Review: Engineering in situ biosensors for tracking cellular events

This review will focus on advances in the development of such biosensor in tracking cellular events with a focus on their technical novelty.

[1]  M. Rahman,et al.  Insights into the Potential Role of Mercury in Alzheimer’s Disease , 2019, Journal of Molecular Neuroscience.

[2]  Bing Ren,et al.  Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors , 2018, Proceedings of the National Academy of Sciences.

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[4]  A. Queen,et al.  Genetically encoded FRET-based optical sensor for Hg2+ detection and intracellular imaging in living cells , 2019, Journal of Industrial Microbiology & Biotechnology.

[5]  A. Jäschke,et al.  SRB-2: a promiscuous rainbow aptamer for live-cell RNA imaging , 2018, Nucleic acids research.

[6]  Xiaobing Zhang,et al.  Fluorescence Resonance Energy Transfer-Based DNA Nanoprism with a Split Aptamer for Adenosine Triphosphate Sensing in Living Cells. , 2017, Analytical chemistry.

[7]  George W. Jackson,et al.  Aptamer–gold nanoparticle conjugates for the colorimetric detection of arboviruses and vector mosquito species , 2019, RSC advances.

[8]  Aviv Regev,et al.  RNA targeting with CRISPR–Cas13 , 2017, Nature.

[9]  Walther Akemann,et al.  Engineering of a Genetically Encodable Fluorescent Voltage Sensor Exploiting Fast Ci-VSP Voltage-Sensing Movements , 2008, PloS one.

[10]  Robert Tjian,et al.  CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells , 2015, Proceedings of the National Academy of Sciences.

[11]  M. Mohsin,et al.  Real time quantification of intracellular nickel using genetically encoded FRET-based nanosensor. , 2019, International journal of biological macromolecules.

[12]  Kenichiro Hata,et al.  Targeted DNA demethylation in vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions , 2016, Nature Biotechnology.

[13]  Shaojie Zhang,et al.  Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow , 2016, Nature Biotechnology.

[14]  S. Hennig,et al.  Using a Specific RNA-Protein Interaction To Quench the Fluorescent RNA Spinach. , 2017, ACS chemical biology.

[15]  K. Kim,et al.  Labeling RNAs in live cells using malachite green aptamer scaffolds as fluorescent probes , 2017, bioRxiv.

[16]  Kemin Wang,et al.  Aptamer-based FRET nanoflares for imaging potassium ions in living cells. , 2016, Chemical communications.

[17]  A. Bird,et al.  Engineering a high-affinity methyl-CpG-binding protein , 2006, Nucleic acids research.

[18]  D. Kleinfeld,et al.  An in vivo biosensor for neurotransmitter release and in situ receptor activity , 2009, Nature Neuroscience.

[19]  Chi Bun Ching,et al.  Development of Colorimetric-Based Whole-Cell Biosensor for Organophosphorus Compounds by Engineering Transcription Regulator DmpR. , 2016, ACS synthetic biology.

[20]  Peng Xu,et al.  Design and kinetic analysis of a hybrid promoter-regulator system for malonyl-CoA sensing in Escherichia coli. , 2014, ACS chemical biology.

[21]  Da Xing,et al.  High-Fidelity and Rapid Quantification of miRNA Combining crRNA Programmability and CRISPR/Cas13a trans-Cleavage Activity. , 2019, Analytical chemistry.

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[23]  Aviv Regev,et al.  Nucleic acid detection with CRISPR-Cas13a/C2c2 , 2017, Science.

[24]  Parvez Khan,et al.  Engineering genetically encoded FRET-based nanosensors for real time display of arsenic (As3+) dynamics in living cells , 2019, Scientific Reports.

[25]  Walther Akemann,et al.  Imaging neural circuit dynamics with a voltage-sensitive fluorescent protein. , 2012, Journal of neurophysiology.

[26]  S. Jaffrey,et al.  RNA Mimics of Green Fluorescent Protein , 2011, Science.

[27]  A DNA aptamer efficiently inhibits the infectivity of Bovine herpesvirus 1 by blocking viral entry , 2017, Scientific Reports.

[28]  Dong-Il Kim,et al.  Acid-Sensing Ion Channel 2a (ASIC2a) Promotes Surface Trafficking of ASIC2b via Heteromeric Assembly , 2016, Scientific Reports.

