1
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Chung K, Booth MJ. Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids. Chem Sci 2023; 14:12693-12706. [PMID: 38020373 PMCID: PMC10646958 DOI: 10.1039/d3sc02761a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Plasmids are ubiquitous in biology, where they are used to study gene-function relationships and intricate molecular networks, and hold potential as therapeutic devices. Developing methods to control their function will advance their application in research and may also expedite their translation to clinical settings. Light is an attractive stimulus to conditionally regulate plasmid expression as it is non-invasive, and its properties such as wavelength, intensity, and duration can be adjusted to minimise cellular toxicity and increase penetration. Herein, we have developed a method to site-specifically introduce photocages into plasmids, by resynthesising one strand in a manner similar to Kunkel mutagenesis. Unlike alternative approaches to chemically modify plasmids, this method is sequence-independent at the site of modification and uses commercially available phosphoramidites. To generate our light-activated (LA) plasmids, photocleavable biotinylated nucleobases were introduced at specific sites across the T7 and CMV promoters on plasmids and bound to streptavidin to sterically block access. These LA-plasmids were then successfully used to control expression in both cell-free systems (T7 promoter) and mammalian cells (CMV promoter). These light-activated plasmids might be used to remotely control cellular activity and reduce off-target toxicity for future medical use. Our simple approach to plasmid modification might also be used to introduce novel chemical moieties for advanced function.
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Affiliation(s)
- Khoa Chung
- Department of Chemistry, University of Oxford Mansfield Road OX1 3TA Oxford UK
| | - Michael J Booth
- Department of Chemistry, University of Oxford Mansfield Road OX1 3TA Oxford UK
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
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2
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Bollu A, Klöcker N, Špaček P, P Weissenboeck F, Hüwel S, Rentmeister A. Light-Activated Translation of Different mRNAs in Cells via Wavelength-Dependent Photouncaging. Angew Chem Int Ed Engl 2023; 62:e202209975. [PMID: 36417319 PMCID: PMC10107135 DOI: 10.1002/anie.202209975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/24/2022]
Abstract
The 5' cap is a hallmark of eukaryotic mRNA involved in the initiation of translation. Its modification with a single photo-cleavable group can bring translation of mRNA under the control of light. However, UV irradiation causes cell stress and downregulation of translation. Furthermore, complex processes often involve timed expression of more than one gene. The approach would thus greatly benefit from the ability to photo-cleave by blue light and to control more than one mRNA at a time. We report the synthesis of a 5' cap modified with a 7-(diethylamino)coumarin (CouCap) and adapted conditions for in vitro transcription. Translation of the resulting CouCap-mRNA is muted in vitro and in mammalian cells, and can be initiated by irradiation with 450 nm. The native cap is restored and no non-natural residues nor sequence alterations remain in the mRNA. Multiplexing for two different mRNAs was achieved by combining cap analogs with coumarin- and ortho-nitrobenzyl-based photo-cleavable groups.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Špaček
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Florian P Weissenboeck
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
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3
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Klöcker N, Anhäuser L, Rentmeister A. Enzymatic Modification of the 5' Cap with Photocleavable ONB-Derivatives Using GlaTgs V34A. Chembiochem 2023; 24:e202200522. [PMID: 36408753 PMCID: PMC10108117 DOI: 10.1002/cbic.202200522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/22/2022]
Abstract
The 5' cap of mRNA plays a critical role in mRNA processing, quality control and turnover. Enzymatic availability of the 5' cap governs translation and could be a tool to investigate cell fate decisions and protein functions or develop protein replacement therapies. We have previously reported on the chemical synthesis of 5' cap analogues with photocleavable groups for this purpose. However, the synthesis is complex and post-synthetic enzymatic installation may make the technique more applicable to biological researchers. Common 5' cap analogues, like the cap 0, are commercially available and routinely used for in vitro transcription. Here, we report a facile enzymatic approach to attach photocleavable groups site-specifically to the N2 position of m7 G of the 5' cap. By expanding the substrate scope of the methyltransferase variant GlaTgs V34A and using synthetic co-substrate analogues, we could enzymatically photocage the 5' cap and recover it after irradiation.
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Affiliation(s)
- Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
| | - Lea Anhäuser
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, Münster, Germany
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4
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Feng Z, Ducos B, Scerbo P, Aujard I, Jullien L, Bensimon D. The Development and Application of Opto-Chemical Tools in the Zebrafish. Molecules 2022; 27:6231. [PMID: 36234767 PMCID: PMC9572478 DOI: 10.3390/molecules27196231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
The zebrafish is one of the most widely adopted animal models in both basic and translational research. This popularity of the zebrafish results from several advantages such as a high degree of similarity to the human genome, the ease of genetic and chemical perturbations, external fertilization with high fecundity, transparent and fast-developing embryos, and relatively low cost-effective maintenance. In particular, body translucency is a unique feature of zebrafish that is not adequately obtained with other vertebrate organisms. The animal's distinctive optical clarity and small size therefore make it a successful model for optical modulation and observation. Furthermore, the convenience of microinjection and high embryonic permeability readily allow for efficient delivery of large and small molecules into live animals. Finally, the numerous number of siblings obtained from a single pair of animals offers large replicates and improved statistical analysis of the results. In this review, we describe the development of opto-chemical tools based on various strategies that control biological activities with unprecedented spatiotemporal resolution. We also discuss the reported applications of these tools in zebrafish and highlight the current challenges and future possibilities of opto-chemical approaches, particularly at the single cell level.
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Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Bertrand Ducos
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Letters University, 46 Rue d’Ulm, 75005 Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Inovarion, 75005 Paris, France
| | - Isabelle Aujard
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - Ludovic Jullien
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - David Bensimon
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
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5
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Tavakoli A, Min JH. Photochemical modifications for DNA/RNA oligonucleotides. RSC Adv 2022; 12:6484-6507. [PMID: 35424630 PMCID: PMC8982246 DOI: 10.1039/d1ra05951c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022] Open
Abstract
Light-triggered chemical reactions can provide excellent tools to investigate the fundamental mechanisms important in biology. Light is easily applicable and orthogonal to most cellular events, and its dose and locality can be controlled in tissues and cells. Light-induced conversion of photochemical groups installed on small molecules, proteins, and oligonucleotides can alter their functional states and thus the ensuing biological events. Recently, photochemical control of DNA/RNA structure and function has garnered attention thanks to the rapidly expanding photochemistry used in diverse biological applications. Photoconvertible groups can be incorporated in the backbone, ribose, and nucleobase of an oligonucleotide to undergo various irreversible and reversible light-induced reactions such as cleavage, crosslinking, isomerization, and intramolecular cyclization reactions. In this review, we gather a list of photoconvertible groups used in oligonucleotides and summarize their reaction characteristics, impacts on DNA/RNA thermal stability and structure, as well as their biological applications.
