1
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Liu J, Kang W, Wang W. Photocleavage-based Photoresponsive Drug Delivery. Photochem Photobiol 2021; 98:288-302. [PMID: 34861053 DOI: 10.1111/php.13570] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 11/27/2021] [Indexed: 02/06/2023]
Abstract
Targeted drug delivery has been extensively studied in the last decade, whereas both passive and active targeting strategies still face many challenges, such as off-target drug release. Light-responsive drug delivery systems have been developed with high controllability and spatio-temporal resolution to improve drug efficacy and reduce off-target drug release. Photoremovable protecting groups are light-responsive moieties that undergo irreversible photocleavage reactions upon light irradiation. They can be covalently linked to the molecule of interest to control its structure and function with light. In this review, we will summarize recent applications of photocleavage technologies in nanoparticle-based drug delivery for precise targeting and controlled drug release, with a highlight of strategies to achieve long-wavelength light excitation. A greater understanding of these mechanisms and emerging studies will help design more efficient photocleavage-based nanosystems to advance photoresponsive drug delivery.
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Affiliation(s)
- Jinzhao Liu
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Dr. Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong, China.,HKU-Shenzhen Institute of Research and Innovation, Shenzhen, 518053, China
| | - Weirong Kang
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Dr. Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong, China.,HKU-Shenzhen Institute of Research and Innovation, Shenzhen, 518053, China
| | - Weiping Wang
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Dr. Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong, China.,HKU-Shenzhen Institute of Research and Innovation, Shenzhen, 518053, China
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2
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van der Leun AM, Hoekstra ME, Reinalda L, Scheele CLGJ, Toebes M, van de Graaff MJ, Chen LYY, Li H, Bercovich A, Lubling Y, David E, Thommen DS, Tanay A, van Rheenen J, Amit I, van Kasteren SI, Schumacher TN. Single-cell analysis of regions of interest (SCARI) using a photosensitive tag. Nat Chem Biol 2021; 17:1139-1147. [PMID: 34504322 PMCID: PMC7611907 DOI: 10.1038/s41589-021-00839-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/24/2021] [Indexed: 11/25/2022]
Abstract
The functional activity and differentiation potential of cells are determined by their interactions with surrounding cells. Approaches that allow unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a tradeoff between spatial resolution and cell profiling depth. Here, we develop a photocage-based technology that allows isolation and in-depth analysis of live cells from regions of interest in complex ex vivo systems, including primary human tissues. The use of a highly sensitive 4-nitrophenyl(benzofuran) cage coupled to a set of nanobodies allows high-resolution photo-uncaging of different cell types in areas of interest. Single-cell RNA-sequencing of spatially defined CD8+ T cells is used to exemplify the feasibility of identifying location-dependent cell states. The technology described here provides a valuable tool for the analysis of spatially defined cells in diverse biological systems, including clinical samples.
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Affiliation(s)
- Anne M van der Leun
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mirjam E Hoekstra
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Luuk Reinalda
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Colinda L G J Scheele
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
- VIB-KULeuven Center for Cancer Biology, Leuven, Belgium
| | - Mireille Toebes
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Michel J van de Graaff
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
- SeraNovo, Leiden, Netherlands
| | - Linda Y Y Chen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Hanjie Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
- Shenzhen Institute of Synthetic Biology, Shenzhen, China
| | - Akhiad Bercovich
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Yaniv Lubling
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniela S Thommen
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Sander I van Kasteren
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands.
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.
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3
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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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4
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Lu S, Shen J, Fan C, Li Q, Yang X. DNA Assembly-Based Stimuli-Responsive Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100328. [PMID: 34258165 PMCID: PMC8261508 DOI: 10.1002/advs.202100328] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Indexed: 05/06/2023]
Abstract
Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.
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Affiliation(s)
- Shasha Lu
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jianlei Shen
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Chunhai Fan
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineDepartment of UrologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qian Li
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Xiurong Yang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
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5
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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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 12/18/2020] [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.
