1
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Cornelissen NV, Hoffmann A, Rentmeister A. DNA‐Methyltransferasen und AdoMet‐Analoga als Werkzeuge für die Molekularbiologie und Biotechnologie. CHEM-ING-TECH 2023. [DOI: 10.1002/cite.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Nicolas V. Cornelissen
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Arne Hoffmann
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
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2
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White LJ, Boles JE, Clifford M, Patenall BL, Hilton KHLF, Ng KKL, Ellaby RJ, Hind CK, Mulvihill DP, Hiscock JR. Di-anionic self-associating supramolecular amphiphiles (SSAs) as antimicrobial agents against MRSA and Escherichia coli. Chem Commun (Camb) 2021; 57:11839-11842. [PMID: 34698738 DOI: 10.1039/d1cc05455d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report a series of di-anionic supramolecular self-associating amphiphiles (SSAs). We elucidate the antimicrobial properties of these SSAs against both methicillin resistant Staphylococcus aureus and Escherichia coli. In addition, we show this class of compound to form both intra- and intermolecular hydrogen bonded macrocyclic structures in the solid state.
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Affiliation(s)
- Lisa J White
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Jessica E Boles
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK. .,School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
| | - Melanie Clifford
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | - Bethany L Patenall
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | - Kira H L F Hilton
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Kendrick K L Ng
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Rebecca J Ellaby
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Charlotte K Hind
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | - Daniel P Mulvihill
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
| | - Jennifer R Hiscock
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.
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3
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King EA, Peairs EM, Uthappa DM, Villa JK, Goff CM, Burrow NK, Deitch RT, Martin AK, Young DD. Photoregulation of PRMT-1 Using a Photolabile Non-Canonical Amino Acid. Molecules 2021; 26:molecules26165072. [PMID: 34443661 PMCID: PMC8398576 DOI: 10.3390/molecules26165072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/24/2022] Open
Abstract
Protein methyltransferases are vital to the epigenetic modification of gene expression. Thus, obtaining a better understanding of and control over the regulation of these crucial proteins has significant implications for the study and treatment of numerous diseases. One ideal mechanism of protein regulation is the specific installation of a photolabile-protecting group through the use of photocaged non-canonical amino acids. Consequently, PRMT1 was caged at a key tyrosine residue with a nitrobenzyl-protected Schultz amino acid to modulate protein function. Subsequent irradiation with UV light removes the caging group and restores normal methyltransferase activity, facilitating the spatial and temporal control of PRMT1 activity. Ultimately, this caged PRMT1 affords the ability to better understand the protein’s mechanism of action and potentially regulate the epigenetic impacts of this vital protein.
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4
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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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/04/2021] [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.
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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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5
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Acevedo-Jake A, Ball AT, Galli M, Kukwikila M, Denis M, Singleton DG, Tavassoli A, Goldup SM. AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides. J Am Chem Soc 2020; 142:5985-5990. [PMID: 32155338 PMCID: PMC8016193 DOI: 10.1021/jacs.0c01670] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/22/2022]
Abstract
We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.
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Affiliation(s)
- Amanda Acevedo-Jake
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Andrew T. Ball
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Marzia Galli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mikiembo Kukwikila
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mathieu Denis
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Daniel G. Singleton
- ATDBio
Ltd, School of Chemistry, University of
Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Ali Tavassoli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Stephen M. Goldup
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
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6
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Tang S, Cannon J, Yang K, Krummel MF, Baker JR, Choi SK. Spacer-Mediated Control of Coumarin Uncaging for Photocaged Thymidine. J Org Chem 2020; 85:2945-2955. [PMID: 32020803 PMCID: PMC7293860 DOI: 10.1021/acs.joc.9b02617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Despite its importance in the design of photocaged molecules, less attention is focused on linker chemistry than the cage itself. Here, we describe unique uncaging properties displayed by two coumarin-caged thymidine compounds, each conjugated with (2) or without (1) an extended, self-immolative spacer. Photolysis of 1 using long-wavelength UVA (365 nm) or visible (420, 455 nm) light led to the release of free thymidine along with the competitive generation of a thymidine-bearing recombination product. The occurrence of this undesired side reaction, which is previously unreported, was not present with the photolysis of 2, which released thymidine exclusively with higher quantum efficiency. We propose that the spatial separation between the cage and the substrate molecule conferred by the extended linker can play a critical role in circumventing this unproductive reaction. This report reinforces the importance of linker selection in the design of coumarin-caged oligonucleosides and other conjugates.
