301
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Yang S, Wu F, Peng S, Wang F, Chen Y, Yuan Y, Weng X, Zhou X. A m 6 A Sensing Method by Its Impact on the Stability of RNA Double Helix. Chem Biodivers 2020; 17:e2000050. [PMID: 32372485 DOI: 10.1002/cbdv.202000050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/05/2020] [Indexed: 01/05/2023]
Abstract
N6 -Methyladenosine (m6 A) is one of the most important RNA modifications in epigenetics. The development of detection method for m6 A is limited by its abundance and structure. Although it has been previously reported that its presence has an impact on the complementary pairing of RNA, few assays have been developed using this finding. We used this discovery and designed a detection method based on Cas13a system, which has different fluorescence signals for target RNAs containing m6 A modification and target RNAs without m6 A modification. We verified the fact that the presence of m6 A could cause the instability of dsRNA using the Cas13a system and provided a new direction and strategy for the development of m6 A detection methods in the future.
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Affiliation(s)
- Shixi Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Fan Wu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Shuang Peng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, P. R. China
| | - Yi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Yushu Yuan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, 430072, P. R. China
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302
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Kunii A, Yamamoto T, Sakuma T. Various strategies of effector accumulation to improve the efficiency of genome editing and derivative methodologies. In Vitro Cell Dev Biol Anim 2020; 56:359-366. [PMID: 32514717 DOI: 10.1007/s11626-020-00469-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/21/2020] [Indexed: 12/30/2022]
Abstract
CRISPR-Cas9 is a sophisticated tool in which Cas9/sgRNA complexes bind to the programmed target sequences and induce DNA double-strand breaks (DSBs) enabling highly efficient genome editing. Moreover, when nuclease-inactive Cas9 (dCas9) is employed, its specific DNA-binding activity provides a variety of derivative technologies such as transcriptional activation/repression, epigenome editing, and chromosome visualization. In these derivative technologies, particular effector molecules are fused with dCas9 or recruited to the target site. However, there had been room for improvement, because both genome editing and derivative technologies require not only the DNA-binding tools but also the additional components for their efficient and flexible outcomes. For genome editing, DSB repair molecules and knock-in donor templates need to act at the DSB sites. Derivative technologies also require their various effector domains to be gathered onto the target sites. Recently, many groups have developed and utilized inventive platforms to accumulate these additional components to the target sequence by modifying Cas9 protein and/or sgRNA. Here, we summarize the strategies of CRISPR-based effector accumulation and the improved methodologies using these creative platforms.
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Affiliation(s)
- Atsushi Kunii
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, 739-8526, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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303
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de Puig H, Bosch I, Collins JJ, Gehrke L. Point-of-Care Devices to Detect Zika and Other Emerging Viruses. Annu Rev Biomed Eng 2020; 22:371-386. [DOI: 10.1146/annurev-bioeng-060418-052240] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rapid diagnostic tests (point-of-care devices) are critical components of informed patient care and public health monitoring (surveillance applications). We propose that among the many rapid diagnostics platforms that have been tested or are in development, lateral flow immunoassays and synthetic biology–based diagnostics (including CRISPR-based diagnostics) represent the best overall options given their ease of use, scalability for manufacturing, sensitivity, and specificity. This review describes the identification of lateral flow immunoassay monoclonal antibody pairs that detect and distinguish between closely related pathogens and that are used in combination with functionalized multicolored nanoparticles and computational methods to deconvolute data. We also highlight the promise of synthetic biology–based diagnostic tests, which use synthetic genetic circuits that activate upon recognition of a pathogen-associated nucleic acid sequence, and discuss how the combined or parallel use of lateral flow immunoassays and synthetic biology tools may represent the future of scalable rapid diagnostics.
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Affiliation(s)
- Helena de Puig
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| | - Irene Bosch
- E25Bio Inc., Cambridge, Massachusetts 02139, USA
| | - James J. Collins
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Lee Gehrke
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;, ,
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, USA
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304
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Li J, Yang S, Zuo C, Dai L, Guo Y, Xie G. Applying CRISPR-Cas12a as a Signal Amplifier to Construct Biosensors for Non-DNA Targets in Ultralow Concentrations. ACS Sens 2020; 5:970-977. [PMID: 32157873 DOI: 10.1021/acssensors.9b02305] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Efficient signal amplification is essential to construct ultrasensitive biosensors for biologically relevant species with abundant concomitant interferences. Here, we apply LbaCas12a as a signal amplifier to develop a versatile CRISPR-Cas12a platform to detect a wide range of analytes in ultralow concentrations. The platform relies on the indiscriminate single-stranded DNase activity of LbaCas12a, which recognizes single-stranded DNA intermediates generated by non-DNA targets down to femtomolar concentrations and subsequently enhances the fluorescence signal output. With the help of functional nucleotides (DNAzyme and aptamer), ultrasensitive bioassays for Pb2+ and Acinetobacter baumannii have been designed with a limit of detection down to ∼0.053 nM and ∼3 CFU/mL, respectively. It also allows simultaneous detection of four microRNAs (miRNAs) at a picomolar concentration without significant interferences by other counterparts, suggesting the potential of multiplexed miRNA expression profiles analysis in high throughput. Given the versatility and generality of the CRISPR-Cas12a platform, we expect the current work to advance the application of CRISPR-Cas-based platforms in bioanalysis and provide new insights into ultrasensitive biosensor design.
