Review
Chemistry, Physical
Weiran Su, Junru Li, Chen Ji, Congshuo Chen, Yuzheng Wang, Huili Dai, Fengqin Li, Peifeng Liu
Summary: CRISPR/Cas systems are powerful tools for disease biomarkers detection, capable of detecting nucleic acid and non-nucleic acid targets. This review summarizes the principles and characteristics of various CRISPR/Cas systems, and introduces the applications of CRISPR/Cas systems in detecting nucleic and non-nucleic acid targets. The prospects and challenges of their applications in biosensing are also discussed.
Review
Biophysics
Xinkuan Cheng, Yaru Li, Jun Kou, Dan Liao, Wenlu Zhang, Lijuan Yin, Shuli Man, Long Ma
Summary: CRISPR/Cas tools have shown great potential in biosensing beyond gene editing. However, the application of CRISPR/Cas-based biosensors for non-nucleic acid targets is still in its early stages. This review summarizes the strategies and prospects of CRISPR/Cas toolboxes in recognizing non-nucleic acid targets, providing valuable information for the expansion of these powerful tools into multiple detection fields.
BIOSENSORS & BIOELECTRONICS
(2022)
Review
Chemistry, Analytical
Yuxin Zhang, Yunping Wu, Yanfang Wu, Yangyang Chang, Meng Liu
Summary: The increasing demand for developing biosensors in various fields poses challenges on sensor performance requirements such as sensitivity, selectivity, and operating costs. CRISPR-Cas systems, known as molecular scissors, are highly accurate in cleaving specific DNA and RNA sequences, and recent studies have shown the establishment of versatile biosensing platforms based on CRISPR-Cas. The review introduces the general characteristics and mechanisms of class II CRISPR-Cas systems, highlighting their biosensing strategies for detecting a wide range of nucleic acid and non-nucleic acid analytes.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Review
Chemistry, Analytical
Siyu Chen, Bo Gong, Cong Zhu, Chunyang Lei, Zhou Nie
Summary: Nucleic acid molecules possess attractive properties for biosensing and bioimaging due to their high designability and structural predictability. CRISPR-Cas systems, with high programmability and flexibility, recognize and cleave nucleic acid targets and have been engineered as multifunctional tools. Integration of nucleic acids with CRISPR-Cas systems has advanced biosensing and bioimaging methodologies, holding great promise in biochemical research and clinical diagnosis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Pooja Bhardwaj, Rajni Kant, Sthita Pragnya Behera, Gaurav Raj Dwivedi, Rajeev Singh
Summary: This article emphasizes the importance of CRISPR/Cas technology as a diagnostic tool for early management, diagnosis, and treatment of infections and diseases, and explores its detection capabilities for non-nucleic acid targets as well as the technical challenges and improvements in clinical assessment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Noor Mohammad, Logan Talton, Zach Hetzler, Megha Gongireddy, Qingshan Wei
Summary: In this study, researchers discovered that CRISPR-Cas12a can induce nonspecific trans-cleavage of dsDNA substrate, and the location of the overhang on the substrate affects its susceptibility to trans-activated Cas12a. They attributed this preference to the directional trans-cleavage behavior of Cas12a. They also used this finding to design a hybrid DNA reporter for a sensitive CRISPR-Cas12a detection platform.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Food Science & Technology
Yunhao Lu, Hao Yang, Jinrong Bai, Qiang He, Ruijie Deng
Summary: Foodborne pathogenic infections have caused various problems in human life, and there is a need for advanced detection technologies. CRISPR/Cas-based biosensors have the potential to address the challenges of conventional assays such as insensitivity, long turnaround time, and complex pretreatments. This review focuses on the strategies of CRISPR/Cas-assisted diagnostics for foodborne pathogens, specifically discussing biosensing platforms based on fluorescence, colorimetric, (electro)chemiluminescence, electrochemical, and surface-enhanced Raman scattering detection. The review summarizes the detection principles for foodborne pathogenic bacteria, fungi, and viruses. The current challenges and technical barriers of these methods in broad application are also discussed, along with alternative solutions to improve the potential of CRISPR/Cas for food safety.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Review
Biochemistry & Molecular Biology
Shuo Huang, Rui Dai, Zhiqi Zhang, Han Zhang, Meng Zhang, Zhangjun Li, Kangrui Zhao, Wenjun Xiong, Siyu Cheng, Buhua Wang, Yi Wan
Summary: CRISPR/Cas systems are widely used in gene editing due to their accuracy, programmability, ease of use, and affordability. Additionally, they have been applied in live-cell imaging and bioanalysis, expanding the scope of their use beyond gene editing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Chemistry, Multidisciplinary
Weihong Yin, Jianjian Zhuang, Jiale Li, Liping Xia, Kai Hu, Juxin Yin, Ying Mu
Summary: Digital nucleic acid detection based on microfluidics technology provides a powerful tool for isothermal amplification technologies such as RPA, LAMP, and CRISPR-Cas assisted methods. This technology has low equipment requirements and simple operations, making it widely applicable in clinical and in vitro diagnosis.