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Affiliation(s)
- Amirrasoul Tavakoli
- Department of Chemistry and Biochemistry, Baylor UniversityWacoTX 76798USA+1 254-710-2095
| | - Debamita Paul
- Department of Chemistry and Biochemistry, Baylor UniversityWacoTX 76798USA+1 254-710-2095
| | - Hong Mu
- Department of Biology, New York UniversityNew YorkNY 10003USA
| | - Jagannath Kuchlyan
- Department of Chemistry and Biochemistry, Baylor UniversityWacoTX 76798USA+1 254-710-2095
| | - Saroj Baral
- Department of Physics, University of Illinois at ChicagoChicagoIL 60607USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at ChicagoChicagoIL 60607USA
| | - Suse Broyde
- Department of Biology, New York UniversityNew YorkNY 10003USA
| | - Jung-Hyun Min
- Department of Chemistry and Biochemistry, Baylor UniversityWacoTX 76798USA+1 254-710-2095
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6
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Baumschlager A, Khammash M. Synthetic Biological Approaches for Optogenetics and Tools for Transcriptional Light-Control in Bacteria. Adv Biol (Weinh) 2021; 5:e2000256. [PMID: 34028214 DOI: 10.1002/adbi.202000256] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/11/2021] [Indexed: 12/22/2022]
Abstract
Light has become established as a tool not only to visualize and investigate but also to steer biological systems. This review starts by discussing the unique features that make light such an effective control input in biology. It then gives an overview of how light-control came to progress, starting with photoactivatable compounds and leading up to current genetic implementations using optogenetic approaches. The review then zooms in on optogenetics, focusing on photosensitive proteins, which form the basis for optogenetic engineering using synthetic biological approaches. As the regulation of transcription provides a highly versatile means for steering diverse biological functions, the focus of this review then shifts to transcriptional light regulators, which are presented in the biotechnologically highly relevant model organism Escherichia coli.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich, Mattenstrasse 26, Basel, 4058, Switzerland
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7
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Welleman IM, Hoorens MWH, Feringa BL, Boersma HH, Szymański W. Photoresponsive molecular tools for emerging applications of light in medicine. Chem Sci 2020; 11:11672-11691. [PMID: 34094410 PMCID: PMC8162950 DOI: 10.1039/d0sc04187d] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/14/2020] [Indexed: 12/29/2022] Open
Abstract
Light-based therapeutic and imaging modalities, which emerge in clinical applications, rely on molecular tools, such as photocleavable protecting groups and photoswitches that respond to photonic stimulus and translate it into a biological effect. However, optimisation of their key parameters (activation wavelength, band separation, fatigue resistance and half-life) is necessary to enable application in the medical field. In this perspective, we describe the applications scenarios that can be envisioned in clinical practice and then we use those scenarios to explain the necessary properties that the photoresponsive tools used to control biological function should possess, highlighted by examples from medical imaging, drug delivery and photopharmacology. We then present how the (photo)chemical parameters are currently being optimized and an outlook is given on pharmacological aspects (toxicity, solubility, and stability) of light-responsive molecules. With these interdisciplinary insights, we aim to inspire the future directions for the development of photocontrolled tools that will empower clinical applications of light.