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Affiliation(s)
- Junjie Li
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, China
| | - Shuangshuang Yang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, China
| | - Chen Zuo
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, China
| | - Ling Dai
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, China
| | - Yongcan Guo
- Department of Laboratory Medicine, Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing 400016, China
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305
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Baker C, Hayden MS. Gene editing in dermatology: Harnessing CRISPR for the treatment of cutaneous disease. F1000Res 2020; 9:281. [PMID: 32528662 DOI: 10.12688/f1000research.23185.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/16/2020] [Indexed: 12/26/2022] Open
Abstract
The discovery of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system has revolutionized gene editing research. Through the repurposing of programmable RNA-guided CRISPR-associated (Cas) nucleases, CRISPR-based genome editing systems allow for the precise modification of specific sites in the human genome and inspire novel approaches for the study and treatment of inherited and acquired human diseases. Here, we review how CRISPR technologies have stimulated key advances in dermatologic research. We discuss the role of CRISPR in genome editing for cutaneous disease and highlight studies on the use of CRISPR-Cas technologies for genodermatoses, cutaneous viruses and bacteria, and melanoma. Additionally, we examine key limitations of current CRISPR technologies, including the challenges these limitations pose for the widespread therapeutic application of CRISPR-based therapeutics.
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Affiliation(s)
- Catherine Baker
- Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Matthew S Hayden
- Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.,Section of Dermatology, Surgery, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, 03766, USA
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306
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Dong T, Mansour H, Hu H, Wang GA, Watson CJF, Yousef M, Matamoros G, Sanchez AL, MacNeil AJ, Wu P, Li F. Colorimetric Polymerase Chain Reaction Enabled by a Fast Light-Activated Substrate Chromogenic Detection Platform. Anal Chem 2020; 92:6456-6461. [PMID: 32259426 DOI: 10.1021/acs.analchem.9b05591] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Miniaturization of nucleic acid tests (NATs) into portable, inexpensive detection platforms may aid disease diagnosis in point-of-care (POC) settings. Colorimetric signals are ideal readouts for portable NATs, and it remains of high demand to develop color readouts that are simple, quantitative, and versatile. Thus motivated, we report a fast light-activated substrate chromogenic polymerase chain reaction (FLASH PCR) that uses DNA intercalating dyes (DIDs) to enable colorimetric nucleic acid detection and quantification. The FLASH system is established on our finding that DID-DNA intercalation can promote the rapid photooxidation of chromogenic substrates through light-induced production of singlet oxygen. Using this principle, we have successfully converted DID-based fluorescent PCR assays into colorimetric FLASH PCR. To demonstrate the practical applicability of FLASH PCR to POC diagnosis, we also fabricated two readout platforms, including a portable electronic FLASH reader and a paper-based FLASH strip. Using the FLASH reader, we were able to detect as low as 60 copies of DNA standards, a limit of detection (LOD) comparable with commercial quantitative PCR. The FLASH strip further enables the reader-free detection of PCR amplicons by converting the colorimetric signal into the visual measurement of distance as a readout. Finally, the practical applicability of the FLASH PCR was demonstrated by the detection and/or quantification of nucleic acid markers in diverse clinical and biological samples.
