1
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Caldwell S, Demyan IR, Falcone GN, Parikh A, Lohmueller J, Deiters A. Conditional Control of Benzylguanine Reaction with the Self-Labeling SNAP-tag Protein. Bioconjug Chem 2025; 36:540-548. [PMID: 39977950 PMCID: PMC11926790 DOI: 10.1021/acs.bioconjchem.5c00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2025] [Revised: 01/30/2025] [Accepted: 02/05/2025] [Indexed: 02/22/2025]
Abstract
SNAP-tag, a mutant of the O6-alkylguanine-DNA-alkyltransferase, self-labels by reacting with benzylguanine (BG) substrates, thereby forming a thioether bond. SNAP-tag has been genetically fused to a wide range of proteins of interest in order to covalently modify them. In the context of both diagnostic and therapeutic applications, as well as use as a biological recording device, precise control in a spatial and temporal fashion over the covalent bond-forming reaction is desired to direct inputs, readouts, or therapeutic actions to specific locations, at specific time points, in cells and organisms. Here, we introduce a comprehensive suite of six caged BG molecules: one light-triggered and five others that can be activated through various chemical and biochemical stimuli, such as small molecules, transition metal catalysts, reactive oxygen species, and enzymes. These molecules are unable to react with SNAP-tag until the trigger is present, which leads to near complete SNAP-tag conjugation, as illustrated both in biochemical assays and on human cell surfaces. This approach holds promise for targeted therapeutic assembly at disease sites, offering the potential to reduce off-target effects and toxicity through precise trigger titration.
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Affiliation(s)
- Steven
E. Caldwell
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Isabella R. Demyan
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Gianna N. Falcone
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Avani Parikh
- Department
of Surgery, Division of Surgical Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Jason Lohmueller
- Department
of Surgery, Division of Surgical Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
- Center
for Systems Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
- Center
for Systems Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
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2
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Kiy Z, Chaud J, Xu L, Brandhorst E, Kamali T, Vargas C, Keller S, Hong H, Specht A, Cambridge S. Towards a Light-mediated Gene Therapy for the Eye using Caged Ethinylestradiol and the Inducible Cre/lox System. Angew Chem Int Ed Engl 2024; 63:e202317675. [PMID: 38127455 DOI: 10.1002/anie.202317675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Increasingly, retinal pathologies are being treated with virus-mediated gene therapies. To be able to target viral transgene expression specifically to the pathological regions of the retina with light, we established an in vivo photoactivated gene expression paradigm for retinal tissue. Based on the inducible Cre/lox system, we discovered that ethinylestradiol is a suitable alternative to Tamoxifen as ethinylestradiol is more amenable to modification with photosensitive protecting compounds, i.e., "caging." Identification of ethinylestradiol as a ligand for the mutated human estradiol receptor was supported by in silico binding studies showing the reduced binding of caged ethinylestradiol. Caged ethinylestradiol was injected into the eyes of double transgenic GFAP-CreERT2 mice with a Cre-dependent tdTomato reporter transgene followed by irradiation with light of 450 nm. Photoactivation significantly increased retinal tdTomato expression compared to controls. We thus demonstrated a first step towards the development of a targeted, light-mediated gene therapy for the eyes.