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Affiliation(s)
- Ilse M Welleman
- Department of Radiology, Medical Imaging Center, University Medical Center Groningen Groningen The Netherlands
- Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
| | - Mark W H Hoorens
- Department of Radiology, Medical Imaging Center, University Medical Center Groningen Groningen The Netherlands
- Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
| | - Ben L Feringa
- Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
| | - Hendrikus H Boersma
- Department of Radiology, Medical Imaging Center, University Medical Center Groningen Groningen The Netherlands
- Departments of Clinical Pharmacy and Pharmacology, Nuclear Medicine and Molecular Imaging, University Medical Center Groningen Groningen The Netherlands
| | - Wiktor Szymański
- Department of Radiology, Medical Imaging Center, University Medical Center Groningen Groningen The Netherlands
- Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
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8
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Xiao L, Habibian M, Kool ET. Site-Selective RNA Functionalization via DNA-Induced Structure. J Am Chem Soc 2020; 142:16357-16363. [PMID: 32865995 PMCID: PMC7962339 DOI: 10.1021/jacs.0c06824] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methods for RNA functionalization at specific sites are in high demand but remain a challenge, particularly for RNAs produced by transcription rather than by total synthesis. Recent studies have described acylimidazole reagents that react in high yields at 2'-OH groups stochastically at nonbase-paired regions, covering much of the RNA in scattered acyl esters. Localized reactions, if possible, could prove useful in many applications, providing functional handles at specific sites and sequences of the biopolymer. Here, we describe a DNA-directed strategy for in vitro functionalization of RNA at site-localized 2'-OH groups. The method, RNA Acylation at Induced Loops (RAIL), utilizes complementary helper DNA oligonucleotides that expose gaps or loops at selected positions while protecting the remainder in DNA-RNA duplexes. Reaction with an acylimidazole reagent is then carried out, providing high yields of 2'-OH conjugation at predetermined sites. Experiments reveal optimal helper oligodeoxynucleotide designs and conditions for the reaction, and tests of the approach are carried out to control localized ribozyme activities and to label RNAs with dual-color fluorescent dyes. The RAIL approach offers a simple and novel strategy for site-selective labeling and control of RNAs, potentially of any length and origin.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, ChEM-H Institute and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
| | - Maryam Habibian
- Department of Chemistry, ChEM-H Institute and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, ChEM-H Institute and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
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9
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Wrist A, Sun W, Summers RM. The Theophylline Aptamer: 25 Years as an Important Tool in Cellular Engineering Research. ACS Synth Biol 2020; 9:682-697. [PMID: 32142605 DOI: 10.1021/acssynbio.9b00475] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The theophylline aptamer was isolated from an oligonucleotide library in 1994. Since that time, the aptamer has found wide utility, particularly in synthetic biology, cellular engineering, and diagnostic applications. The primary application of the theophylline aptamer is in the construction and characterization of synthetic riboswitches for regulation of gene expression. These riboswitches have been used to control cellular motility, regulate carbon metabolism, construct logic gates, screen for mutant enzymes, and control apoptosis. Other applications of the theophylline aptamer in cellular engineering include regulation of RNA interference and genome editing through CRISPR systems. Here we describe the uses of the theophylline aptamer for cellular engineering over the past 25 years. In so doing, we also highlight important synthetic biology applications to control gene expression in a ligand-dependent manner.
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Affiliation(s)
- Alexandra Wrist
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Wanqi Sun
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Ryan M. Summers
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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10
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Boháčová S, Ludvíková L, Poštová Slavětínská L, Vaníková Z, Klán P, Hocek M. Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA. Org Biomol Chem 2019; 16:1527-1535. [PMID: 29431832 DOI: 10.1039/c8ob00160j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleosides, nucleotides and 2'-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleotides and DNA. Photodeprotection (photorelease) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined. Photocaged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR. DNA probes containing photocaged or free 5-hydroxymethylU in the recognition sequence of restriction endonucleases were prepared and used for the study of photorelease of caged DNA by UV or visible light at different wavelengths. The nitropiperonyl-protected nucleotide was found to be a superior building block because the corresponding dNTP is a good substrate for DNA polymerases, and the protecting group is efficiently cleavable by irradiation by UV or visible light (up to 425 nm).
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Affiliation(s)
- Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
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11
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Light-triggered release of photocaged therapeutics - Where are we now? J Control Release 2019; 298:154-176. [PMID: 30742854 DOI: 10.1016/j.jconrel.2019.02.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/02/2023]
Abstract
The current available therapeutics face several challenges such as the development of ideal drug delivery systems towards the goal of personalized treatments for patients benefit. The application of light as an exogenous activation mechanism has shown promising outcomes, owning to the spatiotemporal confinement of the treatment in the vicinity of the diseased tissue, which offers many intriguing possibilities. Engineering therapeutics with light responsive moieties have been explored to enhance the bioavailability, and drug efficacy either in vitro or in vivo. The tailor-made character turns the so-called photocaged compounds highly desirable to reduce the side effects of drugs and, therefore, have received wide research attention. Herein, we seek to highlight the potential of photocaged compounds to obtain a clear understanding of the mechanisms behind its use in therapeutic delivery. A deep overview on the progress achieved in the design, fabrication as well as current and possible future applications in therapeutics of photocaged compounds is provided, so that novel formulations for biomedical field can be designed.