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Affiliation(s)
- Tianyu Dong
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, P. R. China 610064.,Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Hayam Mansour
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada.,Department of Cell Biology, National Research Center, Cairo Governorate 12622, Egypt
| | - Hao Hu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, P. R. China 610064
| | - Guan A Wang
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Colton J F Watson
- Department of Health Sciences, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Michael Yousef
- Department of Health Sciences, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Gabriela Matamoros
- Department of Health Sciences, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Ana L Sanchez
- Department of Health Sciences, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Adam J MacNeil
- Department of Health Sciences, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Peng Wu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, P. R. China 610064
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, College of Chemistry, Analytical & Testing Centre, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, P. R. China 610064.,Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
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307
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Kaminski MM, Alcantar MA, Lape IT, Greensmith R, Huske AC, Valeri JA, Marty FM, Klämbt V, Azzi J, Akalin E, Riella LV, Collins JJ. A CRISPR-based assay for the detection of opportunistic infections post-transplantation and for the monitoring of transplant rejection. Nat Biomed Eng 2020; 4:601-609. [PMID: 32284553 DOI: 10.1038/s41551-020-0546-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/06/2020] [Indexed: 12/26/2022]
Abstract
In organ transplantation, infection and rejection are major causes of graft loss. They are linked by the net state of immunosuppression. To diagnose and treat these conditions earlier, and to improve long-term patient outcomes, refined strategies for the monitoring of patients after graft transplantation are needed. Here, we show that a fast and inexpensive assay based on CRISPR-Cas13 accurately detects BK polyomavirus DNA and cytomegalovirus DNA from patient-derived blood and urine samples, as well as CXCL9 messenger RNA (a marker of graft rejection) at elevated levels in urine samples from patients experiencing acute kidney transplant rejection. The assay, which we adapted for lateral-flow readout, enables-via simple visualization-the post-transplantation monitoring of common opportunistic viral infections and of graft rejection, and should facilitate point-of-care post-transplantation monitoring.
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Affiliation(s)
- Michael M Kaminski
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Miguel A Alcantar
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Isadora T Lape
- Schuster Transplantation Research Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert Greensmith
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Allison C Huske
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacqueline A Valeri
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Francisco M Marty
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Verena Klämbt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jamil Azzi
- Schuster Transplantation Research Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Enver Akalin
- Montefiore Einstein Center for Transplantation, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Leonardo V Riella
- Schuster Transplantation Research Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - James J Collins
- Institute for Medical Engineering and Science and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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308
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Garcia-Cortadella R, Masvidal-Codina E, De la Cruz JM, Schäfer N, Schwesig G, Jeschke C, Martinez-Aguilar J, Sanchez-Vives MV, Villa R, Illa X, Sirota A, Guimerà A, Garrido JA. Distortion-Free Sensing of Neural Activity Using Graphene Transistors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1906640. [PMID: 32187840 DOI: 10.1002/smll.201906640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/26/2020] [Accepted: 02/21/2020] [Indexed: 06/10/2023]
Abstract
Graphene solution-gated field-effect transistors (g-SGFETs) are promising sensing devices to transduce electrochemical potential signals in an electrolyte bath. However, distortion mechanisms in g-SGFET, which can affect signals of large amplitude or high frequency, have not been evaluated. Here, a detailed characterization and modeling of the harmonic distortion and non-ideal frequency response in g-SGFETs is presented. This accurate description of the input-output relation of the g-SGFETs allows to define the voltage- and frequency-dependent transfer functions, which can be used to correct distortions in the transduced signals. The effect of signal distortion and its subsequent calibration are shown for different types of electrophysiological signals, spanning from large amplitude and low frequency cortical spreading depression events to low amplitude and high frequency action potentials. The thorough description of the distortion mechanisms presented in this article demonstrates that g-SGFETs can be used as distortion-free signal transducers not only for neural sensing, but also for a broader range of applications in which g-SGFET sensors are used.