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Affiliation(s)
- Shengzhuang Tang
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Ann Arbor, Michigan 48109, United States of America
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
| | - Jayme Cannon
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Ann Arbor, Michigan 48109, United States of America
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
| | - Kelly Yang
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
| | - Matthew F. Krummel
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, California 94143, United States of America
| | - James R. Baker
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Ann Arbor, Michigan 48109, United States of America
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
| | - Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Ann Arbor, Michigan 48109, United States of America
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
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7
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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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8
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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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9
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Hughes RM. A compendium of chemical and genetic approaches to light-regulated gene transcription. Crit Rev Biochem Mol Biol 2018; 53:453-474. [PMID: 30040498 DOI: 10.1080/10409238.2018.1487382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
On-cue regulation of gene transcription is an invaluable tool for the study of biological processes and the development and integration of next-generation therapeutics. Ideal reagents for the precise regulation of gene transcription should be nontoxic to the host system, highly tunable, and provide a high level of spatial and temporal control. Light, when coupled with protein or small molecule-linked photoresponsive elements, presents an attractive means of meeting the demands of an ideal system for regulating gene transcription. In this review, we cover recent developments in the burgeoning field of light-regulated gene transcription, covering both genetically encoded and small-molecule based strategies for optical regulation of transcription during the period 2012 till present.
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Affiliation(s)
- Robert M Hughes
- a Department of Chemistry , East Carolina University , Greenville , NC , USA
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10
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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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11
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Boháčová S, Vaníková Z, Poštová Slavětínská L, Hocek M. Protected 2′-deoxyribonucleoside triphosphate building blocks for the photocaging of epigenetic 5-(hydroxymethyl)cytosine in DNA. Org Biomol Chem 2018; 16:5427-5432. [DOI: 10.1039/c8ob01106k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
2′-Deoxyribonucleoside triphosphates containing 5-(hydroxymethyl)cytosine protected with photocleavable groups were prepared and studied as substrates for the enzymatic synthesis of DNA containing a photocaged epigenetic 5hmC base.
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Affiliation(s)
- Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
| | - Zuzana Vaníková
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
- Department of Organic Chemistry
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
- Department of Organic Chemistry
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12
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Wong PT, Roberts EW, Tang S, Mukherjee J, Cannon J, Nip AJ, Corbin K, Krummel MF, Choi SK. Control of an Unusual Photo-Claisen Rearrangement in Coumarin Caged Tamoxifen through an Extended Spacer. ACS Chem Biol 2017; 12:1001-1010. [PMID: 28191924 PMCID: PMC5404426 DOI: 10.1021/acschembio.6b00999] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The use of coumarin
caged molecules has been well documented in
numerous photocaging applications including for the spatiotemporal
control of Cre-estrogen receptor (Cre-ERT2) recombinase activity.
In this article, we report that 4-hydroxytamoxifen (4OHT) caged with
coumarin via a conventional ether linkage led to
an unexpected photo-Claisen rearrangement which significantly competed
with the release of free 4OHT. The basis for this unwanted reaction
appears to be related to the coumarin structure and its radical-based
mechanism of uncaging, as it did not occur in ortho-nitrobenzyl (ONB) caged 4OHT that was otherwise linked in the same
manner. In an effort to perform design optimization, we introduced
a self-immolative linker longer than the ether linkage and identified
an optimal linker which allowed rapid 4OHT release by both single-photon
and two-photon absorption mechanisms. The ability of this construct
to actively control Cre-ERT2 mediated gene modifications was investigated
in mouse embryonic fibroblasts (MEFs) in which the expression of a
green fluorescent protein (GFP) reporter dependent gene recombination
was controlled by 4OHT release and measured by confocal fluorescence
microscopy and flow cytometry. In summary, we report the implications
of this photo-Claisen rearrangement in coumarin caged compounds and
demonstrate a rational linker strategy for addressing this unwanted
side reaction.
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Affiliation(s)
| | - Edward W. Roberts
- Department
of Pathology, University of California, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, California 94143, United States
| | | | | | | | - Alyssa J. Nip
- Department
of Pathology, University of California, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, California 94143, United States
| | - Kaitlin Corbin
- Department
of Pathology, University of California, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, California 94143, United States
| | - Matthew F. Krummel
- Department
of Pathology, University of California, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, California 94143, United States
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13
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Padilla MS, Farley CA, Chatkewitz LE, Young DD. Synthesis and incorporation of a caged tyrosine amino acid possessing a bioorthogonal handle. Tetrahedron Lett 2016; 57:4709-4712. [PMID: 28533567 PMCID: PMC5438197 DOI: 10.1016/j.tetlet.2016.09.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Reversing a bioconjugation in a spatial and temporal fashion has widespread applications, especially toward targeted drug delivery. We report the synthesis and incorporation of an unnatural amino acid with an alkyne modified dimethoxy-ortho-nitrobenzyl caging group. This unnatural amino acid can be utilized in a Glaser-Hay conjugation to generate a bioconjugate, but also is able to disrupt the bioconjugate when irradiated with light. These combined features allow for the preparation of bioconjugates with a high degree of site-specificity and allow for the separation of the two components if necessary.