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12
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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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13
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Dhamodharan V, Nomura Y, Dwidar M, Yokobayashi Y. Optochemical control of gene expression by photocaged guanine and riboswitches. Chem Commun (Camb) 2018; 54:6181-6183. [DOI: 10.1039/c8cc02290a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A photocaged guanine was synthesized to optically control gene expression in cells using synthetic riboswitches.
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Affiliation(s)
- V. Dhamodharan
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Okinawa
- Japan
| | - Yoko Nomura
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Okinawa
- Japan
| | - Mohammed Dwidar
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Okinawa
- Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit
- Okinawa Institute of Science and Technology Graduate University
- Onna
- Okinawa
- Japan
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14
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Binder D, Bier C, Grünberger A, Drobietz D, Hage-Hülsmann J, Wandrey G, Büchs J, Kohlheyer D, Loeschcke A, Wiechert W, Jaeger KE, Pietruszka J, Drepper T. Photocaged Arabinose: A Novel Optogenetic Switch for Rapid and Gradual Control of Microbial Gene Expression. Chembiochem 2016; 17:296-9. [DOI: 10.1002/cbic.201500609] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Dennis Binder
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Claus Bier
- Institute of Bioorganic Chemistry; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences (IBG-1); Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Dagmar Drobietz
- Institute of Bioorganic Chemistry; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Georg Wandrey
- AVT-Biochemical Engineering; RWTH Aachen University; Worringer Weg 1 52074 Aachen Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering; RWTH Aachen University; Worringer Weg 1 52074 Aachen Germany
| | - Dietrich Kohlheyer
- Institute of Bio- and Geosciences (IBG-1); Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences (IBG-1); Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
- Institute of Bio- and Geosciences (IBG-1); Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
- Institute of Bio- and Geosciences (IBG-1); Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology; Heinrich-Heine-University Düsseldorf; Forschungszentrum Jülich; Stetternicher Forst 52426 Jülich Germany
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15
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Efficient Photochemical Approaches for Spatially Resolved Surface Functionalization. Angew Chem Int Ed Engl 2015; 54:11388-403. [DOI: 10.1002/anie.201504920] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Indexed: 12/18/2022]
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16
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Delaittre G, Goldmann AS, Mueller JO, Barner-Kowollik C. Effiziente photochemische Verfahren für die räumlich aufgelöste Oberflächenfunktionalisierung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504920] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Walsh S, Gardner L, Deiters A, Williams GJ. Intracellular light-activation of riboswitch activity. Chembiochem 2014; 15:1346-51. [PMID: 24861567 DOI: 10.1002/cbic.201400024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Indexed: 12/18/2022]
Abstract
By combining a riboswitch with a cell-permeable photocaged small-molecule ligand, an optochemical gene control element was constructed that enabled spatial and temporal control of gene expression in bacterial cells. The simplicity of this strategy, coupled with the ability to create synthetic riboswitches with tailored ligand specificities and output in a variety of microorganisms, plants, and fungi might afford a general strategy to photocontrol gene expression in vivo. The ability to activate riboswitches by using light enables the interrogation and manipulation of a wide range of biological processes with high precision, and will have broad utility in the regulation of artificial genetic circuits.
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Affiliation(s)
- Steven Walsh
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, NC 27695-8204 (USA)
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18
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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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19
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Klán P, Šolomek T, Bochet CG, Blanc A, Givens R, Rubina M, Popik V, Kostikov A, Wirz J. Photoremovable protecting groups in chemistry and biology: reaction mechanisms and efficacy. Chem Rev 2013; 113:119-91. [PMID: 23256727 PMCID: PMC3557858 DOI: 10.1021/cr300177k] [Citation(s) in RCA: 1248] [Impact Index Per Article: 113.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Petr Klán
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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20
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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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21
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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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22
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Pauloehrl T, Delaittre G, Bruns M, Meißler M, Börner HG, Bastmeyer M, Barner-Kowollik C. (Bio)Molecular Surface Patterning by Phototriggered Oxime Ligation. Angew Chem Int Ed Engl 2012; 51:9181-4. [DOI: 10.1002/anie.201202684] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/08/2012] [Indexed: 12/19/2022]
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23
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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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24
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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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25
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Russell AG, Sadler MJ, Laidlaw HJ, Gutiérrez-Loriente A, Wharton CW, Carteau D, Bassani DM, Snaith JS. Photorelease of tyrosine from α-carboxy-6-nitroveratryl (αCNV) derivatives. Photochem Photobiol Sci 2012; 11:556-63. [PMID: 22249211 DOI: 10.1039/c2pp05320a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of photolabile tyrosine derivatives protected on the phenolic oxygen by the α-carboxy-6-nitroveratryl (αCNV) protecting group is described. The compounds undergo rapid photolysis at wavelengths longer than 300 nm to liberate the corresponding phenol in excellent yield (quantum yield for the deprotection of tyrosine = 0.19). Further protection of caged tyrosine is possible, yielding N-Fmoc protected derivatives suitable for direct incorporation of caged tyrosine in solid-phase peptide synthesis.