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Affiliation(s)
- Zoe Kiy
- Heidelberg University, 69120, Heidelberg, Germany
| | - Juliane Chaud
- Laboratoire de Conception et Application de Molécules Bioactives, Equipe de Chimie et Neurobiologie Moléculaire, Université de Strasbourg, CNRS, CAMB UMR 7199, 67000, Strasbourg, France
| | - Liang Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Eric Brandhorst
- Sektion Endokrinologie, Medizinische Fakultät Mannheim, 68167, Mannheim, Germany
| | - Tschackad Kamali
- Heidelberg Engineering GmbH, Max-Jarecki-Straße 8, 69115, Heidelberg, Germany
| | - Carolyn Vargas
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Sandro Keller
- Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Humboldtstr. 50/III, 8010, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Alexandre Specht
- Laboratoire de Conception et Application de Molécules Bioactives, Equipe de Chimie et Neurobiologie Moléculaire, Université de Strasbourg, CNRS, CAMB UMR 7199, 67000, Strasbourg, France
| | - Sidney Cambridge
- Heidelberg University, 69120, Heidelberg, Germany
- Institute for Anatomy II, Dr. Senckenberg Anatomy, Goethe-University Frankfurt am Main, 60590, Frankfurt am Main, Germany
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3
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Darrah K, Albright S, Kumbhare R, Tsang M, Chen JK, Deiters A. Antisense Oligonucleotide Activation via Enzymatic Antibiotic Resistance Mechanism. ACS Chem Biol 2023; 18:2176-2182. [PMID: 37326511 PMCID: PMC10592181 DOI: 10.1021/acschembio.3c00027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
The structure and mechanism of the bacterial enzyme β-lactamase have been well-studied due to its clinical role in antibiotic resistance. β-Lactamase is known to hydrolyze the β-lactam ring of the cephalosporin scaffold, allowing a spontaneous self-immolation to occur. Previously, cephalosporin-based sensors have been developed to evaluate β-lactamase expression in both mammalian cells and zebrafish embryos. Here, we present a circular caged morpholino oligonucleotide (cMO) activated by β-lactamase-mediated cleavage of a cephalosporin motif capable of silencing the expression of T-box transcription factor Ta (tbxta), also referred to as no tail a (ntla), eliciting a distinct, observable phenotype. We explore the use of β-lactamase to elicit a biological response in aquatic embryos for the first time and expand the utility of cephalosporin as a cleavable linker beyond targeting antibiotic-resistant bacteria. The addition of β-lactamase to the current suite of enzymatic triggers presents unique opportunities for robust, orthogonal control over endogenous gene expression in a spatially resolved manner.
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Affiliation(s)
- Kristie
E. Darrah
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Savannah Albright
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Rohan Kumbhare
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department
of Developmental Biology, University of
Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - James K. Chen
- Department
of Chemical and Systems Biology, Stanford
University School of Medicine, Stanford, California 94305, United States
| | - Alexander Deiters
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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4
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Pattanayak S, Sarode BR, Deiters A, Chen JK. Bicyclic Caged Morpholino Oligonucleotides for Optical Gene Silencing. Chembiochem 2022; 23:e202200374. [PMID: 36068175 PMCID: PMC9637763 DOI: 10.1002/cbic.202200374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/02/2022] [Indexed: 11/07/2022]
Abstract
Caged morpholino oligonucleotides (cMOs) are synthetic tools that allow light-inducible gene silencing in live organisms. Previously reported cMOs have utilized hairpin, duplex, and cyclic structures, as well as caged nucleobases. While these antisense technologies enable efficient optical control of RNA splicing and translation, they can have limited dynamic range. A new caging strategy was developed where the two MO termini are conjugated to an internal position through a self-immolative trifunctional linker, thereby generating a bicyclic cMO that is conformationally resistant to RNA binding. The efficacy of this alternative cMO design has been demonstrated in zebrafish embryos and compared to linear MOs and monocyclic constructs.
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Affiliation(s)
- Sankha Pattanayak
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Present Address, Creyon Bio, Inc., San Diego, CA 92121, USA
| | - Bhagyesh R Sarode
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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5
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Darrah K, Wesalo J, Lukasak B, Tsang M, Chen JK, Deiters A. Small Molecule Control of Morpholino Antisense Oligonucleotide Function through Staudinger Reduction. J Am Chem Soc 2021; 143:18665-18671. [PMID: 34705461 DOI: 10.1021/jacs.1c08723] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conditionally activated, caged morpholino antisense agents (cMOs) are tools that enable the temporal and spatial investigation of gene expression, regulation, and function during embryonic development. Cyclic MOs are conformationally gated oligonucleotide analogs that do not block gene expression until they are linearized through the application of an external trigger, such as light or enzyme activity. Here, we describe the first examples of small molecule-responsive cMOs, which undergo rapid and efficient decaging via a Staudinger reduction. This is enabled by a highly flexible linker design that offers opportunities for the installation of chemically activated, self-immolative motifs. We synthesized cyclic cMOs against two distinct, developmentally relevant genes and demonstrated phosphine-triggered knockdown of gene expression in zebrafish embryos. This represents the first report of a small molecule-triggered antisense agent for gene knockdown, adding another bioorthogonal entry to the growing arsenal of gene knockdown tools.