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Affiliation(s)
- Marshall S Padilla
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Christopher A Farley
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Lindsay E Chatkewitz
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
| | - Douglas D Young
- Department of Chemistry, College of William & Mary, P.O. Box 8795, Williamsburg, VA 23187, USA
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14
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Seio K, Ohno Y, Ohno K, Takeshita L, Kanamori T, Masaki Y, Sekine M. Photo-controlled binding of MutS to photo-caged DNA duplexes incorporating 4- O -(2-nitrobenzyl) or 4- O -[2-(2-nitrophenyl)propyl]thymidine. Bioorg Med Chem Lett 2016; 26:4861-4863. [DOI: 10.1016/j.bmcl.2016.07.075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 07/14/2016] [Accepted: 07/29/2016] [Indexed: 10/21/2022]
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15
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Struntz NB, Harki DA. Catch and Release DNA Decoys: Capture and Photochemical Dissociation of NF-κB Transcription Factors. ACS Chem Biol 2016; 11:1631-8. [PMID: 27054264 DOI: 10.1021/acschembio.6b00130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Catch and release DNA decoys (CRDDs) are a new class of non-natural DNA probes that capture and dissociate from DNA-binding proteins using a light trigger. Photolytic cleavage of non-natural nucleobases in the CRDD yields abasic sites and truncation products that lower the affinity of the CRDD for its protein target. Herein, we demonstrate the ability of the first-generation CRDD to bind and release NF-κB proteins. This platform technology should be applicable to other DNA-binding proteins by modification of the target sequence.
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Affiliation(s)
- Nicholas B. Struntz
- Department
of Medicinal Chemistry, University of Minnesota, 2231 6th Street S.E., Minneapolis, Minnesota 55455, United States
| | - Daniel A. Harki
- Department
of Medicinal Chemistry, University of Minnesota, 2231 6th Street S.E., Minneapolis, Minnesota 55455, United States
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16
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Mikutis G, Mora CA, Puddu M, Paunescu D, Grass RN, Stark WJ. DNA-Based Sensor Particles Enable Measuring Light Intensity in Single Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:2765-2770. [PMID: 26866714 DOI: 10.1002/adma.201504892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/04/2015] [Indexed: 06/05/2023]
Abstract
"Lab on a particle" architecture is employed in designing a light nanosensor. Light-sensitive protecting groups are installed on DNA, which is encapsulated in silica particles, qualifying as a self-sufficient light sensor. The nanosensors allow measuring light intensity and duration in very small volumes, such as single cells, and store the irradiation information until readout.
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Affiliation(s)
- Gediminas Mikutis
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Carlos A Mora
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Michela Puddu
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Daniela Paunescu
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Robert N Grass
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Wendelin J Stark
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
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17
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Baldassarre M, Barth A. The carbonate/bicarbonate system as a pH indicator for infrared spectroscopy. Analyst 2015; 139:2167-76. [PMID: 24622696 DOI: 10.1039/c3an02331a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Caged compounds capable of inducing large pH-jumps upon UV illumination have represented a breakthrough in time-resolved infrared spectroscopy of acidification-triggered phenomena, but their use is hampered by the inability to control the initial pH as well as to measure the final pH in μL volumes. We have developed an experimental approach that accurately measures the initial and final pH values in pH-jump experiments. Our approach exploits the concomitant presence of two or more inorganic ions, such as carbonate and bicarbonate, that are added to the sample at a known concentration. The difference spectrum obtained in the infrared measurement is fitted to isolate the bands arising from the appearance or disappearance of either protonation state, and is then compared to a synthetic library of difference spectra generated using both qualitative (band position and width, extinction coefficient, pK) and quantitative (concentration, pathlength) parameters of the reporter ions. We have tested this approach in UV-photolysis experiments of 1-(2-nitrophenyl)ethyl sulfate in the presence of different concentrations of Na2CO3 and successfully used the infrared absorption of the carbonate and the bicarbonate ions to determine the initial and final pH values before and after the pH-jump, respectively.
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Affiliation(s)
- Maurizio Baldassarre
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden.