Article
Biochemical Research Methods
Matthew S. Verosloff, Sarah J. Shapiro, Elizabeth M. Hawkins, Emel Alpay, Deepika Verma, Emma G. Stanfield, Lior Kreindler, Sonal Jain, Bridget McKay, Shae A. Hubbell, Carley G. Hendriks, Benjamin A. Blizard, James P. Broughton, Janice S. Chen
Summary: The programmable nature of CRISPR-Cas nucleases has led to new methods for molecular diagnostics. Emerging from the intersection of CRISPR biology and engineering, CRISPR-based diagnostics offer timely, accurate, and actionable solutions across a wide range of testing applications.
BIOTECHNOLOGY JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Joon Soo Park, Kuangwen Hsieh, Liben Chen, Aniruddha Kaushik, Alexander Y. Trick, Tza-Huei Wang
Summary: The digital-enhanced CRISPR/Cas-assisted one-pot virus detection (deCOViD) is a novel assay that allows qualitative and quantitative detection of SARS-CoV-2 in a very short time with high sensitivity and a broad dynamic range. It outperforms current benchtop-based counterparts and represents one of the fastest and most sensitive CRISPR/Cas-assisted SARS-CoV-2 detection methods to date.
Review
Biochemical Research Methods
Mingzhu Yuan, Ronghua Ding, Shuaiyin Chen, Guangcai Duan
Summary: The CRISPR/Cas system provides a rapid and accurate nucleic acid detection method for on-site POCT, with features such as short detection cycles, low cost, and high sensitivity, which are crucial in interrupting outbreaks of infectious diseases.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Luoxi Li, Guanwang Shen, Min Wu, Jianxin Jiang, Qingyou Xia, Ping Lin
Summary: This article discusses the application of CRISPR-Cas technology in the field of molecular diagnostics and emphasizes the revolutionary advancements it brings.
TRENDS IN BIOTECHNOLOGY
(2022)
Review
Food Science & Technology
Jiali Qiao, Zhiying Zhao, Yaru Li, Minghui Lu, Shuli Man, Shengying Ye, Qiang Zhang, Long Ma
Summary: Food safety issues are of utmost importance in public health worldwide, and the development of rapid and effective detection methods is crucial. Nucleic acid isothermal amplification (NAIA) plays a significant role in food safety detection, and the integration of NAIA with the CRISPR/Cas system offers improved sensitivity, specificity, adaptability, versatility, and dependability. However, there is currently a lack of comprehensive summaries on the integration of NAIA and CRISPR/Cas in the field of food safety detection. This review comprehensively examines recent advances in CRISPR/Cas-integrated NAIA for food safety detection and discusses current challenges and future opportunities.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Review
Chemistry, Analytical
Zhaohe Huang, Sitong Liu, Xiaojing Pei, Shujing Li, Yifan He, Yigang Tong, Guoqi Liu
Summary: This review discusses the importance and development of CRISPR/Cas system in nucleic acid detection applications. The combination of CRISPR with various signal-readout techniques has wide applications in molecular diagnostics. Fluorescence is a dominant read-out technique, and understanding fluorescence readout types and variables affecting the signals can improve experimental designs.
Review
Chemistry, Multidisciplinary
Devleena Samanta, Wenjie Zhou, Sasha B. Ebrahimi, Sarah Hurst Petrosko, Chad A. Mirkin
Summary: Colloidal crystal engineering with DNA has made significant advances in bottom-up materials synthesis and fundamental concepts in chemistry, allowing the independent tuning of nanoparticle characteristics and DNA properties to create designer materials with unique properties.
ADVANCED MATERIALS
(2022)
Article
Biochemical Research Methods
Sasha B. Ebrahimi, Devleena Samanta, Caroline D. Kusmierz, Chad A. Mirkin
Summary: The synthesis of protein spherical nucleic acids (ProSNAs) enables the development of a versatile nanoplatform for intracellular delivery of functional proteins, addressing the challenges of low cellular uptake and susceptibility to degradation.