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Affiliation(s)
- Ramon Garcia-Cortadella
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Eduard Masvidal-Codina
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Esfera UAB, Bellaterra, 08193, Spain
| | - Jose M De la Cruz
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Nathan Schäfer
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Gerrit Schwesig
- Bernstein Center for Computational Neuroscience Munich, Munich Cluster of Systems Neurology (SyNergy), Faculty of Medicine, Ludwig-Maximilians Universität München, Planegg-Martinsried, 82152, Germany
| | | | - Javier Martinez-Aguilar
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Esfera UAB, Bellaterra, 08193, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, 50018, Spain
| | - Maria V Sanchez-Vives
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, 08036, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain
| | - Rosa Villa
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Esfera UAB, Bellaterra, 08193, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, 50018, Spain
| | - Xavi Illa
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Esfera UAB, Bellaterra, 08193, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, 50018, Spain
| | - Anton Sirota
- Bernstein Center for Computational Neuroscience Munich, Munich Cluster of Systems Neurology (SyNergy), Faculty of Medicine, Ludwig-Maximilians Universität München, Planegg-Martinsried, 82152, Germany
| | - Anton Guimerà
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Esfera UAB, Bellaterra, 08193, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, 50018, Spain
| | - Jose A Garrido
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain
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309
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Nucleic acid amplification free biosensors for pathogen detection. Biosens Bioelectron 2020; 153:112049. [DOI: 10.1016/j.bios.2020.112049] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/11/2022]
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310
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Song J, Hegge JW, Mauk MG, Chen J, Till JE, Bhagwat N, Azink LT, Peng J, Sen M, Mays J, Carpenter EL, van der Oost J, Bau HH. Highly specific enrichment of rare nucleic acid fractions using Thermus thermophilus argonaute with applications in cancer diagnostics. Nucleic Acids Res 2020; 48:e19. [PMID: 31828328 PMCID: PMC7038991 DOI: 10.1093/nar/gkz1165] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/12/2019] [Accepted: 12/03/2019] [Indexed: 12/26/2022] Open
Abstract
Detection of disease-associated, cell-free nucleic acids in body fluids enables early diagnostics, genotyping and personalized therapy, but is challenged by the low concentrations of clinically significant nucleic acids and their sequence homology with abundant wild-type nucleic acids. We describe a novel approach, dubbed NAVIGATER, for increasing the fractions of Nucleic Acids of clinical interest Via DNA-Guided Argonaute from Thermus thermophilus (TtAgo). TtAgo cleaves specifically guide-complementary DNA and RNA with single nucleotide precision, greatly increasing the fractions of rare alleles and, enhancing the sensitivity of downstream detection methods such as ddPCR, sequencing, and clamped enzymatic amplification. We demonstrated 60-fold enrichment of the cancer biomarker KRAS G12D and ∼100-fold increased sensitivity of Peptide Nucleic Acid (PNA) and Xenonucleic Acid (XNA) clamp PCR, enabling detection of low-frequency (<0.01%) mutant alleles (∼1 copy) in blood samples of pancreatic cancer patients. NAVIGATER surpasses Cas9-based assays (e.g. DASH, Depletion of Abundant Sequences by Hybridization), identifying more mutation-positive samples when combined with XNA-PCR. Moreover, TtAgo does not require targets to contain any specific protospacer-adjacent motifs (PAM); is a multi-turnover enzyme; cleaves ssDNA, dsDNA and RNA targets in a single assay; and operates at elevated temperatures, providing high selectivity and compatibility with polymerases.
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Affiliation(s)
- Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
| | - Jorrit W Hegge
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University,The Netherlands
| | - Michael G Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
| | - Junman Chen
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
| | - Jacob E Till
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neha Bhagwat
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lotte T Azink
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University,The Netherlands
| | - Jing Peng
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
| | - Moen Sen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jazmine Mays
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erica L Carpenter
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University,The Netherlands
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia PA, USA
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311
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Adashi EY, Cohen IG. What would responsible remedial human germline editing look like? Nat Biotechnol 2020; 38:398-400. [DOI: 10.1038/s41587-020-0482-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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312
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Single-molecule analysis of nucleic acid biomarkers - A review. Anal Chim Acta 2020; 1115:61-85. [PMID: 32370870 DOI: 10.1016/j.aca.2020.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.
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313
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Zhang J, Lan T, Lu Y. Translating in vitro diagnostics from centralized laboratories to point-of-care locations using commercially-available handheld meters. Trends Analyt Chem 2020; 124:115782. [PMID: 32194293 PMCID: PMC7081941 DOI: 10.1016/j.trac.2019.115782] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is a growing demand for high-performance point-of-care (POC) diagnostic technologies where in vitro diagnostics (IVD) is fundamental for prevention, identification, and treatment of many diseases. Over the past decade, a shift of IVDs from the centralized laboratories to POC settings is emerging. In this review, we summarize recent progress in translating IVDs from centralized labs to POC settings using commercially available handheld meters. After introducing typical workflows for IVDs and highlight innovative technologies in this area, we discuss advantages of using commercially available handheld meters for translating IVDs from centralized labs to POC settings. We then provide comprehensive coverage of different signal transduction strategies to repurpose the commercially-available handheld meters, including personal glucose meter, pH meter, thermometer and pressure meter, for detecting a wide range of targets by integrating biochemical assays with the meters for POC testing. Finally, we identify remaining challenges and offer future outlook in this area.