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Affiliation(s)
- Amirrasoul Tavakoli
- Department of Chemistry & Biochemistry, Baylor University Waco TX 76706 USA +1-254-710-2095
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University Waco TX 76706 USA +1-254-710-2095
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6
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Darrah KE, Deiters A. Translational control of gene function through optically regulated nucleic acids. Chem Soc Rev 2021; 50:13253-13267. [PMID: 34739027 DOI: 10.1039/d1cs00257k] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Translation of mRNA into protein is one of the most fundamental processes within biological systems. Gene expression is tightly regulated both in space and time, often involving complex signaling or gene regulatory networks, as most prominently observed in embryo development. Thus, studies of gene function require tools with a matching level of external control. Light is an excellent conditional trigger as it is minimally invasive, can be easily tuned in wavelength and amplitude, and can be applied with excellent spatial and temporal resolution. To this end, modification of established oligonucleotide-based technologies with optical control elements, in the form of photocaging groups and photoswitches, has rendered these tools capable of navigating the dynamic regulatory pathways of mRNA translation in cellular and in vivo models. In this review, we discuss the different optochemical approaches used to generate photoresponsive nucleic acids that activate and deactivate gene expression and function at the translational level.
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Affiliation(s)
- Kristie E Darrah
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA.
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA.
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7
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Matinkhoo K, Pryyma A, Wong AAWL, Perrin DM. Synthesis and evaluation of " Ama-Flash", a photocaged amatoxin prodrug for light-activated RNA Pol II inhibition and cell death. Chem Commun (Camb) 2021; 57:9558-9561. [PMID: 34477193 DOI: 10.1039/d1cc03279h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Amanitin is used extensively as a research tool to inhibit RNA Pol II thereby implicating its role in mRNA transcription. Recently, amanitin has gained traction as a toxic payload for targeted therapy. Here we report the first-ever photocaged amanitin analog, that is non-toxic and can be pre-loaded into cells. Light provides a means to inhibit RNA Pol II and provoke cell death on-demand.
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Affiliation(s)
- Kaveh Matinkhoo
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
| | - Alla Pryyma
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
| | - Antonio A W L Wong
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
| | - David M Perrin
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
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8
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Yang L, Trentini D, Kim H, Sul J, Eberwine JH, Dmochowski IJ. Photoactivatable Circular Caged Oligonucleotides for Transcriptome In Vivo Analysis (TIVA). CHEMPHOTOCHEM 2021; 5:940-946. [DOI: 10.1002/cptc.202100098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Linlin Yang
- Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
| | - Dora Trentini
- Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
| | - HyunBum Kim
- Department of Pharmacology University of Pennsylvania 38 John Morgan Building 3620 Hamilton Walk Philadelphia PA 19104-6084 USA
| | - Jai‐Yoon Sul
- Department of Pharmacology University of Pennsylvania 38 John Morgan Building 3620 Hamilton Walk Philadelphia PA 19104-6084 USA
| | - James H. Eberwine
- Department of Pharmacology University of Pennsylvania 38 John Morgan Building 3620 Hamilton Walk Philadelphia PA 19104-6084 USA
| | - Ivan J. Dmochowski
- Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
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9
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Kabza AM, Kundu N, Zhong W, Sczepanski JT. Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 14:e1743. [PMID: 34328690 DOI: 10.1002/wnan.1743] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/26/2021] [Accepted: 07/06/2021] [Indexed: 01/21/2023]
Abstract
Watson-Crick base pairing rules provide a powerful approach for engineering DNA-based nanodevices with programmable and predictable behaviors. In particular, DNA strand displacement reactions have enabled the development of an impressive repertoire of molecular devices with complex functionalities. By relying on DNA to function, dynamic strand displacement devices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation in living systems has been a slow process due to several persistent challenges, including nuclease degradation. To circumvent these issues, researchers are increasingly turning to chemically modified nucleotides as a means to increase device performance and reliability within harsh biological environments. In this review, we summarize recent progress toward the integration of chemically modified nucleotides with DNA strand displacement reactions, highlighting key successes in the development of robust systems and devices that operate in living cells and in vivo. We discuss the advantages and disadvantages of commonly employed modifications as they pertain to DNA strand displacement, as well as considerations that must be taken into account when applying modified oligonucleotide to living cells. Finally, we explore how chemically modified nucleotides fit into the broader goal of bringing dynamic DNA nanotechnology into the cell, and the challenges that remain. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > Biosensing.
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Affiliation(s)
- Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Wenrui Zhong
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
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10
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Yang L, Dmochowski IJ. Conditionally Activated ("Caged") Oligonucleotides. Molecules 2021; 26:1481. [PMID: 33803234 PMCID: PMC7963183 DOI: 10.3390/molecules26051481] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 01/09/2023] Open
Abstract
Conditionally activated ("caged") oligonucleotides provide useful spatiotemporal control for studying dynamic biological processes, e.g., regulating in vivo gene expression or probing specific oligonucleotide targets. This review summarizes recent advances in caging strategies, which involve different stimuli in the activation step. Oligo cyclization is a particularly attractive caging strategy, which simplifies the probe design and affords oligo stabilization. Our laboratory developed an efficient synthesis for circular caged oligos, and a circular caged antisense DNA oligo was successfully applied in gene regulation. A second technology is Transcriptome In Vivo Analysis (TIVA), where caged oligos enable mRNA isolation from single cells in living tissue. We highlight our development of TIVA probes with improved caging stability. Finally, we illustrate the first protease-activated oligo probe, which was designed for caspase-3. This expands the toolkit for investigating the transcriptome under a specific physiologic condition (e.g., apoptosis), particularly in specimens where light activation is impractical.
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Affiliation(s)
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA;
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11
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Patel R, Sarma S, Shukla A, Parmar P, Goswami D, Saraf M. Walking through the wonder years of artificial DNA: peptide nucleic acid. Mol Biol Rep 2020; 47:8113-8131. [PMID: 32990905 DOI: 10.1007/s11033-020-05819-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 09/04/2020] [Indexed: 11/26/2022]
Abstract
Peptide Nucleic Acid (PNA) serves as an artificial functional analog of DNA. Being immune to enzymatic degradation and possessing strong affinity towards DNA and RNA, it is an ideal candidate for many medical and biotechnological applications that are of antisense and antigene in nature. PNAs are anticipated to have its application in DNA and RNA detection as well as quantification, to serve as antibacterial and antiviral agents, and silencing gene for developing anticancer strategies. Although, their restricted entry in both eukaryotic and prokaryotic cells limit their applications. In addition, aggregation of PNA in storage containers reduces the quality and quantity of functional PNA that makes it inadequate for their mass production and storage. To overcome these limitations, researchers have modified PNA either by the addition of diverse functional groups at various loci on its backbone, or by synthesizing chimeras with other moieties associated with various delivery agents that aids their entry into the cell. Here, this review article summarizes few of the structural modifications that are performed with PNA, methods used to improve their cellular uptake and shedding light on the applications of PNA in various prospects in biological sciences.
