1
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Bardhan A, Brown W, Albright S, Tsang M, Davidson LA, Deiters A. Direct Activation of Nucleobases with Small Molecules for the Conditional Control of Antisense Function. Angew Chem Int Ed Engl 2024; 63:e202318773. [PMID: 38411401 DOI: 10.1002/anie.202318773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Conditionally controlled antisense oligonucleotides provide precise interrogation of gene function at different developmental stages in animal models. Only one example of small molecule-induced activation of antisense function exist. This has been restricted to cyclic caged morpholinos that, based on sequence, can have significant background activity in the absence of the trigger. Here, we provide a new approach using azido-caged nucleobases that are site-specifically introduced into antisense morpholinos. The caging group design is a simple azidomethylene (Azm) group that, despite its very small size, efficiently blocks Watson-Crick base pairing in a programmable fashion. Furthermore, it undergoes facile decaging via Staudinger reduction when exposed to a small molecule phosphine, generating the native antisense oligonucleotide under conditions compatible with biological environments. We demonstrated small molecule-induced gene knockdown in mammalian cells, zebrafish embryos, and frog embryos. We validated the general applicability of this approach by targeting three different genes.
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Affiliation(s)
- Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Savannah Albright
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Michael Tsang
- Department of Cell Biology, Center for Integrative Organ Systems., University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Lance A Davidson
- Department of Bioengineering, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
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2
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Hamerla C, Mondal P, Hegger R, Burghardt I. Controlled destabilization of caged circularized DNA oligonucleotides predicted by replica exchange molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:26132-26144. [PMID: 37740309 DOI: 10.1039/d3cp02961a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Spatiotemporal control is a critical issue in the design of strategies for the photoregulation of oligonucleotide activity. Efficient uncaging, i.e., activation by removal of photolabile protecting groups (PPGs), often necessitates multiple PPGs. An alternative approach is based on circularization strategies, exemplified by intrasequential circularization, also denoted photo-tethering, as introduced in [Seyfried et al., Angew. Chem., Int. Ed., 2017, 56, 359]. Here, we develop a computational protocol, relying on replica exchange molecular dynamics (REMD), in order to characterize the destabilization of a series of circularized, caged DNA oligonucleotides addressed in the aforementioned study. For these medium-sized (32 nt) oligonucleotides, melting temperatures are computed, whose trend is in good agreement with experiment, exhibiting a large destabilization and, hence, reduction of the melting temperature of the order of ΔTm ∼ 30 K as compared with the native species. The analysis of free energy landscapes confirms the destabilization pattern experienced by the circularized oligonucleotides. The present study underscores that computational protocols that capture controlled destabilization and uncaging of oligonucleotides are promising as predictive tools in the tailored photocontrol of nucleic acids.
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Affiliation(s)
- Carsten Hamerla
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Padmabati Mondal
- Department of Chemistry and Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Indian Institute of Science Education and Research (IISER) Tirupati, Panguru (G.P), Yerpedu Mandal, 517619 - Tirupati Dist., Andhra Pradesh, India
| | - Rainer Hegger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
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3
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Zhang L, Xie X, Djokovic N, Nikolic K, Kosenkov D, Abendroth F, Vázquez O. Reversible Control of RNA Splicing by Photoswitchable Small Molecules. J Am Chem Soc 2023. [PMID: 37276581 DOI: 10.1021/jacs.3c03275] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Dynamics are intrinsic to both RNA function and structure. Yet, the available means to precisely provide RNA-based processes with spatiotemporal resolution are scarce. Here, our work pioneers a reversible approach to regulate RNA splicing within primary patient-derived cells by synthetic photoswitches. Our small molecule enables conditional real-time control at mRNA and protein levels. NMR experiments, together with theoretical calculations, photochemical characterization, fluorescence polarization measurements, and living cell-based assays, confirmed light-dependent exon inclusion as well as an increase in the target functional protein. Therefore, we first demonstrated the potential of photopharmacology modulation in splicing, tweaking the current optochemical toolkit. The timeliness on the consolidation of RNA research as the driving force toward therapeutical innovation holds the promise that our approach will contribute to redrawing the vision of RNA.
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Affiliation(s)
- Lei Zhang
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
| | - Xiulan Xie
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, University of Belgrade, Belgrade, 11000, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, University of Belgrade, Belgrade, 11000, Serbia
| | - Dmitri Kosenkov
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey 07764, United States
| | - Frank Abendroth
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
| | - Olalla Vázquez
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, D-35043, Germany
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4
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Ji H, Xiong W, Zhang K, Tian T, Zhou X. Hydrogen Peroxide-triggered Chemical Strategy for Controlling CRISPR systems. Chem Asian J 2022; 17:e202200214. [PMID: 35483968 DOI: 10.1002/asia.202200214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Indexed: 11/09/2022]
Abstract
The function of the CRISPR system can be conditionally controlled through rationally guided RNA engineering such that the target sequences can be precisely selected and manipulated. In particular, gRNA, as an important component of the CRISPR system, provides a unique tool for multifunctional control of the system based on the structure of the RNA itself. Therefore, we introduced here a protective group on the 2'-OH position of RNA to inhibit RNA-guided nucleic acid cleavage. Next, the modified gRNA can restore its original function under the chemical stimulation of hydrogen peroxide to realize the control of the CRISPR system. The experiment result demonstrated that the operating mechanism of this strategy may be based on chemical modifications that reduce the number of complementary base pairs between RNAs and targets, and the RNA-protein interaction. This further enriches the toolbox of conditional control of CRISPR function and has broad potential for gene editing in living cells and disease treatment using endogenous hydrogen peroxide.