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Affiliation(s)
- Kristie Darrah
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joshua Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Bradley Lukasak
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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6
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Ho C, Morsut L. Novel synthetic biology approaches for developmental systems. Stem Cell Reports 2021; 16:1051-1064. [PMID: 33979593 PMCID: PMC8185972 DOI: 10.1016/j.stemcr.2021.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Recently, developmental systems are investigated with increasing technological power. Still, open questions remain, especially concerning self-organization capacity and its control. Here, we present three areas where synthetic biology tools are used in top-down and bottom-up approaches for studying and constructing developmental systems. First, we discuss how synthetic biology tools can improve stem cell-based organoid models. Second, we discuss recent studies employing user-defined perturbations to study embryonic patterning in model species. Third, we present "toy models" of patterning and morphogenesis using synthetic genetic circuits in non-developmental systems. Finally, we discuss how these tools and approaches can specifically benefit the field of embryo models.
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Affiliation(s)
- Christine Ho
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Leonardo Morsut
- Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA.
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7
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Abou Nakad E, Bolze F, Specht A. o-Nitrobenzyl photoremovable groups with fluorescence uncaging reporting properties. Org Biomol Chem 2019; 16:6115-6122. [PMID: 30094422 DOI: 10.1039/c8ob01330f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
o-Nitrobenzyl (o-NB) derivatives are the most widely applied photoremovable groups for the study of dynamic biological processes. By introducing different substituents to the benzylic position we were able to generate a fluorescence signal upon irradiation. This signal originates from the formation of a nitrosoketone by-product able to achieve a keto-enol tautomerism leading to pi-conjugated α-hydroxystilbene derivatives. These o-NB caging groups can be used to directly monitor the uncaging event by the release of a detectable fluorescent side-product.
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Affiliation(s)
- E Abou Nakad
- Laboratoire de Conception et Application de Molécules Bioactives, Equipe de Chimie et Neurobiologie Moléculaire, Université de Strasbourg, CNRS, CAMB UMR 7199, F-67000 Strasbourg, France.
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8
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O’Connor MJ, Beebe LL, Deodato D, Ball RE, Page AT, VanLeuven AJ, Harris KT, Park S, Hariharan V, Lauderdale JD, Dore TM. Bypassing Glutamic Acid Decarboxylase 1 (Gad1) Induced Craniofacial Defects with a Photoactivatable Translation Blocker Morpholino. ACS Chem Neurosci 2019; 10:266-278. [PMID: 30200754 PMCID: PMC6337688 DOI: 10.1021/acschemneuro.8b00231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
![]()
γ-Amino
butyric acid (GABA) mediated signaling is critical
in the central and enteric nervous systems, pancreas, lungs, and other
tissues. It is associated with many neurological disorders and craniofacial
development. Glutamic acid decarboxylase (GAD) synthesizes GABA from
glutamate, and knockdown of the gad1 gene results
in craniofacial defects that are lethal in zebrafish. To bypass this
and enable observation of the neurological defects resulting from
knocking down gad1 expression, a photoactivatable
morpholino oligonucleotide (MO) against gad1 was
prepared by cyclization with a photocleavable linker rendering the
MO inactive. The cyclized MO was stable in the dark and toward degradative
enzymes and was completely linearized upon brief exposure to 405 nm
light. In the course of investigating the function of the ccMOs in
zebrafish, we discovered that zebrafish possess paralogous gad1 genes, gad1a and gad1b. A gad1b MO injected at the 1–4 cell stage
caused severe morphological defects in head development, which could
be bypassed, enabling the fish to develop normally, if the fish were
injected with a photoactivatable, cyclized gad1b MO
and grown in the dark. At 1 day post fertilization (dpf), light activation
of the gad1b MO followed by observation at 3 and
7 dpf led to increased and abnormal electrophysiological brain activity
compared to wild type animals. The photocleavable linker can be used
to cyclize and inactivate any MO, and represents a general strategy
to parse the function of developmentally important genes in a spatiotemporal
manner.