[29]  B. Ducommun,et al.  Chromatibody, a novel non-invasive molecular tool to explore and manipulate chromatin in living cells , 2016, Journal of Cell Science.

[30]  B. Deplancke,et al.  Engineered Multivalent Sensors to Detect Coexisting Histone Modifications in Living Stem Cells. , 2017, Cell chemical biology.

[31]  S. Muyldermans,et al.  Naturally occurring antibodies devoid of light chains , 1993, Nature.

[32]  Chongli Yuan,et al.  Monitoring Histone Methylation (H3K9me3) Changes in Live Cells , 2019, ACS omega.

[33]  Jens Rudat,et al.  FoldX as Protein Engineering Tool: Better Than Random Based Approaches? , 2018, Computational and structural biotechnology journal.

[34]  Minoru Yoshida,et al.  A Genetically Encoded FRET Probe to Detect Intranucleosomal Histone H3K9 or H3K14 Acetylation Using BRD4, a BET Family Member. , 2016, ACS chemical biology.

[35]  Tai-Yu Chiu,et al.  Live-Cell Dynamic Sensing of Cd2+ with a FRET-Based Indicator , 2013, PloS one.

[36]  Michael J. Ziller,et al.  Genome-wide tracking of dCas9-methyltransferase footprints , 2018, Nature Communications.

[37]  A. Jeltsch,et al.  Modular fluorescence complementation sensors for live cell detection of epigenetic signals at endogenous genomic sites , 2017, Nature Communications.

[38]  Xiangkai Li,et al.  Advances in Understanding How Heavy Metal Pollution Triggers Gastric Cancer , 2016, BioMed research international.

[39]  Zhan Wu,et al.  Genetically Encoded Fluorescent RNA Sensor for Ratiometric Imaging of MicroRNA in Living Tumor Cells. , 2017, Journal of the American Chemical Society.

[40]  Adrian T. Grzybowski,et al.  Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation , 2016, Proceedings of the National Academy of Sciences.

[41]  A. Borst,et al.  A genetically encoded calcium indicator for chronic in vivo two-photon imaging , 2008, Nature Methods.

[42]  Andrew J. Steckl,et al.  Aptamer-based lateral flow assay for point of care cortisol detection in sweat , 2019, Sensors and Actuators B: Chemical.

[43]  Chongli Yuan,et al.  Engineering Recombinant Protein Sensors for Quantifying Histone Acetylation. , 2017, ACS sensors.

[44]  Mark T. Harnett,et al.  An optimized fluorescent probe for visualizing glutamate neurotransmission , 2013, Nature Methods.

[45]  P. Gao,et al.  SiRA: A Silicon Rhodamine-Binding Aptamer for Live-Cell Super-Resolution RNA Imaging. , 2019, Journal of the American Chemical Society.

[46]  Dinshaw J. Patel,et al.  Structure, recognition and adaptive binding in RNA aptamer complexes. , 1997, Journal of molecular biology.

[47]  Lucy J. Colwell,et al.  Comparative analysis of nanobody sequence and structure data , 2018, Proteins.

[48]  Michael Z. Lin,et al.  High-fidelity optical reporting of neuronal electrical activity with an ultrafast fluorescent voltage sensor , 2014, Nature Neuroscience.

[49]  M. Alini,et al.  Monitoring live human mesenchymal stromal cell differentiation and subsequent selection using fluorescent RNA-based probes , 2016, Scientific Reports.

[50]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[51]  Li I. Zhang,et al.  ED SUM: Signaling by the neurotransmitter acetylcholine is monitored in cells and animals with a sensitive reporter. , 2018, Nature Biotechnology.

[52]  S. Jaffrey,et al.  RNA Imaging with Dimeric Broccoli in Live Bacterial and Mammalian Cells , 2016, Current protocols in chemical biology.

[53]  BaeHyunjung,et al.  Sol-Gel SELEX Circumventing Chemical Conjugation of Low Molecular Weight Metabolites Discovers Aptamers Selective to Xanthine , 2013 .

[54]  A. Bird,et al.  Identification and Characterization of a Family of Mammalian Methyl-CpG Binding Proteins , 1998, Molecular and Cellular Biology.

[55]  A. Nimmerjahn,et al.  Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors , 2018, Science.