significance with the emergence of effective therapy. However, existing techniques to identify SMA patients rely on cumbersome instruments, hindering their accessibility and application. An SMA-Cas12a-strip assay was developed with the integration of Cas12a-based nucleic acid detection, isothermal amplification, and lateral flow strip. The analytical performance of the assay was assessed with clinical samples. To explore its extensible utility, various specimens were tested. Validated with 168 clinical samples, the sensitivity and specificity of the SMA-Cas12a-strip assay were both 100%. The minimum detectable concentration of genomic DNA containing the target gene achieved 526 aM. The assay was compatible with specimens from several sources, and the turnaround time could be within 1.5 h. We developed a simple, cost-effective, and highly sensitive and specific assay to detect SMA patients. With little and field-portable equipment, the assay holds great promise in the detection of SMA patients, particularly in low-resource regions. Full article
(This article belongs to the Special Issue Application of CRISPR Cas Systems for Biosensing)
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12 pages, 2158 KiB  
Communication
Detection of CRISPR-Cas9-Mediated Mutations Using a Carbon Nanotube-Modified Electrochemical Genosensor
by Ezgi Kivrak, Tekle Pauzaite, Nikki A. Copeland, John G. Hardy, Pinar Kara, Melike Firlak, Atike I. Yardimci, Selahattin Yilmaz, Fahreddin Palaz and Mehmet Ozsoz
Biosensors 2021, 11(1), 17; https://doi.org/10.3390/bios11010017 - 8 Jan 2021
Cited by 10 | Viewed by 6538
Abstract
The CRISPR-Cas9 system has facilitated the genetic modification of various model organisms and cell lines. The outcomes of any CRISPR-Cas9 assay should be investigated to ensure/improve the precision of genome engineering. In this study, carbon nanotube-modified disposable pencil graphite electrodes (CNT/PGEs) were used [...] Read more.
The CRISPR-Cas9 system has facilitated the genetic modification of various model organisms and cell lines. The outcomes of any CRISPR-Cas9 assay should be investigated to ensure/improve the precision of genome engineering. In this study, carbon nanotube-modified disposable pencil graphite electrodes (CNT/PGEs) were used to develop a label-free electrochemical nanogenosensor for the detection of point mutations generated in the genome by using the CRISPR-Cas9 system. Carbodiimide chemistry was used to immobilize the 5′-aminohexyl-linked inosine-substituted probe on the surface of the sensor. After hybridization between the target sequence and probe at the sensor surface, guanine oxidation signals were monitored using differential pulse voltammetry (DPV). Optimization of the sensitivity of the nanogenoassay resulted in a lower detection limit of 213.7 nM. The nanogenosensor was highly specific for the detection of the precisely edited DNA sequence. This method allows for a rapid and easy investigation of the products of CRISPR-based gene editing and can be further developed to an array system for multiplex detection of different-gene editing outcomes. Full article
(This article belongs to the Special Issue Application of CRISPR Cas Systems for Biosensing)
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Review

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15 pages, 1189 KiB  
Review
How to Find the Right RNA-Sensing CRISPR-Cas System for an In Vitro Application
by Escarlet Díaz-Galicia, Raik Grünberg and Stefan T. Arold
Biosensors 2022, 12(2), 53; https://doi.org/10.3390/bios12020053 - 19 Jan 2022
Cited by 8 | Viewed by 4890
Abstract
CRISPR-Cas systems have a great and still largely untapped potential for in vitro applications, in particular, for RNA biosensing. However, there is currently no systematic guide on selecting the most appropriate RNA-targeting CRISPR-Cas system for a given application among thousands of potential candidates. [...] Read more.
CRISPR-Cas systems have a great and still largely untapped potential for in vitro applications, in particular, for RNA biosensing. However, there is currently no systematic guide on selecting the most appropriate RNA-targeting CRISPR-Cas system for a given application among thousands of potential candidates. We provide an overview of the currently described Cas effector systems and review existing Cas-based RNA detection methods. We then propose a set of systematic selection criteria for selecting CRISPR-Cas candidates for new applications. Using this approach, we identify four candidates for in vitro RNA. Full article
(This article belongs to the Special Issue Application of CRISPR Cas Systems for Biosensing)
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