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Affiliation(s)
- Rohit Patel
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Sameera Sarma
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Arpit Shukla
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Paritosh Parmar
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dweipayan Goswami
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Meenu Saraf
- Department of Microbiology and Biotechnology, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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12
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Hartmann D, Smith JM, Mazzotti G, Chowdhry R, Booth MJ. Controlling gene expression with light: a multidisciplinary endeavour. Biochem Soc Trans 2020; 48:1645-1659. [PMID: 32657338 PMCID: PMC7458398 DOI: 10.1042/bst20200014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022]
Abstract
The expression of a gene to a protein is one of the most vital biological processes. The use of light to control biology offers unparalleled spatiotemporal resolution from an external, orthogonal signal. A variety of methods have been developed that use light to control the steps of transcription and translation of specific genes into proteins, for cell-free to in vivo biotechnology applications. These methods employ techniques ranging from the modification of small molecules, nucleic acids and proteins with photocages, to the engineering of proteins involved in gene expression using naturally light-sensitive proteins. Although the majority of currently available technologies employ ultraviolet light, there has been a recent increase in the use of functionalities that work at longer wavelengths of light, to minimise cellular damage and increase tissue penetration. Here, we discuss the different chemical and biological methods employed to control gene expression, while also highlighting the central themes and the most exciting applications within this diverse field.
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Affiliation(s)
- Denis Hartmann
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Jefferson M. Smith
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Giacomo Mazzotti
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Razia Chowdhry
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Michael J. Booth
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
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13
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Zhang D, Jin S, Piao X, Devaraj NK. Multiplexed Photoactivation of mRNA with Single-Cell Resolution. ACS Chem Biol 2020; 15:1773-1779. [PMID: 32484653 DOI: 10.1021/acschembio.0c00205] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We demonstrate sequential optical activation of two types of mRNAs in the same mammalian cell through the sequential photocleavage of small molecule caging groups ("photocages") tethered to the 5'-untranslated region (5'-UTR) of mRNAs. Synthetic photocages were conjugated onto target mRNA using RNA-TAG, an enzymatic site-specific RNA modification technique. Translation of mRNA was severely reduced upon conjugation of the photocages onto the 5'-UTR. However, subsequent photorelease of the cages from the mRNA transcript triggered activation of translation with single-cell spatiotemporal resolution. To achieve sequential photoactivation of two mRNAs in the same cell, we synthesized a pair of photocages that can be selectively cleaved from mRNA upon photoirradiation with different wavelengths of light. Sequential photoactivation of two mRNAs enabled precise optical control of translation of two unique transcripts. We believe that this modular approach to precisely and rapidly control gene expression will serve as a powerful tool in future biological studies that require controlling translation of multiple transcripts with high spatiotemporal resolution.
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Affiliation(s)
- Dongyang Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Shuaijiang Jin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Xijun Piao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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14
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Tam DY, Zhuang X, Wong SW, Lo PK. Photoresponsive Self-Assembled DNA Nanomaterials: Design, Working Principles, and Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805481. [PMID: 30861628 DOI: 10.1002/smll.201805481] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/30/2019] [Indexed: 05/23/2023]
Abstract
Photoresponsive DNA nanomaterials represent a new class of remarkable functional materials. By adjusting the irradiation wavelength, light intensity, and exposure time, various photocontrolled DNA-based systems can be reversibly or irreversibly regulated in respect of their size, shape, conformation, movement, and dissociation/association. This Review introduces the most updated progress in the development of photoresponsive DNA-based system and emphasizes their advantages over other stimuli-responsive systems. Their design and mechanisms to trigger the photoresponses are shown and discussed. The potential application of these photon-responsive DNA nanomaterials in biology, biomedicine, materials science, nanophotonic and nanoelectronic are also covered and described. The challenges faced and further directions of the development of photocontrolled DNA-based systems are also highlighted.
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Affiliation(s)
- Dick Yan Tam
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Xinyu Zhuang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Sze Wing Wong
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
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15
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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: 3.4] [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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16
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Cheong H, Kim J, Mu J, Zhang W, Li J, Yang H, Xing B. Spatiotemporal‐Controlled Reporter for Cell‐Surface Proteolytic Enzyme Activity Visualization. Chembiochem 2018; 20:561-567. [DOI: 10.1002/cbic.201800445] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/08/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Haolun Cheong
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
| | - Jisu Kim
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
| | - Jing Mu
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
| | - Wenmin Zhang
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
- College of ChemistryFuzhou University Fuzhou Fujian 350116 P.R. China
| | - Juan Li
- College of ChemistryFuzhou University Fuzhou Fujian 350116 P.R. China
| | - HuangHao Yang
- College of ChemistryFuzhou University Fuzhou Fujian 350116 P.R. China
| | - Bengang Xing
- Division of Chemistry and Biological ChemistrySchool of Physical and Mathematical SciencesNanyang Technological University Singapore 637371 Singapore
- College of ChemistryFuzhou University Fuzhou Fujian 350116 P.R. China
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17
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Zhang C, Cheng L, Dong G, Han G, Yang X, Tang C, Li X, Zhou Y, Du L, Li M. Novel photoactivatable substrates for Renilla luciferase imaging in vitro and in vivo. Org Biomol Chem 2018; 16:4789-4792. [PMID: 29926875 PMCID: PMC6165844 DOI: 10.1039/c8ob01192c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To develop a photoactivatable bioluminescence imaging technique, a set of high and efficient photoactivatable substrates for Renilla luciferase has been well designed and synthesized. Surprisingly, all of them could release the free luciferin that presented robust bioluminescent signals ex vivo and in living animals after UV irradiation at 365 nm.
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Affiliation(s)
- Chaochao Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, School of Pharmacy, Shandong University, Jinan, Shandong 250012, China, ; Fax: +86-531-8838-2076; Tel: +86-531-8838-2076
| | - Lin Cheng
- Department of Ultrasound, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Gaopan Dong
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, School of Pharmacy, Shandong University, Jinan, Shandong 250012, China, ; Fax: +86-531-8838-2076; Tel: +86-531-8838-2076
| | - Guangxi Han
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, School of Pharmacy, Shandong University, Jinan, Shandong 250012, China, ; Fax: +86-531-8838-2076; Tel: +86-531-8838-2076
| | - Xingye Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, School of Pharmacy, Shandong University, Jinan, Shandong 250012, China, ; Fax: +86-531-8838-2076; Tel: +86-531-8838-2076
| | - Chunchao Tang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, School of Pharmacy, Shandong University, Jinan, Shandong 250012, China, ; Fax: +86-531-8838-2076; Tel: +86-531-8838-2076
| | - Xiang Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, School of Pharmacy, Shandong University, Jinan, Shandong 250012, China, ; Fax: +86-531-8838-2076; Tel: +86-531-8838-2076
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Lupei Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, School of Pharmacy, Shandong University, Jinan, Shandong 250012, China, ; Fax: +86-531-8838-2076; Tel: +86-531-8838-2076
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, School of Pharmacy, Shandong University, Jinan, Shandong 250012, China, ; Fax: +86-531-8838-2076; Tel: +86-531-8838-2076
- Shenzhen Research Institute, Shandong University, Shenzhen, Guangdong 518057, China
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18
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Yang L, Kim HB, Sul JY, Yeldell SB, Eberwine JH, Dmochowski IJ. Efficient Synthesis of Light-Triggered Circular Antisense Oligonucleotides Targeting Cellular Protein Expression. Chembiochem 2018; 19:1250-1254. [PMID: 29479781 PMCID: PMC6248878 DOI: 10.1002/cbic.201800012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 02/06/2023]
Abstract
Light-activated ("caged") antisense oligonucleotides are powerful molecules for regulating gene expression at submicron spatial resolution through the focal modulation of endogenous cellular processes. Cyclized caged oligos are particularly promising structures because of their inherent stability and similarity to naturally occurring circular DNA and RNA molecules. Here, we introduce an efficient route for cyclizing an antisense oligodeoxynucleotide incorporating a photocleavable linker. Oligo cyclization was achieved for several sequences in nearly quantitative yields through intramolecular copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). Caging stability and light activation were characterized by FRET efficiency, denaturing gel assay, and melting temperature measurements. Finally, a cyclized caged oligo was designed to target gfap, and it gave a tenfold reduction in glial fibrillary acidic protein upon photoactivation in astrocytes.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, USA
| | - Hyun Bum Kim
- Department of Pharmacology, University of Pennsylvania, 38 John Morgan Building, 3620 Hamilton Walk, Philadelphia, PA, 19104-6084, USA
| | - Jai-Yoon Sul
- Department of Pharmacology, University of Pennsylvania, 38 John Morgan Building, 3620 Hamilton Walk, Philadelphia, PA, 19104-6084, USA
| | - Sean B Yeldell
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, USA
| | - James H Eberwine
- Department of Pharmacology, University of Pennsylvania, 38 John Morgan Building, 3620 Hamilton Walk, Philadelphia, PA, 19104-6084, USA
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, USA
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19
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Abstract
External photocontrol over RNA function has emerged as a useful tool for studying nucleic acid biology. Most current methods rely on fully synthetic nucleic acids with photocaged nucleobases, limiting application to relatively short synthetic RNAs. Here we report a method to gain photocontrol over RNA by postsynthetic acylation of 2'-hydroxyls with photoprotecting groups. One-step introduction of these groups efficiently blocks hybridization, which is restored after light exposure. Polyacylation (termed cloaking) enables control over a hammerhead ribozyme, illustrating optical control of RNA catalytic function. Use of the new approach on a transcribed 237 nt RNA aptamer demonstrates the utility of this method to switch on RNA folding in a cellular context, and underlines the potential for application in biological studies.