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26
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Wulffen B, Buff MCR, Pofahl M, Mayer G, Heckel A. Caged glucosamine-6-phosphate for the light-control of riboswitch activity. Photochem Photobiol Sci 2012; 11:489-92. [DOI: 10.1039/c1pp05242j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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27
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Georgianna WE, Young DD. Development and utilization of non-coding RNA–small molecule interactions. Org Biomol Chem 2011; 9:7969-78. [DOI: 10.1039/c1ob06324c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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28
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Young DD, Lively MO, Deiters A. Activation and deactivation of DNAzyme and antisense function with light for the photochemical regulation of gene expression in mammalian cells. J Am Chem Soc 2010; 132:6183-93. [PMID: 20392038 DOI: 10.1021/ja100710j] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The photochemical regulation of biological systems represents a very precise means of achieving high-resolution control over gene expression in both a spatial and a temporal fashion. DNAzymes are enzymatically active deoxyoligonucleotides that enable the site-specific cleavage of RNA and have been used in a variety of in vitro applications. We have previously reported the photochemical activation of DNAzymes and antisense agents through the preparation of a caged DNA phosphoramidite and its site-specific incorporation into oligonucleotides. The presence of the caging group disrupts either DNA:RNA hybridization or catalytic activity until removed via a brief irradiation with UV light. Here, we are expanding this concept by investigating the photochemical deactivation of DNAzymes and antisense agents. Moreover, we report the application of light-activated and light-deactivated antisense agents to the regulation of gene function in mammalian cells. This represents the first example of gene silencing antisense agents that can be turned on and turned off in mammalian tissue culture.
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Affiliation(s)
- Douglas D Young
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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29
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Lusic H, Uprety R, Deiters A. Improved synthesis of the two-photon caging group 3-nitro-2-ethyldibenzofuran and its application to a caged thymidine phosphoramidite. Org Lett 2010; 12:916-9. [PMID: 20112966 DOI: 10.1021/ol902807q] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new and efficient route to the recently reported 3-nitro-2-ethyldibenzofuran caging group was developed. Furthermore, its installation on a thymidine phosphoramidite is described. This caging group is efficiently removed through light-irradiation at 365 nm.
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Affiliation(s)
- Hrvoje Lusic
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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30
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Nierth A, Singer M, Jäschke A. Efficient photoactivation of a Diels-Alderase ribozyme. Chem Commun (Camb) 2010; 46:7975-7. [DOI: 10.1039/c0cc03162c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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31
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Reymond C, Beaudoin JD, Perreault JP. Modulating RNA structure and catalysis: lessons from small cleaving ribozymes. Cell Mol Life Sci 2009; 66:3937-50. [PMID: 19718544 PMCID: PMC2777235 DOI: 10.1007/s00018-009-0124-1] [Citation(s) in RCA: 20] [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: 04/24/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 01/12/2023]
Abstract
RNA is a key molecule in life, and comprehending its structure/function relationships is a crucial step towards a more complete understanding of molecular biology. Even though most of the information required for their correct folding is contained in their primary sequences, we are as yet unable to accurately predict both the folding pathways and active tertiary structures of RNA species. Ribozymes are interesting molecules to study when addressing these questions because any modifications in their structures are often reflected in their catalytic properties. The recent progress in the study of the structures, the folding pathways and the modulation of the small ribozymes derived from natural, self-cleaving, RNA motifs have significantly contributed to today's knowledge in the field.