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Vaníková Z, Hocek M. Polymerase Synthesis of Photocaged DNA Resistant against Cleavage by Restriction Endonucleases. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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19
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Vaníková Z, Hocek M. Polymerase synthesis of photocaged DNA resistant against cleavage by restriction endonucleases. Angew Chem Int Ed Engl 2014; 53:6734-7. [PMID: 24850380 DOI: 10.1002/anie.201402370] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/23/2014] [Indexed: 12/12/2022]
Abstract
5-[(2-Nitrobenzyl)oxymethyl]-2'-deoxyuridine 5'-O-triphosphate was used for polymerase (primer extension or PCR) synthesis of photocaged DNA that is resistant to the cleavage by restriction endonucleases. Photodeprotection of the caged DNA released 5-hydroxymethyluracil-modified nucleic acids, which were fully recognized and cleaved by restriction enzymes.
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Affiliation(s)
- Zuzana Vaníková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic) http://www.uochb.cas.cz/hocekgroup
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Teraoka A, Murakoshi K, Fukamauchi K, Suzuki AZ, Watanabe S, Furuta T. Preparation and affinity-based purification of caged linear DNA for light-controlled gene expression in mammalian cells. Chem Commun (Camb) 2014; 50:664-6. [DOI: 10.1039/c3cc46607h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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21
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Preus S, Jønck S, Pittelkow M, Dierckx A, Karpkird T, Albinsson B, Wilhelmsson LM. The photoinduced transformation of fluorescent DNA base analogue tC triggers DNA melting. Photochem Photobiol Sci 2013; 12:1416-22. [PMID: 23689311 DOI: 10.1039/c3pp50057h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
While fluorescent analogues of the canonical nucleobases have proven to be highly valuable in a large number of applications, up until today, fluorescent DNA base analogues remain virtually inapplicable for single-molecule fluorescence experiments which require extremely bright and photostable dyes. Insight into the photodegradation processes of these fluorophores is thus a key step in the continuous development towards dyes with improved performances. Here, we show that the commercially available fluorescent nucleobase analogue tC under intense long-term illumination and in the presence of O2 is degraded to form a single photoreaction product which we suggest to be the sulfoxide form of tC. The photoproduct is characterized by a blue-shifted absorption and a less intense fluorescence compared to that of tC. Interestingly, when tC is positioned inside double-stranded DNA this photodriven conversion of tC to its photoproduct greatly reduces the duplex stability of the overall double helix in which the probe is positioned. Since tC can be excited selectively at 400 nm, well outside the absorption band of the natural DNA bases, this observation points towards the application of tC as a general light-triggered switch of DNA duplex stability.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Copenhagen, DK-2100, Denmark
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22
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Ahmed I, Fruk L. The power of light: photosensitive tools for chemical biology. ACTA ACUST UNITED AC 2013; 9:565-70. [DOI: 10.1039/c2mb25407g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Polstein LR, Gersbach CA. Light-inducible spatiotemporal control of gene activation by customizable zinc finger transcription factors. J Am Chem Soc 2012; 134:16480-3. [PMID: 22963237 PMCID: PMC3468123 DOI: 10.1021/ja3065667] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Advanced gene regulatory systems are necessary for scientific
research,
synthetic biology, and gene-based medicine. An ideal system would
allow facile spatiotemporal manipulation of gene expression within
a cell population that is tunable, reversible, repeatable, and can
be targeted to diverse DNA sequences. To meet these criteria, a gene
regulation system was engineered that combines light-sensitive proteins
and programmable zinc finger transcription factors. This system, light-inducible
transcription using engineered zinc finger proteins (LITEZ), uses
two light-inducible dimerizing proteins from Arabidopsis thaliana, GIGANTEA and the LOV domain of FKF1, to control synthetic zinc
finger transcription factor activity in human cells. Activation of
gene expression in human cells engineered with LITEZ was reversible
and repeatable by modulating the duration of illumination. The level
of gene expression could also be controlled by modulating light intensity.
Finally, gene expression could be activated in a spatially defined
pattern by illuminating the human cell culture through a photomask
of arbitrary geometry. LITEZ enables new approaches for precisely
regulating gene expression in biotechnology and medicine, as well
as studying gene function, cell–cell interactions, and tissue
morphogenesis.
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Affiliation(s)
- Lauren R Polstein
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
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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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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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Lehner R, Hunziker P. Why not just switch on the light?: light and its versatile applications in the field of nanomedicine. EUROPEAN JOURNAL OF NANOMEDICINE 2012. [DOI: 10.1515/ejnm-2012-0012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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