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Affiliation(s)
- JingJing Zhang
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing
210023, China
| | - Tian Lan
- GlucoSentient, Inc., 2100 S. Oak Street, Suite 101,
Champaign, IL 61820, USA
| | - Yi Lu
- Department of Chemistry, University of Illinois at
Urbana–Champaign, Urbana, Illinois 61801, United States
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314
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Zhang D, Yan Y, Que H, Yang T, Cheng X, Ding S, Zhang X, Cheng W. CRISPR/Cas12a-Mediated Interfacial Cleaving of Hairpin DNA Reporter for Electrochemical Nucleic Acid Sensing. ACS Sens 2020; 5:557-562. [PMID: 32013399 DOI: 10.1021/acssensors.9b02461] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A rapid and sensitive isothermal method is crucial for point-of-care (POC) nucleic acid testing. Recently, RNA-guided CRISPR/Cas12a proteins were discovered to exhibit target-triggered nonspecific single-stranded deoxyribonuclease (ssDNase) activity. Herein, the ssDNase cleavage capacity of the CRISPR/Cas12a system for interfacial hairpin DNA (hpDNA) and linear DNA was investigated in detailed. A novel electrochemical DNA biosensor was then developed via target-induced Cas12a cleaving interfacial hpDNA. In this strategy, the RNA-guided target DNA binding activates the robust Cas12a ssDNase activity. The immobilized hpDNA electrochemical reporters with a low surface coverage and incompact morphological structure present accessible substrates for highly efficient Cas12a cleavage, leading to a highly sensitive electrochemical DNA biosensor. Under the optimal conditions, as low as 30 pM target DNA was detected in about 60 min with 3.5 orders of magnitude dynamic range from 50 pM to 100 nM. Furthermore, the practical application ability of the established sensing method for detecting the target in complex matrices was also demonstrated. The proposed strategy enables rapid and sensitive DNA determination, providing a potential tool for POC molecular diagnostics.
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Affiliation(s)
- Decai Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Haiying Que
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tiantian Yang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaoxue Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiuming Zhang
- Department of Laboratory Diagnosis, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen 518000, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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315
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Wang X, Xiong E, Tian T, Cheng M, Lin W, Wang H, Zhang G, Sun J, Zhou X. Clustered Regularly Interspaced Short Palindromic Repeats/Cas9-Mediated Lateral Flow Nucleic Acid Assay. ACS NANO 2020; 14:2497-2508. [PMID: 32045522 DOI: 10.1021/acsnano.0c00022] [Citation(s) in RCA: 182] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The lateral flow assay is one of the most convenient analytical techniques for analyzing the immune response, but its applicability to precise genetic analyses is limited by the false-positive signal and tedious and inefficient hybridization steps. Here, we introduce the CRISPR (clustered regularly interspaced short palindromic repeats) /Cas system into the lateral flow assay, termed CRISPR/Cas9-mediated lateral flow nucleic acid assay (CASLFA), to address such issues. In this study, CASLFA is utilized to identify Listeria monocytogenes, genetically modified organisms (GMOs), and African swine fever virus (ASFV) at a detection limit of hundreds of copies of genome samples with high specificity within 1 h. We further evaluated the performance of CASLFA in a nonlaboratory environment and successfully confirmed 27 ASFV-infected samples from 110 suspected swine serum samples, with an accuracy of 100% when compared to real-time PCR (RT-PCR) assay. CASLFA satisfies some of the characteristics of a next-generation molecular diagnostics tool due to its rapidity and accuracy, allowing for point-of-care use without the need for technical expertise and complex ancillary equipment. This method has great potential for gene analysis in resource-poor or nonlaboratory environments.
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Affiliation(s)
- Xusheng Wang
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Erhu Xiong
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Tian Tian
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Meng Cheng
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Wei Lin
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
| | - Heng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture , Guangzhou 510642 , China
- Research Center for African Swine Fever Prevention and Control , South China Agricultural University , Guangzhou 510642 , China
| | - Guihong Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture , Guangzhou 510642 , China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria , South China Agricultural University , Guangzhou 510642 , China
- Research Center for African Swine Fever Prevention and Control , South China Agricultural University , Guangzhou 510642 , China
| | - Jian Sun
- Guangdong Laboratory for Lingnan Modern Agriculture , Guangzhou 510642 , China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria , South China Agricultural University , Guangzhou 510642 , China
- Research Center for African Swine Fever Prevention and Control , South China Agricultural University , Guangzhou 510642 , China
| | - Xiaoming Zhou
- College of Biophotonics & School of Life Sciences , South China Normal University , Guangzhou 510631 , China
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316
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English MA, Soenksen LR, Gayet RV, de Puig H, Angenent-Mari NM, Mao AS, Nguyen PQ, Collins JJ. Programmable CRISPR-responsive smart materials. Science 2020; 365:780-785. [PMID: 31439791 DOI: 10.1126/science.aaw5122] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/27/2019] [Indexed: 12/26/2022]
Abstract
Stimuli-responsive materials activated by biological signals play an increasingly important role in biotechnology applications. We exploit the programmability of CRISPR-associated nucleases to actuate hydrogels containing DNA as a structural element or as an anchor for pendant groups. After activation by guide RNA-defined inputs, Cas12a cleaves DNA in the gels, thereby converting biological information into changes in material properties. We report four applications: (i) branched poly(ethylene glycol) hydrogels releasing DNA-anchored compounds, (ii) degradable polyacrylamide-DNA hydrogels encapsulating nanoparticles and live cells, (iii) conductive carbon-black-DNA hydrogels acting as degradable electrical fuses, and (iv) a polyacrylamide-DNA hydrogel operating as a fluidic valve with an electrical readout for remote signaling. These materials allow for a range of in vitro applications in tissue engineering, bioelectronics, and diagnostics.