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Affiliation(s)
- Huimin Ji
- The Institute of Molecular Medicine, Wuhan University People's Hospital, Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, 430072, Wuhan, Hubei, P. R. China
| | - Wei Xiong
- The Institute of Molecular Medicine, Wuhan University People's Hospital, Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, 430072, Wuhan, Hubei, P. R. China
| | - Kaisong Zhang
- The Institute of Molecular Medicine, Wuhan University People's Hospital, Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, 430072, Wuhan, Hubei, P. R. China
| | - Tian Tian
- The Institute of Molecular Medicine, Wuhan University People's Hospital, Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, 430072, Wuhan, Hubei, P. R. China
| | - Xiang Zhou
- The Institute of Molecular Medicine, Wuhan University People's Hospital, Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, 430072, Wuhan, Hubei, P. R. China
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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: 0] [Impact Index Per Article: 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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Ren X, Li J. In Situ Imaging of mRNA Splicing Variants by SpliceRCA. Methods Mol Biol 2022; 2537:197-209. [PMID: 35895266 DOI: 10.1007/978-1-0716-2521-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We present a method for multiplexed in situ imaging of individual RNA splicing variants. This method enables quantifying RNA splicing variants with single-molecule resolution, discriminating splicing isoforms with single-base precision as well as analyzing the subcellular localization of transcripts. With this technology, it is possible to study cell heterogeneity of gene expression, potentially helping to decipher rich diversity in posttranscriptional function and assist clinical monitoring.
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Affiliation(s)
- Xiaojun Ren
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology, Beijing, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, China.
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7
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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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8
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Abstract
DNA-based Boolean logic gates (for example, AND, OR, and NOT) can be assembled into complex computational circuits that generate an output signal in response to specific patterns of oligonucleotide inputs. However, the fundamental nature of NOT gates, which convert the absence of an input into an output, makes their implementation within DNA-based circuits difficult. Premature execution of a NOT gate before completion of its upstream computation introduces an irreversible error into the circuit. By utilizing photocaging groups, we developed a novel DNA gate design that prevents gate function until irradiation at a certain time point. Optical activation provides temporal control over circuit performance by preventing premature computation and is orthogonal to all other components of DNA computation devices. Using this approach, we designed NAND and NOR logic gates that respond to synthetic microRNA sequences. We further demonstrate the utility of the NOT gate within multilayer circuits in response to a specific pattern of four microRNAs.
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Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anirban Bardhan
- Department of Chemistry, 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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9
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Gu C, Xiao L, Shang J, Xu X, He L, Xiang Y. Chemical synthesis of stimuli-responsive guide RNA for conditional control of CRISPR-Cas9 gene editing. Chem Sci 2021; 12:9934-9945. [PMID: 34377390 PMCID: PMC8317661 DOI: 10.1039/d1sc01194d] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022] Open
Abstract
CRISPR-Cas9 promotes changes in identity or abundance of nucleic acids in live cells and is a programmable modality of broad biotechnological and therapeutic interest. To reduce off-target effects, tools for conditional control of CRISPR-Cas9 functions are under active research, such as stimuli-responsive guide RNA (gRNA). However, the types of physiologically relevant stimuli that can trigger gRNA are largely limited due to the lack of a versatile synthetic approach in chemistry to introduce diverse labile modifications into gRNA. In this work, we developed such a general method to prepare stimuli-responsive gRNA based on site-specific derivatization of 2′-O-methylribonucleotide phosphorothioate (PS-2′-OMe). We demonstrated CRISPR-Cas9-mediated gene editing in human cells triggered by oxidative stress and visible light, respectively. Our study tackles the synthetic challenge and paves the way for chemically modified RNA to play more active roles in gene therapy. Conditional control of CRISPR-Cas9 activity by reactive oxygen species and visible light is achieved using stimuli-responsive guide RNA synthesized by a general method based on RNA 2′-O-methylribonucleotide phosphorothioate.![]()
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Affiliation(s)
- Chunmei Gu
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
| | - Lu Xiao
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
| | - Xiao Xu
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
| | - Luo He
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University Beijing 100084 China
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10
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Tavakoli A, Paul D, Mu H, Kuchlyan J, Baral S, Ansari A, Broyde S, Min JH. Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein. RSC Chem Biol 2021; 2:523-536. [PMID: 34041491 PMCID: PMC8142930 DOI: 10.1039/d0cb00192a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Biomolecular structural changes upon binding/unbinding are key to their functions. However, characterization of such dynamical processes is difficult as it requires ways to rapidly and specifically trigger the assembly/disassembly as well as ways to monitor the resulting changes over time. Recently, various chemical strategies have been developed to use light to trigger changes in oligonucleotide structures, and thereby their activities. Here we report that photocleavable DNA can be used to modulate the DNA binding of the Rad4/XPC DNA repair complex using light. Rad4/XPC specifically recognizes diverse helix-destabilizing/distorting lesions including bulky organic adduct lesions and functions as a key initiator for the eukaryotic nucleotide excision repair (NER) pathway. We show that the 6-nitropiperonyloxymethyl (NPOM)-modified DNA is recognized by the Rad4 protein as a specific substrate and that the specific binding can be abolished by light-induced cleavage of the NPOM group from DNA in a dose-dependent manner. Fluorescence lifetime-based analyses of the DNA conformations suggest that free NPOM-DNA retains B-DNA-like conformations despite its bulky NPOM adduct, but Rad4-binding causes it to be heterogeneously distorted. Subsequent extensive conformational searches and molecular dynamics simulations demonstrate that NPOM in DNA can be housed in the major groove of the DNA, with stacking interactions among the nucleotide pairs remaining largely unperturbed and thus retaining overall B-DNA conformation. Our work suggests that photoactivable DNA may be used as a DNA lesion surrogate to study DNA repair mechanisms such as nucleotide excision repair. Rad4/XPC DNA damage sensor protein specifically binds to a photocleavable NPOM-DNA adduct, and this recognition is abolished upon photo-cleavage of NPOM.![]()