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Affiliation(s)
- Willem A Velema
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Anna M. Kietrys
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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20
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Zhang L, Chen C, Fan X, Tang X. Photomodulating Gene Expression by Using Caged siRNAs with Single-Aptamer Modification. Chembiochem 2018; 19:1259-1263. [PMID: 29488297 DOI: 10.1002/cbic.201700623] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Indexed: 12/21/2022]
Abstract
Caged siRNAs incorporating terminal modification were rationally designed for photochemical regulation of gene silencing induced by RNA interference (RNAi). Through the conjugation of a single oligonucleotide aptamer at the 5' terminus of the antisense RNA strand, enhancement of the blocking effect for RNA-induced silencing complex (RISC) formation/processing was expected, due both/either to the aptamers themselves and/or to their interaction with large binding proteins. Two oligonucleotide aptamers (AS1411 and MUC-1) were chosen for aptamer-siRNA conjugation through a photolabile linker. This caging strategy was successfully used to photoregulate gene expression both of firefly luciferase and of green fluorescent protein (GFP) in cells. Further patterning experiments revealed that spatial regulation of GFP expression was successfully achieved by using the aptamer-modified caged siRNA and light activation. We expect that further optimized caged siRNAs featuring aptamer conjugation will be promising for practical applications to spatiotemporal photoregulation of gene expression in the future.
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Affiliation(s)
- Liangliang Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
| | - Changmai Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
| | - Xinli Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
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21
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Debart F, Dupouy C, Vasseur JJ. Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing. Beilstein J Org Chem 2018; 14:436-469. [PMID: 29520308 PMCID: PMC5827813 DOI: 10.3762/bjoc.14.32] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
Oligonucleotides (ONs) have been envisaged for therapeutic applications for more than thirty years. However, their broad use requires overcoming several hurdles such as instability in biological fluids, low cell penetration, limited tissue distribution, and off-target effects. With this aim, many chemical modifications have been introduced into ONs definitively as a means of modifying and better improving their properties as gene silencing agents and some of them have been successful. Moreover, in the search for an alternative way to make efficient ON-based drugs, the general concept of prodrugs was applied to the oligonucleotide field. A prodrug is defined as a compound that undergoes transformations in vivo to yield the parent active drug under different stimuli. The interest in stimuli-responsive ONs for gene silencing functions has been notable in recent years. The ON prodrug strategies usually help to overcome limitations of natural ONs due to their low metabolic stability and poor delivery. Nevertheless, compared to permanent ON modifications, transient modifications in prodrugs offer the opportunity to regulate ON activity as a function of stimuli acting as switches. Generally, the ON prodrug is not active until it is triggered to release an unmodified ON. However, as it will be described in some examples, the opposite effect can be sought. This review examines ON modifications in response to various stimuli. These stimuli may be internal or external to the cell, chemical (glutathione), biochemical (enzymes), or physical (heat, light). For each stimulus, the discussion has been separated into sections corresponding to the site of the modification in the nucleotide: the internucleosidic phosphate, the nucleobase, the sugar or the extremities of ONs. Moreover, the review provides a current and detailed account of stimuli-responsive ONs with the main goal of gene silencing. However, for some stimuli-responsive ONs reported in this review, no application for controlling gene expression has been shown, but a certain potential in this field could be demonstrated. Additionally, other applications in different domains have been mentioned to extend the interest in such molecules.
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Affiliation(s)
- Françoise Debart
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
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22
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Zhang L, Liang D, Wang Y, Li D, Zhang J, Wu L, Feng M, Yi F, Xu L, Lei L, Du Q, Tang X. Caged circular siRNAs for photomodulation of gene expression in cells and mice. Chem Sci 2017; 9:44-51. [PMID: 29629072 PMCID: PMC5869302 DOI: 10.1039/c7sc03842a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 10/18/2017] [Indexed: 12/12/2022] Open
Abstract
Caged siRNAs with a circular structure were successfully used for photoregulation of target genes in both cells and mice.
By means of RNA interference (RNAi), small interfering RNAs (siRNAs) play important roles in gene function study and drug development. Recently, photolabile siRNAs were developed to elucidate the process of gene silencing in terms of space, time and degree through chemical modification of siRNAs. We report herein a novel type of photolabile siRNA that was synthesized through cyclizing two ends of a single stranded RNA with a photocleavable linker. These circular siRNAs became more resistant to serum degradation. Using reporter assays of firefly/Renilla luciferase and GFP/RFP, the gene silencing activities of caged circular siRNAs for both genes were evaluated in HEK293 cells. The results indicated that the target genes were successfully photomodulated using these caged circular siRNAs that were formed by caged circular antisense guide RNAs and their linear complementary sense RNAs. Using the caged circular siRNA targeting GFP, we also successfully achieved photomodulation of GFP expression in mice. Upon further optimization, this new type of caged circular siRNA is expected to be a promising tool for studying gene therapy.
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Affiliation(s)
- Liangliang Zhang
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Duanwei Liang
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Yuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Dong Li
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Jinhao Zhang
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Li Wu
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Mengke Feng
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Fan Yi
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - Luzheng Xu
- Medical and Health Analytical Center , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China
| | - Liandi Lei
- Medical and Health Analytical Center , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China
| | - Quan Du
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
| | - XinJing Tang
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , No. 38, Xueyuan Rd , Beijing 100191 , China .