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Affiliation(s)
- Matthew J. O’Connor
- New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Lindsey L. Beebe
- Department of Genetics, University of Georgia, Athens, Georgia 30602, United States
| | - Davide Deodato
- New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Rebecca E. Ball
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - A. Tyler Page
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Ariel J. VanLeuven
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Kyle T. Harris
- Department of Chemistry, University of Georgia, Athens, Georgia 30602 United States
| | - Sungdae Park
- Department of Genetics, University of Georgia, Athens, Georgia 30602, United States
| | - Vani Hariharan
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - James D. Lauderdale
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
- Neuroscience
Division
of the Biomedical and Health Sciences Institute, Athens, Georgia 30602, United States
| | - Timothy M. Dore
- New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
- Department of Chemistry, University of Georgia, Athens, Georgia 30602 United States
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9
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Goegan B, Terzi F, Bolze F, Cambridge S, Specht A. Synthesis and Characterization of Photoactivatable Doxycycline Analogues Bearing Two-Photon-Sensitive Photoremovable Groups Suitable for Light-Induced Gene Expression. Chembiochem 2018; 19:1341-1348. [DOI: 10.1002/cbic.201700628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Bastien Goegan
- Laboratoire de Conception et Application de Molécules Bioactives; UMR 7199; CNRS; Faculté de Pharmacie; Université de Strasbourg; 74 Route du Rhin 67400 Illkirch France
| | - Firat Terzi
- University of Heidelberg; Department of Functional Neuroanatomy; Im Neuenheimer Feld 307 69120 Heidelberg Germany
| | - Frédéric Bolze
- Laboratoire de Conception et Application de Molécules Bioactives; UMR 7199; CNRS; Faculté de Pharmacie; Université de Strasbourg; 74 Route du Rhin 67400 Illkirch France
| | - Sidney Cambridge
- University of Heidelberg; Department of Functional Neuroanatomy; Im Neuenheimer Feld 307 69120 Heidelberg Germany
| | - Alexandre Specht
- Laboratoire de Conception et Application de Molécules Bioactives; UMR 7199; CNRS; Faculté de Pharmacie; Université de Strasbourg; 74 Route du Rhin 67400 Illkirch France
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10
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Zhang Y, Thapaliya ER, Tang S, Baker JD, Raymo FM. Supramolecular delivery of fluorescent probes in developing embryos. RSC Adv 2016. [DOI: 10.1039/c6ra15368b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Self-assembling nanocarriers of amphiphilic polymers encapsulate hydrophobic fluorophores in their hydrophobic interior and, upon injection in Drosophila melanogaster embryos, release their cargo into the cellular blastoderm.
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Affiliation(s)
- Yang Zhang
- Laboratory for Molecular Photonics
- Departments of Biology and Chemistry
- University of Miami
- Coral Gables
- USA
| | - Ek Raj Thapaliya
- Laboratory for Molecular Photonics
- Departments of Biology and Chemistry
- University of Miami
- Coral Gables
- USA
| | - Sicheng Tang
- Laboratory for Molecular Photonics
- Departments of Biology and Chemistry
- University of Miami
- Coral Gables
- USA
| | - James D. Baker
- Laboratory for Molecular Photonics
- Departments of Biology and Chemistry
- University of Miami
- Coral Gables
- USA
| | - Françisco M. Raymo
- Laboratory for Molecular Photonics
- Departments of Biology and Chemistry
- University of Miami
- Coral Gables
- USA
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11
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Zheng C, Zhou H, Liu X, Pang Y, Zhang B, Huang Y. Fish in chips: an automated microfluidic device to study drug dynamics in vivo using zebrafish embryos. Chem Commun (Camb) 2014; 50:981-4. [DOI: 10.1039/c3cc47285j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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12
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Shen J, Chen G, Ohulchanskyy TY, Kesseli SJ, Buchholz S, Li Z, Prasad PN, Han G. Tunable near infrared to ultraviolet upconversion luminescence enhancement in (α-NaYF4 :Yb,Tm)/CaF2 core/shell nanoparticles for in situ real-time recorded biocompatible photoactivation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3213-3217. [PMID: 23696330 DOI: 10.1002/smll.201300234] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Indexed: 06/02/2023]
Abstract
A family of upconverting nanoparticles (UCNPs) with a tunable UV enhancement is developed via a facile approach. The design leads to a maximum 9-fold enhancement in comparison with known optimal β-phase core/shell UCNPs in water. A highly effective and rapid in situ real-time live-cell photoactivation is recorded for the first time with such nanoparticles.