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Affiliation(s)
- Amirrasoul Tavakoli
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Debamita Paul
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Hong Mu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Jagannath Kuchlyan
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Saroj Baral
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Suse Broyde
- Department of Biology, New York University, New York, NY 10003, USA
| | - Jung-Hyun Min
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
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11
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Reichert D, Mootz HD, Rentmeister A. Light-control of cap methylation and mRNA translation via genetic code expansion of Ecm1. Chem Sci 2021; 12:4383-4388. [PMID: 34163701 PMCID: PMC8179545 DOI: 10.1039/d1sc00159k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Gene expression is tightly regulated in all domains of life, with post-transcriptional regulation being more pronounced in higher eukaryotes. Optochemical and optogenetic approaches enable the actuation of many underlying processes by light, which is an excellent tool to exert spatio-temporal control. However, light-mediated control of eukaryotic mRNA processing and the respective enzymes has not been reported. We used genetic code expansion to install a photo-caged tyrosine (Y) in the active site of the cap methyltransferase Ecm1. This enzyme is responsible for guanine N7 methylation of the 5′ cap, which is required for translation. Substituting Y284 with the photocaged ortho-nitrobenzyl-tyrosine (ONBY) almost completely abrogated the methylation activity of Ecm1. Irradiation with light removed the ONB group, restoring the native tyrosine and Ecm1 activity, yielding up to 97% conversion of the minimal substrate GpppA within 60 min after activation. Using luciferase- and eGFP-mRNAs as reporters, we could show that light actuates translation by inducing activation of Ecm1 ONBY284 in a eukaryotic in vitro translation system. A tyrosine in the active site of the 5′ cap methyltransferase Ecm1 was photocaged. Translation of mRNA could be triggered by light in eukaryotic cell lysate.![]()
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Affiliation(s)
- Dennis Reichert
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany .,Cells in Motion Interfaculty Center, University of Münster 48149 Münster Germany
| | - Henning D Mootz
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster Correnstr. 36 48149 Münster Germany .,Cells in Motion Interfaculty Center, University of Münster 48149 Münster Germany
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12
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Wang S, Zhao J, Wang L, Zhang J, Hu H, Yu P, Wang R. Inducible DNA Polymerase Chain Reaction Triggered by Oxidative Species. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202000377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sheng Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Jizhong Zhao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Li Wang
- Wuhan No.1 Hospital 215 Zhongshan Avenue Wuhan Hubei 430022 P. R. China
| | - Jingwen Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Hongmei Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Ping Yu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
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13
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Zhang J, Jing N, Fan X, Tang X. Photoregulation of Gene Expression with Amantadine‐Modified Caged siRNAs through Host–Guest Interactions. Chemistry 2020; 26:14002-14010. [DOI: 10.1002/chem.202003084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/16/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Jinhao Zhang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd. 100191 Beijing P.R. China
| | - Nannan Jing
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd. 100191 Beijing P.R. China
| | - Xinli Fan
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd. 100191 Beijing P.R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences Peking University No. 38 Xueyuan Rd. 100191 Beijing P.R. China
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14
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Zhang J, Ma R, Blanchard A, Petree J, Jo H, Salaita K. Conditional Deoxyribozyme-Nanoparticle Conjugates for miRNA-Triggered Gene Regulation. ACS APPLIED MATERIALS & INTERFACES 2020; 12:37851-37861. [PMID: 32803952 PMCID: PMC8287654 DOI: 10.1021/acsami.0c07609] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
DNA-nanoparticle (NP) conjugates have been used to knockdown gene expression transiently and effectively, making them desirable tools for gene regulation therapy. Because DNA-NPs are constitutively active and are rapidly taken up by most cell types, they offer limited control in terms of tissue or cell type specificity. To take a step toward solving this issue, we incorporate toehold-mediated strand exchange, a versatile molecular programming modality, to switch the DNA-NPs from an inactive state to an active state in the presence of a specific RNA input. Because many transcripts are unique to cell subtype or disease state, this approach could one day lead to responsive nucleic acid therapeutics with enhanced specificity. As a proof of concept, we designed conditional deoxyribozyme-nanoparticles (conditional DzNPs) that knockdown tumor necrosis factor α (TNFα) mRNA upon miR-33 triggering. We demonstrate toehold-mediated strand exchange and restoration of TNFα DNAzyme activity in the presence of miR-33 trigger, with optimization of the preparation, configuration, and toehold length of conditional DzNPs. Our results indicate specific and strong ON/OFF response of conditional DzNPs to the miR-33 trigger in buffer. Furthermore, we demonstrate endogenous miR-33-triggered knockdown of TNFα mRNA in mouse macrophages, implying the potential of conditional gene regulation applications using these DzNPs.