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23
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Weyel XMM, Fichte MAH, Heckel A. A Two-Photon-Photocleavable Linker for Triggering Light-Induced Strand Breaks in Oligonucleotides. ACS Chem Biol 2017; 12:2183-2190. [PMID: 28678467 DOI: 10.1021/acschembio.7b00367] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We synthesized a two-photon-sensitive photocleavable linker based on the 7-diethylaminocoumarin structure and introduced it successfully into DNA strands. First, we demonstrated the inducibility of strand scissions upon irradiation at 365 nm. To verify and visualize the two-photon activity, we used a fluorescence assay based on a DNA strand displacement immobilized in a hydrogel. Additionally, we investigated its use in a new class of DNA decoys that are able to catch and release nuclear factor κB (NF-κB) by using light as an external trigger signal. In cell culture we were able to show the regulation of NF-κB-controlled transcription of green fluorescent protein.
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Affiliation(s)
- Xenia M M Weyel
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Manuela A H Fichte
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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24
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Liu J, Hemphill J, Samanta S, Tsang M, Deiters A. Genetic Code Expansion in Zebrafish Embryos and Its Application to Optical Control of Cell Signaling. J Am Chem Soc 2017; 139:9100-9103. [PMID: 28657738 DOI: 10.1021/jacs.7b02145] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Site-specific incorporation of unnatural amino acids into proteins provides a powerful tool to study protein function. Here we report genetic code expansion in zebrafish embryos and its application to the optogenetic control of cell signaling. We genetically encoded four unnatural amino acids with a diverse set of functional groups, which included a photocaged lysine that was applied to the light-activation of luciferase and kinase activity. This approach enables versatile manipulation of protein function in live zebrafish embryos, a transparent and commonly used model organism to study embryonic development.
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Affiliation(s)
- Jihe Liu
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - James Hemphill
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Subhas Samanta
- 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
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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25
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Pitchers WR, Constantinou SJ, Losilla M, Gallant JR. Electric fish genomics: Progress, prospects, and new tools for neuroethology. ACTA ACUST UNITED AC 2016; 110:259-272. [PMID: 27769923 DOI: 10.1016/j.jphysparis.2016.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/06/2016] [Accepted: 10/16/2016] [Indexed: 01/01/2023]
Abstract
Electric fish have served as a model system in biology since the 18th century, providing deep insight into the nature of bioelectrogenesis, the molecular structure of the synapse, and brain circuitry underlying complex behavior. Neuroethologists have collected extensive phenotypic data that span biological levels of analysis from molecules to ecosystems. This phenotypic data, together with genomic resources obtained over the past decades, have motivated new and exciting hypotheses that position the weakly electric fish model to address fundamental 21st century biological questions. This review article considers the molecular data collected for weakly electric fish over the past three decades, and the insights that data of this nature has motivated. For readers relatively new to molecular genetics techniques, we also provide a table of terminology aimed at clarifying the numerous acronyms and techniques that accompany this field. Next, we pose a research agenda for expanding genomic resources for electric fish research over the next 10years. We conclude by considering some of the exciting research prospects for neuroethology that electric fish genomics may offer over the coming decades, if the electric fish community is successful in these endeavors.
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Affiliation(s)
- William R Pitchers
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA.
| | - Savvas J Constantinou
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA
| | - Mauricio Losilla
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA
| | - Jason R Gallant
- Dept. of Integrative Biology, Michigan State University, 288 Farm Lane RM 203, East Lansing, MI 48824, USA.
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26
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Watanabe T, Hoshida T, Sakyo J, Kishi M, Tanabe S, Matsuura J, Akiyama S, Nakata M, Tanabe Y, Suzuki AZ, Watanabe S, Furuta T. Synthesis of nucleobase-caged peptide nucleic acids having improved photochemical properties. Org Biomol Chem 2015; 12:5089-93. [PMID: 24921960 DOI: 10.1039/c4ob00418c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A nucleobase-caged peptide nucleic acid (PNA) having a (6-bromo-7-methoxycoumarin)-4-ylmethoxycarbonyl (Bmcmoc) caging group was newly synthesized. The Bmcmoc-caged PNAs were photolyzed to produce parent PNAs with a high photochemical efficiency. Introduction of a single Bmcmoc group was sufficient to suppress polymerase chain reaction (PCR) clamping activity and triplex invasion complex formation. Photo-mediated restoration of the PCR clamping activity was also demonstrated.
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Affiliation(s)
- Takayoshi Watanabe
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.
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27
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Griepenburg JC, Rapp TL, Carroll PJ, Eberwine J, Dmochowski IJ. Ruthenium-Caged Antisense Morpholinos for Regulating Gene Expression in Zebrafish Embryos. Chem Sci 2015; 6:2342-2346. [PMID: 26023327 PMCID: PMC4443914 DOI: 10.1039/c4sc03990d] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/29/2015] [Indexed: 11/25/2022] Open
Abstract
Photochemical approaches afford high spatiotemporal control over molecular structure and function, for broad applications in materials and biological science. Here, we present the first example of a visible light responsive ruthenium-based photolinker, Ru(bipyridine)2(3-ethynylpyridine)2 (RuBEP), which was reacted stoichiometrically with a 25mer DNA or morpholino (MO) oligonucleotide functionalized with 3' and 5' terminal azides, via Cu(I)-mediated [3+2] Huisgen cycloaddition reactions. RuBEP-caged circular morpholinos (Ru-MOs) targeting two early developmental zebrafish genes, chordin and notail, were synthesized and tested in vivo. One-cell-stage zebrafish embryos microinjected with Ru-MO and incubated in the dark for 24 h developed normally, consistent with caging, whereas irradiation at 450 nm dissociated one 3-ethynylpyridine ligand (ϕ = 0.33) and uncaged the MO to achieve gene knockdown. As demonstrated, Ru photolinkers provide a versatile method for controlling structure and function of biopolymers.
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Affiliation(s)
- Julianne C. Griepenburg
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , USA .
| | - Teresa L. Rapp
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , USA .
| | - Patrick J. Carroll
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , USA .
| | - James Eberwine
- Department of Systems Pharmacology and Experimental Therapeutics , Perelman School of Medicine , University of Pennsylvania , 37 John Morgan Building, 3620 Hamilton Walk , Philadelphia , Pennsylvania 19104 , USA
| | - Ivan J. Dmochowski
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , USA .
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28
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Caged oligonucleotides for studying biological systems. J Inorg Biochem 2015; 150:182-8. [PMID: 25865001 DOI: 10.1016/j.jinorgbio.2015.03.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/08/2023]
Abstract
Light-activated ("caged") compounds have been widely employed for studying biological processes with high spatial and temporal control. In the past decade, several new approaches for caging the structure and function of DNA and RNA oligonucleotides have been developed. This review focuses on caged oligonucleotides that incorporate site-specifically one or two photocleavable linkers, whose photolysis yields oligonucleotides with dramatic structural and functional changes. This technique has been employed by our laboratory and others to photoregulate gene expression in cells and living organisms, typically using near UV-activated organic chromophores. To improve capabilities for in vivo studies, we harnessed the rich inorganic photochemistry of ruthenium bipyridyl complexes to synthesize Ru-caged morpholino antisense oligonucleotides that remain inactive in zebrafish embryos until uncaged with visible light. Expanding into new caged oligonucleotide applications, our lab has developed Transcriptome In Vivo Analysis (TIVA) technology, which provides the first noninvasive, unbiased method for isolating mRNA from single neurons in brain tissues. TIVA-isolated mRNA can be amplified and then analyzed using next-generation sequencing (RNA-seq).