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Affiliation(s)
- Max A English
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - Luis R Soenksen
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA.,Department of Mechanical Engineering, MIT, Cambridge, Cambridge, MA 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Raphael V Gayet
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA.,Microbiology Graduate Program, MIT, Cambridge, MA 02139, USA
| | - Helena de Puig
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Nicolaas M Angenent-Mari
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Angelo S Mao
- Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.,School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Peter Q Nguyen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.,School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. .,Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.,Synthetic Biology Center, MIT, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
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317
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Williams NX, Watson N, Joh DY, Chilkoti A, Franklin AD. Aerosol jet printing of biological inks by ultrasonic delivery. Biofabrication 2020; 12:025004. [PMID: 31778993 PMCID: PMC7047942 DOI: 10.1088/1758-5090/ab5cf5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Printing is a promising method to reduce the cost of fabricating biomedical devices. While there have been significant advancements in direct-write printing techniques, non-contact printing of biological reagents has been almost exclusively limited to inkjet printing. Motivated by this lacuna, this work investigated aerosol jet printing (AJP) of biological reagents onto a nonfouling polymer brush to fabricate in vitro diagnostic (IVD) assays. The ultrasonication ink delivery process, which had previously been reported to damage DNA molecules, caused no degradation of printed proteins, allowing printing of a streptavidin-biotin binding assay with sub-nanogram ml-1 analytical sensitivity. Furthermore, a carcinoembryogenic antigen IVD was printed and found to have sensitivities in the clinically relevant range (limit of detection of approximately 0.5 ng ml-1 and a dynamic range of approximately three orders of magnitude). Finally, the multi-material printing capabilities of the aerosol jet printer were demonstrated by printing silver nanowires and streptavidin as interconnected patterns in the same print job without removal of the substrate from the printer, which will facilitate the fabrication of mixed-material devices. As cost, versatility, and ink usage become more prominent factors in the development of IVDs, this work has shown that AJP should become a more widely considered technique for fabrication.
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Affiliation(s)
- Nicholas X Williams
- Department of Electrical and Computer Engineering, Duke University, Durham NC 27708, United States of America
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318
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Chai H, Wang M, Zhang C, Tang Y, Miao P. Highly Sensitive Genosensing Coupling Rolling Circle Amplification with Multiple DNAzyme Cores for DNA Walking. Bioconjug Chem 2020; 31:764-769. [DOI: 10.1021/acs.bioconjchem.9b00861] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Hua Chai
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P.R. China
| | | | - Chongyu Zhang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P.R. China
- Jinan Guokeyigong Science and Technology Development Co., Ltd., Jinan 250103, P.R. China
| | - Yuguo Tang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P.R. China
| | - Peng Miao
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, P.R. China
- Department of Chemistry, New York University, New York, New York 10003, United States
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319
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Wang C, Wu J, He Y, Song Z, Shi S, Zhu Y, Jia Y, Ye W. Fully Solid-State Graphene Transistors with Striking Homogeneity and Sensitivity for the Practicalization of Single-Device Electronic Bioassays. NANO LETTERS 2020; 20:166-175. [PMID: 31815482 DOI: 10.1021/acs.nanolett.9b03528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
To break through a critical barrier in the practical application of graphene biosensors, namely, device-to-device performance inhomogeneity, this work presents a novel scenario employing a fully solid-state (FSS) transistor configuration. Herein, the graphene sensing unit is completely encapsulated by a high-κ solid dielectric material, which isolates the sensing unit from solution contaminants and thus homogeneously maintains the extraordinary carrier mobility of pristine graphene in batch-made devices. To create an interface sensitive to biomolecular interactions based on the FSS configuration, a metallic floating gate functionalized by conductive mercapto-phenyl molecular linkers is defined on the top-layer solid dielectric. As the solid dielectric layer beneath the metal floating gate enables a higher capacitive gating efficiency than the regular graphene-solution electrical double layer (EDL) interface, the overall transistor amplification gain is further enhanced. As a proof of principle, a label-free DNAzymatic bioassay of Pb2+ is conducted. Without the traditional one-by-one device normalization, an excellent concentration detection limit of 929.8 fM is achieved, which is almost 2 orders of magnitude lower than that in existing works. The FSS configuration allows enhanced sensitivity and homogeneity, thereby providing new developmental guidelines for graphene biosensors beyond the laboratory investigation stage. Additionally, it has the potential to be universally applicable for cost-efficient single-device bioassays.