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Affiliation(s)
- Jiahui Zhang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Rong Ma
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Aaron Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jessica Petree
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Department of Chemistry, Emory University, Atlanta, GA, USA
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15
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Cao X, Yu H, Xue J, Bai M, Zhao Y, Li Y, Zhao Y, Chen F. RNA-Primed Amplification for Noise-Suppressed Visualization of Single-Cell Splice Variants. Anal Chem 2020; 92:9356-9361. [PMID: 32456418 DOI: 10.1021/acs.analchem.0c01734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Splice variants visualization is pivotal for a deeper understanding of cell growth and development. However, it remains technically challenging due to short lengths, similar sequences, and low abundance. The existing single-cell imaging strategies suffer from nonspecific amplification that causes considerable noise during visualization of the splice variants. Herein we develop a new RNA-primed amplification strategy for noise-suppressed visualization of single-cell splice variants. Block probes were designed to specifically identify the conjugated region of exons in mRNA, which was then digested by endonuclease and provided a hydroxyl group at the 3' terminal. The RNA target can act as primer to trigger rolling circle amplification, achieving visualization of splice variants with noise suppressed to nearly zero. We further explored the expression and distribution of BRCA1 splice variants in three breast cell lines, revealing cell-type specific mapping of this cancer suppressor gene.
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Affiliation(s)
- Xiaowen Cao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Huahang Yu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Yue Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Youjun Li
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
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16
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17
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Keyhani S, Goldau T, Blümler A, Heckel A, Schwalbe H. Chemo-Enzymatic Synthesis of Position-Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sara Keyhani
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Thomas Goldau
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
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18
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Keyhani S, Goldau T, Blümler A, Heckel A, Schwalbe H. Chemo-Enzymatic Synthesis of Position-Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:12017-12021. [PMID: 30007102 DOI: 10.1002/anie.201807125] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Indexed: 02/04/2023]
Abstract
The investigation of non-coding RNAs requires RNAs containing modifications at every possible position within the oligonucleotide. Here, we present the chemo-enzymatic RNA synthesis containing photoactivatable or 13 C,15 N-labelled nucleosides. All four ribonucleotides containing ortho-nitrophenylethyl (NPE) photocages, photoswitchable azobenzene C-nucleotides and 13 C,15 N-labelled nucleotides were incorporated position-specifically in high yields. We applied this approach for the synthesis of light-inducible 2'dG-sensing riboswitch variants and detected ligand-induced structural reorganization upon irradiation by NMR spectroscopy. This chemo-enzymatic method opens the possibility to incorporate a wide range of modifications at any desired position of RNAs of any lengths beyond the limits of solid-phase synthesis.
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Affiliation(s)
- Sara Keyhani
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany.,Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Thomas Goldau
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany.,Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
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19
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Ren X, Deng R, Zhang K, Sun Y, Teng X, Li J. SpliceRCA: in Situ Single-Cell Analysis of mRNA Splicing Variants. ACS CENTRAL SCIENCE 2018; 4:680-687. [PMID: 29974063 PMCID: PMC6026782 DOI: 10.1021/acscentsci.8b00081] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Indexed: 06/08/2023]
Abstract
Immune cell heterogeneity due to the differential expression of RNA splicing variants still remains unexplored. This is mainly because single-cell imaging technologies of splicing variants with precise sequence or base resolution are now not readily available. Herein, we design a splice-junction anchored padlock-probe-mediated rolling circle amplification assay (SpliceRCA) for single-cell imaging of splice isoforms of essential regulatory immune gene (CD45) upon T-cell activation. Two recognition regions in the padlock probe can target the splice-junction sequence, resulting in a close proximity for triggering in situ one-target-one-amplicon amplification. With the read length of ∼30 nucleotides, this method allows discrimination of isoforms with single-base precision and quantification of isoforms with single-molecule resolution. We applied SpliceRCA to single-cell image splice variants of essential regulatory immune gene (CD45) upon T-cell activation. It is found that CD45RO isoform presents a distal nuclear spatial distribution and is coregulated with CD45RB upon activation. Our strategy provides a single-cell analysis platform to investigate the mechanism of complex immune responses and may further guide immunotherapy.