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29
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Wu L, Pei F, Zhang J, Wu J, Feng M, Wang Y, Jin H, Zhang L, Tang X. Synthesis of Site-Specifically Phosphate-Caged siRNAs and Evaluation of Their RNAi Activity and Stability. Chemistry 2014; 20:12114-22. [DOI: 10.1002/chem.201403430] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Indexed: 01/17/2023]
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30
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Hemphill J, Govan J, Uprety R, Tsang M, Deiters A. Site-specific promoter caging enables optochemical gene activation in cells and animals. J Am Chem Soc 2014; 136:7152-8. [PMID: 24802207 PMCID: PMC4333597 DOI: 10.1021/ja500327g] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
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In
cell and molecular biology, double-stranded circular DNA constructs,
known as plasmids, are extensively used to express a gene of interest.
These gene expression systems rely on a specific promoter region to
drive the transcription of genes either constitutively (i.e., in a
continually “ON” state) or conditionally (i.e., in response
to a specific transcription initiator). However, controlling plasmid-based
expression with high spatial and temporal resolution in cellular environments
and in multicellular organisms remains challenging. To overcome this
limitation, we have site-specifically installed nucleobase-caging
groups within a plasmid promoter region to enable optochemical control
of transcription and, thus, gene expression, via photolysis of the
caging groups. Through the light-responsive modification of plasmid-based
gene expression systems, we have demonstrated optochemical activation
of an exogenous fluorescent reporter gene in both tissue culture and
a live animal model, as well as light-induced overexpression of an
endogenous signaling protein.
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Affiliation(s)
- James Hemphill
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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31
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Liu Q, Deiters A. Optochemical control of deoxyoligonucleotide function via a nucleobase-caging approach. Acc Chem Res 2014; 47:45-55. [PMID: 23981235 PMCID: PMC3946944 DOI: 10.1021/ar400036a] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Synthetic oligonucleotides have been extensively applied tocontrol a wide range of biological processes such as gene expression, gene repair, DNA replication, and protein activity. Based on well-established sequence design rules that typically rely on Watson-Crick base pairing interactions researchers can readily program the function of these oligonucleotides. Therefore oligonucleotides provide a flexible platform for targeting a wide range of biological molecules, including DNA, RNA, and proteins. In addition, oligonucleotides are commonly used research tools in cell biology and developmental biology. However, a lack of conditional control methods has hampered the precise spatial and temporal regulation of oligonucleotide activity, which limits the application of these reagents to investigate complex biological questions. Nature controls biological function with a high level of spatial and temporal resolution and in order to elucidate the molecular mechanisms of biological processes, researchers need tools that allow for the perturbation of these processes with Nature's precision. Light represents an excellent external regulatory element since irradiation can be easily controlled spatially and temporally. Thus, researchers have developed several different methods to conditionally control oligonucleotide activity with light. One of the most versatile strategies is optochemical regulation through the installation and removal of photolabile caging groups on oligonucleotides. To produce switches that can control nucleic acid function with light, chemists introduce caging groups into the oligomer backbone or on specific nucleobases to block oligonucleotide function until the caging groups are removed by light exposure. In this Account, we focus on the application of caged nucleobases to the photoregulation of DNA function. Using this approach, we have both activated and deactivated gene expression optochemically at the transcriptional and translational level with spatial and temporal control. Specifically, we have used caged triplex-forming oligomers and DNA decoys to regulate transcription, and we have regulated translation with light-activated antisense agents. Moreover, we also discuss strategies that can trigger DNA enzymatic activity, DNA amplification, and DNA mutagenesis by light illumination. More recently, we have developed light-activated DNA logic operations, an advance that may lay the foundation for the optochemical control of complex DNA calculations.
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Affiliation(s)
- Qingyang Liu
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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32
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Teraoka A, Murakoshi K, Fukamauchi K, Suzuki AZ, Watanabe S, Furuta T. Preparation and affinity-based purification of caged linear DNA for light-controlled gene expression in mammalian cells. Chem Commun (Camb) 2014; 50:664-6. [DOI: 10.1039/c3cc46607h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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33
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The synthesis of tetra-modified RNA for the multidimensional control of gene expression via light-activated RNA interference. Nat Protoc 2013; 9:11-20. [PMID: 24309973 DOI: 10.1038/nprot.2013.165] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Light-activated RNA interference (LARI) is an effective way to control gene expression with light. This, in turn, allows for the spacing, timing and degree of gene expression to be controlled by the spacing, timing and amount of light irradiation. The key mediators of this process are siRNA or dsRNA that have been modified with four photocleavable groups of dimethoxy nitro phenyl ethyl (DMNPE), located on the four terminal phosphate groups of the duplex RNA. These mediators can be easily synthesized and purified using two readily available products: synthetic RNA oligonucleotides and DMNPE-hydrazone. The synthesis of the tetra-DMNPE-modified duplex RNA is made possible by a remarkable regiospecificity of DMNPE for terminal phosphates (over internal phosphates or nucleobases) that we have previously identified. The four installed DMNPE groups effectively limit RNAi until irradiation cleaves them, releasing native, active siRNA. By using the described protocol, any process that is mediated by RNAi can be controlled with light. Although other methods exist to control gene expression with light by using specialized reagents, this method requires only two commercially available products. The protocol takes ∼3 d in total for the preparation of modified RNA.
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34
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Griepenburg JC, Ruble BK, Dmochowski IJ. Caged oligonucleotides for bidirectional photomodulation of let-7 miRNA in zebrafish embryos. Bioorg Med Chem 2013; 21:6198-204. [PMID: 23721917 PMCID: PMC3789856 DOI: 10.1016/j.bmc.2013.04.082] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/20/2013] [Accepted: 04/30/2013] [Indexed: 12/17/2022]
Abstract
Many biological functions of microRNA (miRNA) have been identified in the past decade. However, a single miRNA can regulate multiple gene targets, thus it has been a challenge to elucidate the specific functions of each miRNA in different locations and times. New chemical tools make it possible to modulate miRNA activity with higher spatiotemporal resolution. Here, we describe light-activated (caged) constructs for switching let-7 miRNA 'on' or 'off' with 365 nm light in developing zebrafish embryos.