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Affiliation(s)
| | | | | | | | | | - Yibo Zhu
- Department of Mechanical Engineering , Columbia University , New York 10027 , United States
| | - Yuan Jia
- Jiangsu Key Laboratory of Micro-Nano Biomedical Instrument Design and Manufacture, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Weixiang Ye
- Jiangsu Key Laboratory of Thin Films, School of Physical Science and Technology , Soochow University , Suzhou 215006 , China
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320
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Shi R, Hu Z, Lu H, Liu L, Xu L, Liu Y, Wu H, Huang B, Zhang GJ, Chen S, Yang F. Hierarchical Nanostructuring Array Enhances Mid-Hybridization for Accurate Herbal Identification via ITS2 DNA Barcode. Anal Chem 2019; 92:2136-2144. [DOI: 10.1021/acs.analchem.9b04687] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Ruixue Shi
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Zhigang Hu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Hao Lu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Li Liu
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Lei Xu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Yanju Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Hezhen Wu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Bisheng Huang
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Shilin Chen
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Fan Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
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321
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Bruch R, Baaske J, Chatelle C, Meirich M, Madlener S, Weber W, Dincer C, Urban GA. CRISPR/Cas13a-Powered Electrochemical Microfluidic Biosensor for Nucleic Acid Amplification-Free miRNA Diagnostics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1905311. [PMID: 31663165 DOI: 10.1002/adma.201905311] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/23/2019] [Indexed: 05/17/2023]
Abstract
Noncoding small RNAs, such as microRNAs, are becoming the biomarkers of choice for multiple diseases in clinical diagnostics. A dysregulation of these microRNAs can be associated with many different diseases, such as cancer, dementia, and cardiovascular conditions. The key for effective treatment is an accurate initial diagnosis at an early stage, improving the patient's survival chances. In this work, the first clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a-powered microfluidic, integrated electrochemical biosensor for the on-site detection of microRNAs is introduced. Through this unique combination, the quantification of the potential tumor markers microRNA miR-19b and miR-20a is realized without any nucleic acid amplification. With a readout time of 9 min and an overall process time of less than 4 h, a limit of detection of 10 pm is achieved, using a measuring volume of less than 0.6 µL. Furthermore, the feasibility of the biosensor platform to detect miR-19b in serum samples of children, suffering from brain cancer, is demonstrated. The validation of the obtained results with a standard quantitative real-time polymerase chain reaction method shows the ability of the electrochemical CRISPR-powered system to be a low-cost, easily scalable, and target amplification-free tool for nucleic acid based diagnostics.
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Affiliation(s)
- Richard Bruch
- Department of Microsystems Engineering (IMTEK), Laboratory for Sensors, University of Freiburg, Georges-Koehler Allee 103, 79110, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Koehler-Allee 105, 79110, Freiburg, Germany
| | - Julia Baaske
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestraße 18, 79104, Freiburg, Germany
| | - Claire Chatelle
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestraße 18, 79104, Freiburg, Germany
| | - Mailin Meirich
- Department of Microsystems Engineering (IMTEK), Laboratory for Sensors, University of Freiburg, Georges-Koehler Allee 103, 79110, Freiburg, Germany
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine, Molecular Neuro-Oncology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Wilfried Weber
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestraße 18, 79104, Freiburg, Germany
| | - Can Dincer
- Department of Microsystems Engineering (IMTEK), Laboratory for Sensors, University of Freiburg, Georges-Koehler Allee 103, 79110, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Koehler-Allee 105, 79110, Freiburg, Germany
- Department of Bioengineering, Royal School of Mines, Imperial College London, SW7 2AZ, London, UK
| | - Gerald Anton Urban
- Department of Microsystems Engineering (IMTEK), Laboratory for Sensors, University of Freiburg, Georges-Koehler Allee 103, 79110, Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Straße 21, 79104, Freiburg, Germany
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322
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Mohajeri N, Imani M, Akbarzadeh A, Sadighi A, Zarghami N. An update on advances in new developing DNA conjugation diagnostics and ultra-resolution imaging technologies: Possible applications in medical and biotechnological utilities. Biosens Bioelectron 2019; 144:111633. [DOI: 10.1016/j.bios.2019.111633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
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323
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Kellner MJ, Koob JG, Gootenberg JS, Abudayyeh OO, Zhang F. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat Protoc 2019; 14:2986-3012. [PMID: 31548639 PMCID: PMC6956564 DOI: 10.1038/s41596-019-0210-2] [Citation(s) in RCA: 699] [Impact Index Per Article: 139.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/14/2019] [Indexed: 12/26/2022]