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Affiliation(s)
- Xiaojun Ren
- Department
of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry &
Chemical Biology, Tsinghua University, Beijing 100084, China
- School
of Chemistry and Chemical Engineering, Beijing
Institute of Technology, Beijing 100081, China
| | - Ruijie Deng
- Department
of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry &
Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Kaixiang Zhang
- Department
of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry &
Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yupeng Sun
- Department
of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry &
Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Xucong Teng
- Department
of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry &
Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department
of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry &
Chemical Biology, Tsinghua University, Beijing 100084, China
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20
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemical Control of Biological Processes in Cells and Animals. Angew Chem Int Ed Engl 2018; 57:2768-2798. [PMID: 28521066 PMCID: PMC6026863 DOI: 10.1002/anie.201700171] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/06/2017] [Indexed: 12/13/2022]
Abstract
Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.
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Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Taylor Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Yuta Naro
- 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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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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Mori S, Morihiro K, Okuda T, Kasahara Y, Obika S. Hydrogen peroxide-triggered gene silencing in mammalian cells through boronated antisense oligonucleotides. Chem Sci 2018; 9:1112-1118. [PMID: 29629168 PMCID: PMC5875086 DOI: 10.1039/c7sc04318j] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/21/2017] [Indexed: 12/16/2022] Open
Abstract
Hydrogen peroxide (H2O2) is a reactive oxygen species (ROS) involved in various diseases, including neurodegeneration, diabetes, and cancer. Here, we introduce a new approach to use H2O2 to modulate specific gene expression in mammalian cells. H2O2-responsive nucleoside analogues, in which the Watson-Crick faces of the nucleobases are caged by arylboronate moieties, were synthesized. One of these analogues, boronated thymidine (dTB ), was incorporated into oligodeoxynucleotides (ODNs) using an automated DNA synthesizer. The hybridization ability of this boronated ODN to complementary RNA was clearly switched in the off-to-on direction upon H2O2 addition. Furthermore, we demonstrated H2O2-triggered gene silencing in mammalian cells using antisense oligonucleotides (ASOs) modified with dTB . Our approach can be used for the regulation of any gene of interest by the sequence design of boronated ASOs and will contribute to the development of targeted disease therapeutics.
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Affiliation(s)
- Shohei Mori
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) , 7-6-8 Saito-Asagi , Ibaraki , Osaka 567-0085 , Japan
| | - Takumi Okuda
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
| | - Yuuya Kasahara
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) , 7-6-8 Saito-Asagi , Ibaraki , Osaka 567-0085 , Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences , Osaka University , 1-6 Yamadaoka , Suita , Osaka 565-0871 , Japan . ;
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) , 7-6-8 Saito-Asagi , Ibaraki , Osaka 567-0085 , Japan
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23
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemische Steuerung biologischer Vorgänge in Zellen und Tieren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201700171] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Taylor Courtney
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Yuta Naro
- 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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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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Abstract
Oligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2'-, 3'-, and 5'-positions of the sugar moieties, and the internucleotide phospho-linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Geeta Meher
- Spring Bank Pharmaceuticals, Inc, Milford, Massachusetts
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26
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Ho P, Chen YY. Mammalian synthetic biology in the age of genome editing and personalized medicine. Curr Opin Chem Biol 2017. [PMID: 28628856 DOI: 10.1016/j.cbpa.2017.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The recent expansion of molecular tool kits has propelled synthetic biology toward the design of increasingly sophisticated mammalian systems. Specifically, advances in genome editing, protein engineering, and circuitry design have enabled the programming of cells for diverse applications, including regenerative medicine and cancer immunotherapy. The ease with which molecular and cellular interactions can be harnessed promises to yield novel approaches to elucidate genetic interactions, program cellular functions, and design therapeutic interventions. Here, we review recent advancements in the development of enabling technologies and the practical applications of mammalian synthetic biology.
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Affiliation(s)
- Patrick Ho
- Department of Chemical and Biomolecular Engineering, University of California-Los Angeles, 420 Westwood Plaza, Boelter Hall 5531, Los Angeles, CA 90095, USA
| | - Yvonne Y Chen
- Department of Chemical and Biomolecular Engineering, University of California-Los Angeles, 420 Westwood Plaza, Boelter Hall 5531, Los Angeles, CA 90095, USA.
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27
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Ren X, Deng R, Wang L, Zhang K, Li J. RNA splicing process analysis for identifying antisense oligonucleotide inhibitors with padlock probe-based isothermal amplification. Chem Sci 2017; 8:5692-5698. [PMID: 28989608 PMCID: PMC5621167 DOI: 10.1039/c7sc01336a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 06/07/2017] [Indexed: 12/24/2022] Open
Abstract
We report a highly sensitive method for quantifying the splicing products in different steps, enabling us to analyze the splicing process and identify ASO inhibitors.