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Affiliation(s)
- Julianne C. Griepenburg
- Department of Chemistry, University of Pennsylvania, 231 S.34th Street, Philadelphia, PA 19104 USA
| | - Brittani K. Ruble
- Department of Chemistry, University of Pennsylvania, 231 S.34th Street, Philadelphia, PA 19104 USA
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 S.34th Street, Philadelphia, PA 19104 USA
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35
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Govan JM, Young DD, Lusic H, Liu Q, Lively MO, Deiters A. Optochemical control of RNA interference in mammalian cells. Nucleic Acids Res 2013; 41:10518-28. [PMID: 24021631 PMCID: PMC3905849 DOI: 10.1093/nar/gkt806] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Short interfering RNAs (siRNAs) and microRNAs (miRNAs) have been widely used in mammalian tissue culture and model organisms to selectively silence genes of interest. One limitation of this technology is the lack of precise external control over the gene-silencing event. The use of photocleavable protecting groups installed on nucleobases is a promising strategy to circumvent this limitation, providing high spatial and temporal control over siRNA or miRNA activation. Here, we have designed, synthesized and site-specifically incorporated new photocaged guanosine and uridine RNA phosphoramidites into short RNA duplexes. We demonstrated the applicability of these photocaged siRNAs in the light-regulation of the expression of an exogenous green fluorescent protein reporter gene and an endogenous target gene, the mitosis motor protein, Eg5. Two different approaches were investigated with the caged RNA molecules: the light-regulation of catalytic RNA cleavage by RISC and the light-regulation of seed region recognition. The ability to regulate both functions with light enables the application of this optochemical methodology to a wide range of small regulatory RNA molecules.
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Affiliation(s)
- Jeane M Govan
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA, Department of Chemistry, College of William & Mary, Williamsburg, VA 32187, USA, Center for Structural Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA and Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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36
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Pedro JMNS, Greenberg MM. Photochemical control of DNA structure through radical disproportionation. Chembiochem 2013; 14:1590-6. [PMID: 23940105 PMCID: PMC3807129 DOI: 10.1002/cbic.201300369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Indexed: 11/10/2022]
Abstract
Photolysis of an aryl sulfide-containing 5,6-dihydropyrimidine (1) at 350 nm produces high yields of thymidine and products resulting from trapping of a 5,6-dihydrothymidin-5-yl radical by O₂ or thiols. Thymidine is believed to result from disproportionation of the radical pair originally generated from C--S bond homolysis of 1 on the microsecond timescale, which is significantly shorter than other photochemical transformations of modified nucleotides into their native forms. Duplex DNA containing 1 is destabilized, presumably due to disruption of π-stacking. Incorporation of 1 within the binding site of the restriction endonuclease EcoRV provides a photochemical switch for turning on the enzyme's activity. In contrast, 1 is a substrate for endonuclease VIII and serves as a photochemical off switch for this base excision repair enzyme. Modification 1 also modulates the activity of the 10-23 DNAzyme, despite its incorporation into a nonduplex region. Overall, dihydropyrimidine 1 shows promise as a tool to provide spatiotemporal control over DNA structure on the miscrosecond timescale.
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37
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Basu S, Sachidanandan C. Zebrafish: a multifaceted tool for chemical biologists. Chem Rev 2013; 113:7952-80. [PMID: 23819893 DOI: 10.1021/cr4000013] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Sandeep Basu
- Council of Scientific and Industrial Research-Institute of Genomics & Integrative Biology (CSIR-IGIB) , South Campus, New Delhi 110025, India
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38
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Cao W, Zhang X, Miao X, Yang Z, Xu H. γ-Ray-Responsive Supramolecular Hydrogel Based on a Diselenide-Containing Polymer and a Peptide. Angew Chem Int Ed Engl 2013; 52:6233-7. [DOI: 10.1002/anie.201300662] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/31/2013] [Indexed: 11/11/2022]
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39
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Cao W, Zhang X, Miao X, Yang Z, Xu H. γ-Ray-Responsive Supramolecular Hydrogel Based on a Diselenide-Containing Polymer and a Peptide. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300662] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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40
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Connelly CM, Uprety R, Hemphill J, Deiters A. Spatiotemporal control of microRNA function using light-activated antagomirs. MOLECULAR BIOSYSTEMS 2013; 8:2987-93. [PMID: 22945263 DOI: 10.1039/c2mb25175b] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that act as post-transcriptional gene regulators and have been shown to regulate many biological processes including embryonal development, cell differentiation, apoptosis, and proliferation. Variations in the expression of certain miRNAs have been linked to a wide range of human diseases - especially cancer - and the diversity of miRNA targets suggests that they are involved in various cellular networks. Several tools have been developed to control the function of individual miRNAs and have been applied to study their biogenesis, biological role, and therapeutic potential; however, common methods lack a precise level of control that allows for the study of miRNA function with high spatial and temporal resolution. Light-activated miRNA antagomirs for mature miR-122 and miR-21 were developed through the site-specific installation of caging groups on the bases of selected nucleotides. Installation of caged nucleotides led to complete inhibition of the antagomir-miRNA hybridization and thus inactivation of antagomir function. The miRNA-inhibitory activity of the caged antagomirs was fully restored upon decaging through a brief UV irradiation. The synthesized antagomirs were applied to the photochemical regulation of miRNA function in mammalian cells. Moreover, spatial control over antagomir activity was obtained in mammalian cells through localized UV exposure. The presented approach enables the precise regulation of miRNA function and miRNA networks with unprecedented spatial and temporal resolution using UV irradiation and can be extended to any miRNA of interest.
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Affiliation(s)
- Colleen M Connelly
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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41
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Furuta T, Manabe K, Teraoka A, Murakoshi K, Ohtsubo A, Suzuki A. Design, synthesis, and photochemistry of modular caging groups for photoreleasable nucleotides. Org Lett 2012. [PMID: 23205776 DOI: 10.1021/ol3029093] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A modular approach to preparing caged nucleotides having additional properties has been achieved. The modular caging agent includes three components: an amine reactive NHS ester moiety, a photoactive Bhc group, and tosylhydrazone as a precursor of the diazomethyl group. Various amines including biotin and an Arg-Gly-Asp (RGD) peptide were introduced into the key intermediate via amide linkage. The Bio-Bhc-diazo thus synthesized enables the preparation of a photoreleasable siRNA with additional properties.
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Affiliation(s)
- Toshiaki Furuta
- Department of Biomolecular Science, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, 274-8510, Japan.
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42
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Wu L, Wang Y, Wu J, Lv C, Wang J, Tang X. Caged circular antisense oligonucleotides for photomodulation of RNA digestion and gene expression in cells. Nucleic Acids Res 2012; 41:677-86. [PMID: 23104375 PMCID: PMC3592401 DOI: 10.1093/nar/gks996] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
We synthesized three 20mer caged circular antisense oligodeoxynucleotides (R20, R20B2 and R20B4) with a photocleavable linker and an amide bond linker between two 10mer oligodeoxynucleotides. With these caged circular antisense oligodeoxynucleotides, RNA-binding affinity and its digestion by ribonuclease H were readily photomodulated. RNA cleavage rates were upregulated ∼43-, 25- and 15-fold for R20, R20B2 and R20B4, respectively, upon light activation in vitro. R20B2 and R20B4 with 2- or 4-nt gaps in the target RNA lost their ability to bind the target RNA even though a small amount of RNA digestion was still observed. The loss of binding ability indicated promising gene photoregulation through a non-enzymatic strategy. To test this strategy, three caged circular antisense oligonucleotides (PS1, PS2 and PS3) with 2′-OMe RNA and phosphorothioate modifications were synthesized to target GFP expression. Upon light activation, photomodulation of target hybridization and GFP expression in cells was successfully achieved with PS1, PS2 and PS3. These caged circular antisense oligonucleotides show promising applications of photomodulating gene expression through both ribonuclease H and non-enzyme involved antisense strategies.