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Affiliation(s)
- Jie Shen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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13
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Fournier L, Gauron C, Xu L, Aujard I, Le Saux T, Gagey-Eilstein N, Maurin S, Dubruille S, Baudin JB, Bensimon D, Volovitch M, Vriz S, Jullien L. A blue-absorbing photolabile protecting group for in vivo chromatically orthogonal photoactivation. ACS Chem Biol 2013; 8:1528-36. [PMID: 23651265 DOI: 10.1021/cb400178m] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The small and synthetically easily accessible 7-diethylamino-4-thiocoumarinylmethyl photolabile protecting group has been validated for uncaging with blue light. It exhibits a significant action cross-section for uncaging in the 470-500 nm wavelength range and a low light absorption between 350 and 400 nm. These attractive features have been implemented in living zebrafish embryos to perform chromatic orthogonal photoactivation of two biologically active species controlling biological development with UV and blue-cyan light sources, respectively.
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Affiliation(s)
- Ludovic Fournier
- Ecole Normale Supérieure,
Département de Chimie, UMR CNRS-ENS-UPMC 8640 PASTEUR, 24, rue Lhomond, 75231 Paris Cedex 05, France
| | - Carole Gauron
- Collège de France, Center
for Interdisciplinary Research in Biology (CIRB), CNRS, UMR 7241, INSERM, U1050, 11, Place Marcelin Berthelot,
75231 Paris Cedex 05, France
| | - Lijun Xu
- Ecole Normale Supérieure,
Département de Physique and Département de Biologie,
Laboratoire de Physique Statistique, UMR CNRS-ENS 8550, 24 rue Lhomond, F-75231 Paris, France
| | - Isabelle Aujard
- Ecole Normale Supérieure,
Département de Chimie, UMR CNRS-ENS-UPMC 8640 PASTEUR, 24, rue Lhomond, 75231 Paris Cedex 05, France
| | - Thomas Le Saux
- Ecole Normale Supérieure,
Département de Chimie, UMR CNRS-ENS-UPMC 8640 PASTEUR, 24, rue Lhomond, 75231 Paris Cedex 05, France
- UPMC, 4, Place Jussieu,
75232 Paris Cedex 05, France,
| | - Nathalie Gagey-Eilstein
- Ecole Normale Supérieure,
Département de Chimie, UMR CNRS-ENS-UPMC 8640 PASTEUR, 24, rue Lhomond, 75231 Paris Cedex 05, France
| | - Sylvie Maurin
- Ecole Normale Supérieure,
Département de Chimie, UMR CNRS-ENS-UPMC 8640 PASTEUR, 24, rue Lhomond, 75231 Paris Cedex 05, France
| | - Sylvie Dubruille
- Institut Curie, Centre de Recherche, CNRS, UMR 176, 26, rue d’Ulm, Paris F-75248,
France
| | - Jean-Bernard Baudin
- Ecole Normale Supérieure,
Département de Chimie, UMR CNRS-ENS-UPMC 8640 PASTEUR, 24, rue Lhomond, 75231 Paris Cedex 05, France
| | - David Bensimon
- Ecole Normale Supérieure,
Département de Physique and Département de Biologie,
Laboratoire de Physique Statistique, UMR CNRS-ENS 8550, 24 rue Lhomond, F-75231 Paris, France
- Department of Chemistry
and Biochemistry, University of California, Los Angeles, Los Angeles,
California, United States
| | - Michel Volovitch
- Collège de France, Center
for Interdisciplinary Research in Biology (CIRB), CNRS, UMR 7241, INSERM, U1050, 11, Place Marcelin Berthelot,
75231 Paris Cedex 05, France
| | - Sophie Vriz
- Collège de France, Center
for Interdisciplinary Research in Biology (CIRB), CNRS, UMR 7241, INSERM, U1050, 11, Place Marcelin Berthelot,
75231 Paris Cedex 05, France
| | - Ludovic Jullien
- Ecole Normale Supérieure,
Département de Chimie, UMR CNRS-ENS-UPMC 8640 PASTEUR, 24, rue Lhomond, 75231 Paris Cedex 05, France
- UPMC, 4, Place Jussieu,
75232 Paris Cedex 05, France,
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14