RNA splicing, which mainly involves two transesterification steps, is a fundamental process of gene expression and its abnormal regulation contributes to serious genetic diseases. Antisense oligonucleotides (ASOs) are genetic control tools that can be used to specifically control genes through alteration of the RNA splicing pathway. Despite intensive research, how ASOs or various other factors influence the multiple processes of RNA splicing still remains obscure. This is largely due to an inability to analyze the splicing efficiency of each step in the RNA splicing process with high sensitivity. We addressed this limitation by introducing a padlock probe-based isothermal amplification assay to achieve quantification of the specific products in different splicing steps. With this amplified assay, the roles that ASOs play in RNA splicing inhibition in the first and second steps could be distinguished. We identified that 5′-ASO could block RNA splicing by inhibiting the first step, while 3′-ASO could block RNA splicing by inhibiting the second step. This method provides a versatile tool for assisting efficient ASO design and discovering new splicing modulators and therapeutic drugs.
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Affiliation(s)
- Xiaojun Ren
- School of Chemistry and Chemical Engineering , Beijing Institute of Technology , Beijing 100081 , China.,Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Ruijie Deng
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Lida Wang
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Kaixiang Zhang
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
| | - Jinghong Li
- Department of Chemistry , Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology , Tsinghua University , Beijing 100084 , China .
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28
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Gandioso A, Palau M, Nin‐Hill A, Melnyk I, Rovira C, Nonell S, Velasco D, García‐Amorós J, Marchán V. Sequential Uncaging with Green Light can be Achieved by Fine-Tuning the Structure of a Dicyanocoumarin Chromophore. ChemistryOpen 2017; 6:375-384. [PMID: 28638770 PMCID: PMC5474652 DOI: 10.1002/open.201700067] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Indexed: 12/26/2022] Open
Abstract
We report the synthesis and photochemical properties of a series of dicyanocoumarinylmethyl (DEAdcCM)- and dicyanocoumarinylethyl (DEAdcCE)-based photocages of carboxylic acids and amines with absorption maximum around 500 nm. Photolysis studies with green light have demonstrated that the structure of the coumarin chromophore as well as the nature of the leaving group and the type of bond to be photocleaved (ester or carbamate) have a strong influence on the rate and efficiency of the uncaging process. These experimental observations were also supported by DFT calculations. Such differences in deprotection kinetics have been exploited to sequentially photolyze two dicyanocoumarin-caged model compounds (e.g., benzoic acid and ethylamine), and open the way to increasing the number of functional levels that can be addressed with light in a single system, particularly when combining dicyanocoumarin caging groups with other photocleavable protecting groups, which remain intact under green light irradiation.
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Affiliation(s)
- Albert Gandioso
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB (AG, VM)Universitat de Barcelona08028BarcelonaSpain
| | - Marta Palau
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB (AG, VM)Universitat de Barcelona08028BarcelonaSpain
| | - Alba Nin‐Hill
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB (AG, VM)Universitat de Barcelona08028BarcelonaSpain
- Institut de Química Teòrica i Computacional (IQTCUB)Universitat de Barcelona08028BarcelonaSpain
| | - Ivanna Melnyk
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB (AG, VM)Universitat de Barcelona08028BarcelonaSpain
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB (AG, VM)Universitat de Barcelona08028BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)08010BarcelonaSpain
- Institut de Química Teòrica i Computacional (IQTCUB)Universitat de Barcelona08028BarcelonaSpain
| | - Santi Nonell
- Institut Químic de SarriàUniversitat Ramon Llull08017BarcelonaSpain
| | - Dolores Velasco
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB (AG, VM)Universitat de Barcelona08028BarcelonaSpain
- Institut de Nanociència i Nanotecnologia (IN2UB)Universitat de Barcelona08028BarcelonaSpain
| | - Jaume García‐Amorós
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB (AG, VM)Universitat de Barcelona08028BarcelonaSpain
| | - Vicente Marchán
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB (AG, VM)Universitat de Barcelona08028BarcelonaSpain
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29
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Mathur M, Xiang JS, Smolke CD. Mammalian synthetic biology for studying the cell. J Cell Biol 2016; 216:73-82. [PMID: 27932576 PMCID: PMC5223614 DOI: 10.1083/jcb.201611002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/25/2022] Open
Abstract
Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology.
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Affiliation(s)
- Melina Mathur
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Joy S Xiang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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30
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Huang X, Hu Q, Lai Y, Morales DP, Clegg DO, Reich NO. Light-Patterned RNA Interference of 3D-Cultured Human Embryonic Stem Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:10732-10737. [PMID: 27787919 DOI: 10.1002/adma.201603318] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/15/2016] [Indexed: 06/06/2023]
Abstract
A new method of spatially controlled gene regulation in 3D-cultured human embryonic stem cells is developed using hollow gold nanoshells (HGNs) and near-infrared (NIR) light. Targeted cell(s) are discriminated from neighboring cell(s) by focusing NIR light emitted from a two-photon microscope. Irradiation of cells that have internalized HGNs releases surface attached siRNAs and leads to concomitant gene downregulation.