Review
Chemistry, Multidisciplinary
Seungheon Lee, Shivudu Godhulayyagari, Shadler T. Nguyen, Jasmine K. Lu, Sasha B. Ebrahimi, Devleena Samanta
Summary: The use of DNA-based nanostructures as probes has led to significant advances in chemical and biological sensing, allowing the detection of analytes in complex media, the understanding of fundamental biological processes, and the ability to diagnose diseases based on molecular signatures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Peter H. Winegar, C. Adrian Figg, Michelle H. Teplensky, Namrata Ramani, Chad A. Mirkin
Summary: This study develops a method for organizing proteins into precise oligomers using DNA, which only requires six synthetic oligonucleotides. The technique demonstrates modularity by assembling different antibodies into pentamers with exact stoichiometry and oligomeric sequence. This method is important for studying the impact of protein oligomer sequences on material properties in fields such as pharmaceutical development, cascade catalysis, synthetic photosynthesis, and membrane transport.
Review
Biochemistry & Molecular Biology
Dylan M. Snider, Subrata Pandit, Mackenzie L. Coffin, Sasha B. Ebrahimi, Devleena Samanta
Summary: The development of strategies for controlling protein function in a precise and predictable manner has the potential to revolutionize catalysis, diagnostics, and medicine. The use of DNA as an interface for modulating protein activity offers a powerful approach, allowing for the construction of sophisticated architectures with control over protein position, orientation, and stoichiometry.
Article
Chemistry, Multidisciplinary
Namrata Ramani, C. Adrian Figg, Alex J. Anderson, Peter H. Winegar, EunBi Oh, Sasha B. Ebrahimi, Devleena Samanta, Chad A. Mirkin
Summary: A method to pattern multiple oligonucleotide sequences in hydrogels using thiol-yne photochemistry is introduced, enabling the study of cell behavior and signaling in complex spatial environments.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Nibir Pathak, Cesar A. Patino, Namrata Ramani, Prithvijit Mukherjee, Devleena Samanta, Sasha B. Ebrahimi, Chad A. Mirkin, Horacio D. Espinosa
Summary: We demonstrate the efficient intracellular delivery of large proteins, protein-nucleic acid conjugates, and Cas9-ribonucleoprotein complex using a nanochannel-based localized electroporation platform. This platform also allows for the improved cytosolic delivery of spherical nucleic acids, expanding opportunities for detection and therapy.
Review
Multidisciplinary Sciences
Sasha B. Ebrahimi, Devleena Samanta
Summary: Protein-based therapeutics have revolutionized disease treatment, with proteins projected to be among the top selling drugs in the near future. This review discusses the design strategies that have transformed protein-based structures into effective therapeutics and highlights emerging protein engineering strategies. Such strategies aim to enhance the stability, targetability, cell permeability, and reduce immunogenicity of proteins, paving the way for improved therapeutic properties.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Sasha B. Ebrahimi, Xuan Hong, James Ludlow, Dany Doucet, Renuka Thirumangalathu
Summary: Antibody-drug conjugates (ADCs) are highly targeted and potent therapeutics that combine the selectivity of antibodies with the cytotoxicity of drug payloads. However, due to their complex structure and the need for chemical modifications of the payloads, the stability of ADCs can be a challenge. This study utilized high-throughput experimental screens and computational techniques to optimize the conformational and colloidal behavior of a specific ADC, resulting in a more stable structure. The findings provide insights for the development and stabilization of other ADCs.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Jungsoo Park, Michael Evangelopoulos, Matthew Kuo Vasher, Sergej Kudruk, Namrata Ramani, Vinzenz Mayer, Alexander Carlos Solivan, Andrew Lee, Chad Alexander Mirkin
Summary: Formulating small interfering RNAs (siRNAs) as spherical nucleic acids (SNAs) enhances their stability, cellular uptake, and gene silencing activity. The use of calcium chloride (CaCl2) instead of sodium chloride (NaCl) increases cytosolic delivery and reduces endosomal entrapment, resulting in improved efficacy.
Review
Biotechnology & Applied Microbiology
Rupali Chowdhry, Steven Z. Lu, Seungheon Lee, Shivudu Godhulayyagari, Sasha B. Ebrahimi, Devleena Samanta
Summary: Integrating nanotechnology with CRISPR/Cas systems has the potential to overcome limitations, enhance applications in disease diagnostics and therapeutics, and enable faster, more sensitive, and convenient readouts in detection platforms.
TRENDS IN BIOTECHNOLOGY
(2023)