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Shestopalov IA, Chen JK. Spatiotemporal control of embryonic gene expression using caged morpholinos. Methods Cell Biol 2011; 104:151-72. [PMID: 21924162 DOI: 10.1016/b978-0-12-374814-0.00009-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Embryonic development depends on spatial and temporal control of gene function, and deciphering the molecular mechanisms that underlie pattern formation requires methods for perturbing gene expression with similar precision. Emerging chemical technologies can enable such perturbations, as exemplified by the use of caged morpholino (cMO) oligonucleotides to photo-inactivate genes in zebrafish embryos with spatiotemporal control. This chapter describes general principles for cMO design and methods for cMO assembly in three steps from commercially available reagents. Experimental techniques for the microinjection and photoactivation of these reagents are described in detail, as well as the preparation and application of caged fluorescein dextran (cFD) for labeling irradiated cells. Using these protocols, cMOs can be effective tools for functional genomic studies in zebrafish and other model organisms.
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Affiliation(s)
- Ilya A Shestopalov
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford,California, USA
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Sinha DK, Neveu P, Gagey N, Aujard I, Benbrahim-Bouzidi C, Le Saux T, Rampon C, Gauron C, Goetz B, Dubruille S, Baaden M, Volovitch M, Bensimon D, Vriz S, Jullien L. Photocontrol of protein activity in cultured cells and zebrafish with one- and two-photon illumination. Chembiochem 2010; 11:653-63. [PMID: 20187057 DOI: 10.1002/cbic.201000008] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We have implemented a noninvasive optical method for the fast control of protein activity in a live zebrafish embryo. It relies on releasing a protein fused to a modified estrogen receptor ligand binding domain from its complex with cytoplasmic chaperones, upon the local photoactivation of a nonendogenous caged inducer. Molecular dynamics simulations were used to design cyclofen-OH, a photochemically stable inducer of the receptor specific for 4-hydroxy-tamoxifen (ER(T2)). Cyclofen-OH was easily synthesized in two steps with good yields. At submicromolar concentrations, it activates proteins fused to the ER(T2) receptor. This was shown in cultured cells and in zebrafish embryos through emission properties and subcellular localization of properly engineered fluorescent proteins. Cyclofen-OH was successfully caged with various photolabile protecting groups. One particular caged compound was efficient in photoinducing the nuclear translocation of fluorescent proteins either globally (with 365 nm UV illumination) or locally (with a focused UV laser or with two-photon illumination at 750 nm). The present method for photocontrol of protein activity could be used more generally to investigate important physiological processes (e.g., in embryogenesis, organ regeneration and carcinogenesis) with high spatiotemporal resolution.
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Affiliation(s)
- Deepak Kumar Sinha
- Ecole Normale Supérieure, Département de Physique, Laboratoire de Physique Statistique UMR CNRS-ENS 8550, 24 rue Lhomond, 75231 Paris, France
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Shestopalov IA, Chen JK. Oligonucleotide-based tools for studying zebrafish development. Zebrafish 2010; 7:31-40. [PMID: 20392138 DOI: 10.1089/zeb.2010.0650] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Synthetic and nonnatural oligonucleotides have been used extensively to interrogate gene function in zebrafish. In this review, we survey the capabilities and limitations of various oligonucleotide-based technologies for perturbing RNA function and tracking RNA expression. We also examine recent strategies for achieving spatiotemporal control of oligonucleotide function, particularly light-gated technologies that exploit the optical transparency of zebrafish embryos.