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Affiliation(s)
- Xiao Huang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Qirui Hu
- Center for Stem Cell Biology and Engineering, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Yifan Lai
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Demosthenes P Morales
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Dennis O Clegg
- Center for Stem Cell Biology and Engineering, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
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31
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Seyfried P, Eiden L, Grebenovsky N, Mayer G, Heckel A. Photo‐Tethers for the (Multi‐)Cyclic, Conformational Caging of Long Oligonucleotides. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Patrick Seyfried
- Goethe University Frankfurt Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Laura Eiden
- Life and Medical Science Institute University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Nikolai Grebenovsky
- Goethe University Frankfurt Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Max-von-Laue-Str. 9 60438 Frankfurt Germany
| | - Günter Mayer
- Life and Medical Science Institute University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Alexander Heckel
- Goethe University Frankfurt Institute for Organic Chemistry and Chemical Biology Buchmann Institute for Molecular Life Sciences Max-von-Laue-Str. 9 60438 Frankfurt Germany
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32
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Seyfried P, Eiden L, Grebenovsky N, Mayer G, Heckel A. Photo-Tethers for the (Multi-)Cyclic, Conformational Caging of Long Oligonucleotides. Angew Chem Int Ed Engl 2016; 56:359-363. [PMID: 27897376 DOI: 10.1002/anie.201610025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Indexed: 12/28/2022]
Abstract
Intramolecular circularization of DNA oligonucleotides was accomplished by incorporation of alkyne-modified photolabile nucleosides into DNA sequences, followed by a CuI -catalyzed alkyne-azide cycloaddition with bis-azido linker molecules. We determined a range of ring sizes, in which the caged circular oligonucleotides exhibit superior duplex destabilizing properties. Specific binding of a full-length 90 nt C10 aptamer recognizing human Burkitt's lymphoma cells was then temporarily inhibited by locking the aptamer in a bicircularized structure. Irradiation restored the native aptamer conformation resulting in efficient cell binding and uptake. The photo-tether strategy presented here provides a robust and versatile tool for the light-activation of longer functional oligonucleotides, noteworthy without prior knowledge on the structure and the importance of specific nucleotides within a DNA aptamer.
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Affiliation(s)
- Patrick Seyfried
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Laura Eiden
- Life and Medical Science Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Nikolai Grebenovsky
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Günter Mayer
- Life and Medical Science Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Alexander Heckel
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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33
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Gandioso A, Cano M, Massaguer A, Marchán V. A Green Light-Triggerable RGD Peptide for Photocontrolled Targeted Drug Delivery: Synthesis and Photolysis Studies. J Org Chem 2016; 81:11556-11564. [PMID: 27934458 DOI: 10.1021/acs.joc.6b02415] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We describe for the first time the synthesis and photochemical properties of a coumarin-caged cyclic RGD peptide and demonstrate that uncaging can be efficiently performed with biologically compatible green light. This was accomplished by using a new dicyanocoumarin derivative (DEAdcCE) for the protection of the carboxyl function at the side chain of the aspartic acid residue, which was selected on the basis of Fmoc-tBu SPPS compatibility and photolysis efficiency. The shielding effect of a methyl group incorporated in the coumarin derivative near the ester bond linking both moieties in combination with the use of acidic additives such as HOBt or Oxyma during the basic Fmoc-removal treatment were found to be very effective for minimizing aspartimide-related side reactions. In addition, a conjugate between the dicyanocoumarin-caged cyclic RGD peptide and ruthenocene, which was selected as a metallodrug model cargo, has been synthesized and characterized. The fact that green-light triggered photoactivation can be efficiently performed both with the caged peptide and with its ruthenocenoyl bioconjugate reveals great potential for DEAdcCE-caged peptide sequences as selective drug carriers in the context of photocontrolled targeted anticancer strategies.
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Affiliation(s)
- Albert Gandioso
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB, Universitat de Barcelona , E-08028 Barcelona, Spain
| | - Marc Cano
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB, Universitat de Barcelona , E-08028 Barcelona, Spain
| | - Anna Massaguer
- Departament de Biologia, Universitat de Girona , E-17071 Girona, Spain
| | - Vicente Marchán
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB, Universitat de Barcelona , E-08028 Barcelona, Spain
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34
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Morihiro K, Kodama T, Mori S, Tsunoda S, Obika S. Wavelength-selective light-triggered strand exchange reaction. Org Biomol Chem 2016; 14:1555-8. [PMID: 26739866 DOI: 10.1039/c5ob02369f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We prepared an oligodeoxynucleotide (ODN) bearing two 4-hydroxy-2-mercaptobenzimidazole nucleobase analogues (SB(NV) and SB(NB)) modified with different photolabile groups. This ODN enabled a light-triggered strand exchange reaction in a wavelength-selective manner.
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Affiliation(s)
- K Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. and National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - T Kodama
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - S Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - S Tsunoda
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - S Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. and National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
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35
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Jain PK, Ramanan V, Schepers AG, Dalvie NS, Panda A, Fleming HE, Bhatia SN. Development of Light-Activated CRISPR Using Guide RNAs with Photocleavable Protectors. Angew Chem Int Ed Engl 2016; 55:12440-4. [PMID: 27554600 PMCID: PMC5864249 DOI: 10.1002/anie.201606123] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Indexed: 12/11/2022]
Abstract
The ability to remotely trigger CRISPR/Cas9 activity would enable new strategies to study cellular events with greater precision and complexity. In this work, we have developed a method to photocage the activity of the guide RNA called "CRISPR-plus" (CRISPR-precise light-mediated unveiling of sgRNAs). The photoactivation capability of our CRISPR-plus method is compatible with the simultaneous targeting of multiple DNA sequences and supports numerous modifications that can enable guide RNA labeling for use in imaging and mechanistic investigations.