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Affiliation(s)
- Li Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No 38 Xueyuan Road, Haidian District, Beijing 100191, China
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43
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Wang Y, Wu L, Wang P, Lv C, Yang Z, Tang X. Manipulation of gene expression in zebrafish using caged circular morpholino oligomers. Nucleic Acids Res 2012; 40:11155-62. [PMID: 23002141 PMCID: PMC3505977 DOI: 10.1093/nar/gks840] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Morpholino oligomers (MOs) have been widely used to knock down specific genes in zebrafish, but their constitutive activities limit their experimental applications for studying a gene with multiple functions or within a gene network. We report herein a new design and synthesis of caged circular MOs (caged cMOs) with two ends linked by a photocleavable moiety. These caged cMOs were successfully used to photomodulate β-catenin-2 and no tail expression in zebrafish embryos.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Road, Beijing 100191, China
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44
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Eberwine J, Lovatt D, Buckley P, Dueck H, Francis C, Kim TK, Lee J, Lee M, Miyashiro K, Morris J, Peritz T, Schochet T, Spaethling J, Sul JY, Kim J. Quantitative biology of single neurons. J R Soc Interface 2012; 9:3165-83. [PMID: 22915636 PMCID: PMC3481569 DOI: 10.1098/rsif.2012.0417] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The building blocks of complex biological systems are single cells. Fundamental insights gained from single-cell analysis promise to provide the framework for understanding normal biological systems development as well as the limits on systems/cellular ability to respond to disease. The interplay of cells to create functional systems is not well understood. Until recently, the study of single cells has concentrated primarily on morphological and physiological characterization. With the application of new highly sensitive molecular and genomic technologies, the quantitative biochemistry of single cells is now accessible.
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Affiliation(s)
- James Eberwine
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, 36th and Hamilton Walk, Philadelphia, PA 19104, USA.
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45
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Resendiz MJE, Schön A, Freire E, Greenberg MM. Photochemical control of RNA structure by disrupting π-stacking. J Am Chem Soc 2012; 134:12478-81. [PMID: 22827464 DOI: 10.1021/ja306304w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Photolabile nucleotides that disrupt nucleic acid structure are useful mechanistic probes and can be used as tools for regulating biochemical processes. Previous probes can be limited by the need to incorporate multiple modified nucleotides into oligonucleotides and in kinetic studies by the rate-limiting step in the conversion to the native nucleotide. Photolysis of aryl sulfide 1 produces high yields of 5-methyluridine, and product formation is complete in less than a microsecond. Aryl sulfide 1 prevents RNA hairpin formation and complete folding of the preQ(1) class I riboswitch. Proper folding is achieved in each instance upon photolysis at 350 nm. Aryl sulfide 1 is a novel tool for modulating RNA structure, and formation of 5-methyluridine within a radical cage suggests that it will be useful in kinetic studies.
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Affiliation(s)
- Marino J E Resendiz
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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46
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Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Light-controlled tools. Angew Chem Int Ed Engl 2012; 51:8446-76. [PMID: 22829531 DOI: 10.1002/anie.201202134] [Citation(s) in RCA: 738] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Indexed: 12/21/2022]
Abstract
Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.
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Affiliation(s)
- Clara Brieke
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
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47
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Brieke C, Rohrbach F, Gottschalk A, Mayer G, Heckel A. Lichtgesteuerte Werkzeuge. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202134] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clara Brieke
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
| | - Falk Rohrbach
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Gottschalk
- Buchmann‐Institut für Molekulare Lebenswissenschaften, Institut für Biochemie, Max‐von‐Laue‐Straße 15, 60438 Frankfurt/Main (Deutschland)
| | - Günter Mayer
- Universität Bonn, LIMES‐Institut, Gerhard‐Domagk‐Straße 1, 53121 Bonn (Deutschland)
| | - Alexander Heckel
- Goethe‐Universität Frankfurt, Institut für Organische Chemie und Chemische Biologie, Buchmann‐Institut für Molekulare Lebenswissenschaften, Max‐von‐Laue‐Straße 9, 60438 Frankfurt/Main (Deutschland)
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48
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Zhou G, Khan F, Dai Q, Sylvester JE, Kron SJ. Photocleavable peptide-oligonucleotide conjugates for protein kinase assays by MALDI-TOF MS. MOLECULAR BIOSYSTEMS 2012; 8:2395-404. [PMID: 22772337 DOI: 10.1039/c2mb25163a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Robust methods for highly parallel, quantitative analysis of cellular protein tyrosine kinase activities may provide tools critically needed to decipher oncogenic signaling, discover new targeted drugs, diagnose cancer and monitor patients. Here, we describe proof-of-principle for a novel protein kinase assay with the potential to help overcome these challenges. MALDI-TOF mass spectrometry provides an ideal tool for label-free multiplexed analysis of peptide phosphorylation, but is poorly matched to homogeneous assays and complex samples. Thus, we conjugated a common oligonucleotide tag to multiple peptide substrates, offering efficient capture from solution-phase kinase reactions by annealing to the complementary sequence tethered to PEG-passivated superparamagnetic microparticles. To enable reversible conjugation, we developed a novel bifunctional cross-linker allowing simple and efficient preparation of photocleavable peptide-oligonucleotide conjugates. After washing away contaminants and following photorelease, MALDI-TOF analysis yielded relative phosphorylation of each peptide with high sensitivity and specificity. Validating the hybridization-mediated multiplexed kinase assay, when three peptide substrate-oligonucleotide conjugates were mixed with the tyrosine kinase c-Abl and ATP, we readily observed their differential phosphorylation yet measured a common IC(50) for the Abl kinase inhibitor imatinib. This new assay enables analysis of protein kinase activities in a multiplexed format amenable to screening inhibitors against multiple kinases in parallel, an important capability for drug discovery and predictive diagnostics.
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Affiliation(s)
- Guangchang Zhou
- Department of Molecular Genetics and Cell Biology, Gordon Center for Integrative Sciences, W522A, The University of Chicago, Chicago, IL 60637, USA
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49
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Yamazoe S, Shestopalov IA, Provost E, Leach SD, Chen JK. Cyclic Caged Morpholinos: Conformationally Gated Probes of Embryonic Gene Function. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201690] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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50
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Yamazoe S, Shestopalov IA, Provost E, Leach SD, Chen JK. Cyclic caged morpholinos: conformationally gated probes of embryonic gene function. Angew Chem Int Ed Engl 2012; 51:6908-11. [PMID: 22689470 DOI: 10.1002/anie.201201690] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 04/24/2012] [Indexed: 12/21/2022]
Abstract
Feeling a bit cagey: morpholino-based antisense reagents have been caged through oligonucleotide cyclization, enabling photocontrol of gene expression in zebrafish embryos and larvae. Using these reagents, the timing of exocrine cell fate commitment in the developing pancreas has been examined.
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Affiliation(s)
- Sayumi Yamazoe
- Department of Chemical and Systems Biology, Stanford University School of Medicine, CA 94305, USA
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