Abstract
Rapid detection of nucleic acids is integral to applications in clinical diagnostics and biotechnology. We have recently established a CRISPR-based diagnostic platform that combines nucleic acid pre-amplification with CRISPR-Cas enzymology for specific recognition of desired DNA or RNA sequences. This platform, termed specific high-sensitivity enzymatic reporter unlocking (SHERLOCK), allows multiplexed, portable, and ultra-sensitive detection of RNA or DNA from clinically relevant samples. Here, we provide step-by-step instructions for setting up SHERLOCK assays with recombinase-mediated polymerase pre-amplification of DNA or RNA and subsequent Cas13- or Cas12-mediated detection via fluorescence and colorimetric readouts that provide results in <1 h with a setup time of less than 15 min. We also include guidelines for designing efficient CRISPR RNA (crRNA) and isothermal amplification primers, as well as discuss important considerations for multiplex and quantitative SHERLOCK detection assays.
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Affiliation(s)
- Max J Kellner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeremy G Koob
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Omar O Abudayyeh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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324
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CRISPR/Cas Powered Multiplexed Biosensing. Trends Biotechnol 2019; 37:791-792. [DOI: 10.1016/j.tibtech.2019.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 11/24/2022]
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325
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Abstract
Abstract
The development of clustered regularly interspaced short-palindromic repeat (CRISPR)-Cas systems for genome editing has transformed the way life science research is conducted and holds enormous potential for the treatment of disease as well as for many aspects of biotechnology. Here, I provide a personal perspective on the development of CRISPR-Cas9 for genome editing within the broader context of the field and discuss our work to discover novel Cas effectors and develop them into additional molecular tools. The initial demonstration of Cas9-mediated genome editing launched the development of many other technologies, enabled new lines of biological inquiry, and motivated a deeper examination of natural CRISPR-Cas systems, including the discovery of new types of CRISPR-Cas systems. These new discoveries in turn spurred further technological developments. I review these exciting discoveries and technologies as well as provide an overview of the broad array of applications of these technologies in basic research and in the improvement of human health. It is clear that we are only just beginning to unravel the potential within microbial diversity, and it is quite likely that we will continue to discover other exciting phenomena, some of which it may be possible to repurpose as molecular technologies. The transformation of mysterious natural phenomena to powerful tools, however, takes a collective effort to discover, characterize, and engineer them, and it has been a privilege to join the numerous researchers who have contributed to this transformation of CRISPR-Cas systems.
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326
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Affiliation(s)
- Richard Bruch
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Freiburg, Germany
| | - Gerald A Urban
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Freiburg, Germany
| | - Can Dincer
- Laboratory for Sensors, Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany.
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Freiburg, Germany.
- Department of Bioengineering, Royal School of Mines, Imperial College London, London, UK.
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327
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Li Y, Liu L, Liu G. CRISPR/Cas Multiplexed Biosensing: A Challenge or an Insurmountable Obstacle? Trends Biotechnol 2019; 37:792-795. [PMID: 31153632 DOI: 10.1016/j.tibtech.2019.04.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/26/2022]
Abstract
Performing multiplex detection is still an elusive goal for molecular diagnostics. CRISPR/Cas-based biosensing has demonstrated potential for multiplex detection. Instead of being an insurmountable obstacle, CRISPR/Cas multiplexed biosensing is a realistic challenge with some recent successful applications. Strategic considerations are required to fully explore its potential in multiplex diagnostics.
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Affiliation(s)
- Yi Li
- Graduate School of Biomedical Engineering, ARC Centre of Excellence in Nanoscale Biophotonics, Faculty of Engineering, University of New South Wales, Sydney, NSW 2052, Australia; Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Linyang Liu
- Graduate School of Biomedical Engineering, ARC Centre of Excellence in Nanoscale Biophotonics, Faculty of Engineering, University of New South Wales, Sydney, NSW 2052, Australia; Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Guozhen Liu
- Graduate School of Biomedical Engineering, ARC Centre of Excellence in Nanoscale Biophotonics, Faculty of Engineering, University of New South Wales, Sydney, NSW 2052, Australia; Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia; International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.
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