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Affiliation(s)
- Piyush K Jain
- Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Vyas Ramanan
- Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Arnout G Schepers
- Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Nisha S Dalvie
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Apekshya Panda
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Heather E Fleming
- Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sangeeta N Bhatia
- Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Electrical Engineering and Computer Science, Marble Center for Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
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36
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Jain PK, Ramanan V, Schepers AG, Dalvie NS, Panda A, Fleming HE, Bhatia SN. Development of Light-Activated CRISPR Using Guide RNAs with Photocleavable Protectors. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606123] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Piyush K. Jain
- Institute for Medical Engineering & Science; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Vyas Ramanan
- Institute for Medical Engineering & Science; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Arnout G. Schepers
- Institute for Medical Engineering & Science; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Nisha S. Dalvie
- Department of Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Apekshya Panda
- Department of Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Heather E. Fleming
- Institute for Medical Engineering & Science; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Sangeeta N. Bhatia
- Institute for Medical Engineering & Science; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Department of Electrical Engineering and Computer Science; Marble Center for Cancer Nanomedicine; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Department of Medicine; Brigham and Women's Hospital; Boston MA 02115 USA
- Broad Institute of MIT and Harvard; Cambridge MA 02139 USA
- Howard Hughes Medical Institute; Cambridge MA 02139 USA
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37
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Ogura Y, Onishi A, Nishimura T, Tanida J. Optically controlled release of DNA based on nonradiative relaxation process of quenchers. BIOMEDICAL OPTICS EXPRESS 2016; 7:2142-53. [PMID: 27375933 PMCID: PMC4918571 DOI: 10.1364/boe.7.002142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/27/2016] [Accepted: 05/03/2016] [Indexed: 06/02/2023]
Abstract
Optically controlled release of a DNA strand based on a nonradiative relaxation process of black hole quenchers (BHQs), which are a sort of dark quenchers, is presented. BHQs act as efficient energy sources because they relax completely via a nonradiative process, i.e., without fluorescent emission-based energy losses. A DNA strand is modified with BHQs and the release of its complementary strand is controlled by excitation of the BHQs. Experimental results showed that up to 50% of the target strands were released, and these strands were capable of inducing subsequent reactions. The controlled release was localized on a substrate within an area of no more than 5 micrometers in diameter.
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Affiliation(s)
- Yusuke Ogura
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
| | - Atsushi Onishi
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
| | - Takahiro Nishimura
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
| | - Jun Tanida
- Graduate School of Information Science and Technology, Osaka University, Suita, Osaka, 5650871,
Japan
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38
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Reversible Photoregulation of Gene Expression and Translation. Methods Mol Biol 2016. [PMID: 26965115 DOI: 10.1007/978-1-4939-3512-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Several methods for controlling gene expression by light illumination have been reported. Most of these methods control transcription by regulating the interaction between DNA and transcription factors. The use of a photolabile protecting compound (cage compound) is another promising approach for controlling gene expression, although typically in an irreversible manner. We here describe a new approach for reversibly controlling translation using a photoresponsive 8-styryl cap (8ST-cap) that can be reversibly isomerized by illumination with light of a specific wavelength.
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39
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Hanswillemenke A, Kuzdere T, Vogel P, Jékely G, Stafforst T. Site-Directed RNA Editing in Vivo Can Be Triggered by the Light-Driven Assembly of an Artificial Riboprotein. J Am Chem Soc 2015; 137:15875-81. [PMID: 26594902 PMCID: PMC4731850 DOI: 10.1021/jacs.5b10216] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Site-directed
RNA editing allows for the manipulation of RNA and
protein function by reprogramming genetic information at the RNA level.
For this we assemble artificial RNA-guided editases and demonstrate
their transcript repair activity in cells and in developing embryos
of the annelid Platynereis dumerilii. A hallmark
of our assembly strategy is the covalent attachment of guideRNA and
editing enzyme by applying the SNAP-tag technology, a process that
we demonstrate here to be readily triggered by light in vitro, in
mammalian cell culture, and also in P. dumerilii.
Lacking both sophisticated chemistry and extensive genetic engineering,
this technology provides a convenient route for the light-dependent
switching of protein isoforms. The presented strategy may also serve
as a blue-print for the engineering of addressable machineries that
apply tailored nucleic acid analogues to manipulate RNA or DNA site-specifically
in living organisms.
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Affiliation(s)
- Alfred Hanswillemenke
- Interfaculty Institute of Biochemistry, University of Tübingen , Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Tahsin Kuzdere
- Interfaculty Institute of Biochemistry, University of Tübingen , Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Paul Vogel
- Interfaculty Institute of Biochemistry, University of Tübingen , Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Gáspár Jékely
- Max-Planck-Institute for Developmental Biology , Spemannstraße 35, 72076 Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen , Auf der Morgenstelle 15, 72076 Tübingen, Germany
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