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Affiliation(s)
- Ilya A Shestopalov
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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17
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Ouyang X, Shestopalov IA, Sinha S, Zheng G, Pitt CLW, Li WH, Olson AJ, Chen JK. Versatile synthesis and rational design of caged morpholinos. J Am Chem Soc 2010; 131:13255-69. [PMID: 19708646 PMCID: PMC2745229 DOI: 10.1021/ja809933h] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Embryogenesis is regulated by genetic programs that are dynamically executed in a stereotypic manner, and deciphering these molecular mechanisms requires the ability to control embryonic gene function with similar spatial and temporal precision. Chemical technologies can enable such genetic manipulations, as exemplified by the use of caged morpholino (cMO) oligonucleotides to inactivate genes in zebrafish and other optically transparent organisms with spatiotemporal control. Here we report optimized methods for the design and synthesis of hairpin cMOs incorporating a dimethoxynitrobenzyl (DMNB)-based bifunctional linker that permits cMO assembly in only three steps from commercially available reagents. Using this simplified procedure, we have systematically prepared cMOs with differing structural configurations and investigated how the in vitro thermodynamic properties of these reagents correlate with their in vivo activities. Through these studies, we have established general principles for cMO design and successfully applied them to several developmental genes. Our optimized synthetic and design methodologies have also enabled us to prepare a next-generation cMO that contains a bromohydroxyquinoline (BHQ)-based linker for two-photon uncaging. Collectively, these advances establish the generality of cMO technologies and will facilitate the application of these chemical probes in vivo for functional genomic studies.
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Affiliation(s)
- Xiaohu Ouyang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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18
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Yu H, Li J, Wu D, Qiu Z, Zhang Y. Chemistry and biological applications of photo-labile organic molecules. Chem Soc Rev 2010; 39:464-73. [DOI: 10.1039/b901255a] [Citation(s) in RCA: 213] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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A modified consumer inkjet for spatiotemporal control of gene expression. PLoS One 2009; 4:e7086. [PMID: 19763256 PMCID: PMC2739290 DOI: 10.1371/journal.pone.0007086] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 08/19/2009] [Indexed: 01/28/2023] Open
Abstract
This paper presents a low-cost inkjet dosing system capable of continuous, two-dimensional spatiotemporal regulation of gene expression via delivery of diffusible regulators to a custom-mounted gel culture of E. coli. A consumer-grade, inkjet printer was adapted for chemical printing; E. coli cultures were grown on 750 microm thick agar embedded in micro-wells machined into commercial compact discs. Spatio-temporal regulation of the lac operon was demonstrated via the printing of patterns of lactose and glucose directly into the cultures; X-Gal blue patterns were used for visual feedback. We demonstrate how the bistable nature of the lac operon's feedback, when perturbed by patterning lactose (inducer) and glucose (inhibitor), can lead to coordination of cell expression patterns across a field in ways that mimic motifs seen in developmental biology. Examples of this include sharp boundaries and the generation of traveling waves of mRNA expression. To our knowledge, this is the first demonstration of reaction-diffusion effects in the well-studied lac operon. A finite element reaction-diffusion model of the lac operon is also presented which predicts pattern formation with good fidelity.
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Casey JP, Blidner RA, Monroe WT. Caged siRNAs for Spatiotemporal Control of Gene Silencing. Mol Pharm 2009; 6:669-85. [DOI: 10.1021/mp900082q] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- John P. Casey
- Department of Biological and Agricultural Engineering, Louisiana State University and the LSU Agricultural Center, Baton Rouge, Louisiana 70803
| | - Richard A. Blidner
- Department of Biological and Agricultural Engineering, Louisiana State University and the LSU Agricultural Center, Baton Rouge, Louisiana 70803
| | - W. Todd Monroe
- Department of Biological and Agricultural Engineering, Louisiana State University and the LSU Agricultural Center, Baton Rouge, Louisiana 70803
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21
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Patterned delivery and expression of gene constructs into zebrafish embryos using microfabricated interfaces. Biomed Microdevices 2009; 11:633-41. [DOI: 10.1007/s10544-008-9273-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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