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Affiliation(s)
- Cedric Reymond
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
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32
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Kotzur N, Briand B, Beyermann M, Hagen V. Competition between cleavage and decarboxylation in photolysis of alpha-carboxy-2-nitrobenzyl protected cysteine derivatives. Chem Commun (Camb) 2009:3255-7. [PMID: 19587931 DOI: 10.1039/b900865a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photolysis of model peptides containing alpha-carboxy-2-nitrobenzyl (CNB) or alpha-carboxy-4,5-dimethoxy-2-nitrobenzyl (CDMNB) protected cysteines in aqueous solution gives the expected 2-nitrobenzyl-type photocleavage and can be accompanied by photodecarboxylation depending on structural aspects.
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Affiliation(s)
- Nico Kotzur
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
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33
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Richards JL, Tang X, Turetsky A, Dmochowski IJ. RNA bandages for photoregulating in vitro protein synthesis. Bioorg Med Chem Lett 2008; 18:6255-8. [PMID: 18926697 PMCID: PMC2593108 DOI: 10.1016/j.bmcl.2008.09.093] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 09/24/2008] [Accepted: 09/26/2008] [Indexed: 11/24/2022]
Abstract
'RNA bandages' are composed of two 6-12-mer 2'-OMe RNA strands complementary to a mRNA target that are joined by a photocleavable linker. These tandem oligonucleotides typically exhibit much higher affinity for the mRNA than the individual strands. An RNA bandage with binding arms of different lengths and a 4-base gap blocked translation in vitro of GFP mRNA; subsequent near-UV irradiation restored translation. This provides a general method of photomodulating hybridization for a variety of oligonucleotide-based technologies.
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Affiliation(s)
- Julia L. Richards
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - XinJing Tang
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Anna Turetsky
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Ivan J. Dmochowski
- Department of Chemistry, 231 S. 34 St., University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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34
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Affiliation(s)
- Douglas D Young
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695-8204, USA
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35
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Deiters A, Yoder JA. Conditional transgene and gene targeting methodologies in zebrafish. Zebrafish 2008; 3:415-29. [PMID: 18377222 DOI: 10.1089/zeb.2006.3.415] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The zebrafish has become a powerful tool for dissecting vertebrate gene function during embryogenesis. Numerous molecular systems have been developed to examine gene function in zebrafish, including transgenics for creating lineage-tracer lines of zebrafish that express a fluorescent protein as a marker for specific populations of cells, and antisense strategies, primarily morpholinos, for knocking down gene function. The focus of this review is to summarize the pros and cons of the currently available systems for functional genomics in zebrafish, and to discuss the need for future methodologies.
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Affiliation(s)
- Alexander Deiters
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina, USA
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36
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Lusic H, Lively MO, Deiters A. Light-activated deoxyguanosine: photochemical regulation of peroxidase activity. MOLECULAR BIOSYSTEMS 2008; 4:508-11. [PMID: 18493645 DOI: 10.1039/b800166a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochemical activation of a deoxyribozyme with peroxidase activity was achieved by the synthesis and incorporation of a caged deoxyguanosine.
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Affiliation(s)
- Hrvoje Lusic
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695, USA
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37
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Abstract
Drug discovery remains a top priority in medical science. The phenomenon of drug resistance has heightened the need for both new classes of pharmaceutical, as well as novel modes of action. A new paradigm for drug activity is presented, which includes both recognition and subsequent irreversible inactivation of therapeutic targets. Application to both RNA and enzyme therapeutic targets has been demonstrated, while incorporation of both binding and catalytic centers provides a double-filter mechanism for improved target selectivity and lower dosing. In contrast to RNA targets that are subject to strand scission chemistry mediated by ribose H-atom abstraction, proteins appear to be inactivated through oxidative damage to amino acid side chains around the enzyme active site. Methods to monitor both intracellular delivery and activity against RNA targets have been developed based on plasmid expression of the green fluorescent protein (GFP). Herein, the activity of representative metallodrugs is described in the context of both in vitro and cellular assays, and the mechanism of action is discussed. Studies with scavengers of reactive oxygen species (ROS) confirmed hydrogen peroxide to be an obligatory diffusible intermediate, prior to formation of a Cu-bound hydroxyl radical species generated from Fenton-type chemistry.
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38
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Young DD, Edwards WF, Lusic H, Lively MO, Deiters A. Light-triggered polymerase chain reaction. Chem Commun (Camb) 2007:462-4. [PMID: 18188468 DOI: 10.1039/b715152g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochemical control of the polymerase chain reaction has been achieved through the incorporation of light-triggered nucleotides into DNA.
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Affiliation(s)
- Douglas D Young
- North Carolina State University, Department of Chemistry, Raleigh, NC 27695, USA
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39
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Lee HW, Robinson SG, Bandyopadhyay S, Mitchell RH, Sen D. Reversible photo-regulation of a hammerhead ribozyme using a diffusible effector. J Mol Biol 2007; 371:1163-73. [PMID: 17619022 DOI: 10.1016/j.jmb.2007.06.042] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 06/07/2007] [Accepted: 06/12/2007] [Indexed: 11/19/2022]
Abstract
The potential utility of catalytic RNAs and DNAs (ribozymes and deoxyribozymes, respectively) as reagents in molecular biology as well as therapeutic agents for a variety of human diseases, has long been recognized. Although naturally occurring RNA-cleaving ribozymes are typically not subject to feedback control, rational methodologies for the creation of allosteric ribozymes, by functional combination of ribozyme and ligand-responsive aptamer RNA elements, have existed for some years. Here, we report the in vitro selection of RNA aptamers specific for binding one but not the other of two light-induced isomers of a dihydropyrene photo-switch compound, and the utilization of such an aptamer for the construction of the UG-dihydropyrene ribozyme, an allosteric hammerhead ribozyme whose catalysis is controllable by irradiation with visible versus ultraviolet light. In the presence of micromolar concentrations of the photo-switch compound, the ribozyme behaves as a two-state switch, exhibiting a >900-fold difference in catalytic rates between the two irradiation regimes. We anticipate that the UG-dihydropyrene, and other ribozymes like it, may find significant application in the developmental biology of model organisms such as Drosophila melanogaster and Caenorhabditis elegans, as well as in the biomedical sciences.
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Affiliation(s)
- Hyun-Wu Lee
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, B.C., Canada V5A 1S6
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40
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Abstract
Photochemical regulation of biological processes offers a high level of control to study intracellular mechanisms with unprecedented spatial and temporal resolution. This report summarizes the advances made in recent years, focusing predominantly on the in vivo regulation of gene function using irradiation with UV light. The majority of the described applications entail the utilization of photocaging groups installed either on a small molecule modulator of biomolecular function or directly on a biological macromolecule itself.
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Affiliation(s)
- Douglas D Young
- North Carolina State University, Department of Chemistry, Campus Box 8204, Raleigh, NC 27695, USA
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41
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Tang X, Dmochowski IJ. Regulating gene expression with light-activated oligonucleotides. MOLECULAR BIOSYSTEMS 2006; 3:100-10. [PMID: 17245489 DOI: 10.1039/b614349k] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Since the development of light-responsive amino acids, the activity of numerous biomolecules has been photomodulated in biochemical, biophysical, and cellular assays. Biological problems of even greater complexity motivate the development of quantitative methods for controlling gene activity with high spatial and temporal resolution, using light as an external trigger. Photoresponsive DNA and RNA oligonucleotides would optimally serve this purpose, but have proven difficult to expand from proofs-of-concept to in vivo experiments. Until recently, the development of this technology was limited by the synthesis of oligonucleotides whose function could be significantly modulated with near-UV light. New synthetic protocols and strategies for both up- and down-regulating gene activity finally make it possible to address biological considerations. In the near future, we can expect photoresponsive DNA and RNA molecules that are relatively non-toxic, nuclease-resistant, and maintain their specificity and activity in vivo. Quantitative, laser-initiated methods for controlling DNA and RNA function will illuminate new areas in cell and developmental biology.
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Affiliation(s)
- XinJing Tang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA
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