1
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Dohno C, Kimura M, Fujiwara Y, Nakatani K. Photoswitchable molecular glue for RNA: reversible photocontrol of structure and function of the ribozyme. Nucleic Acids Res 2023; 51:9533-9541. [PMID: 37615580 PMCID: PMC10570050 DOI: 10.1093/nar/gkad690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023] Open
Abstract
Single-stranded RNA folds into a variety of secondary and higher-order structures. Distributions and dynamics of multiple RNA conformations are responsible for the biological function of RNA. We here developed a photoswitchable molecular glue for RNA, which could reversibly control the association of two unpaired RNA regions in response to light stimuli. The photoswitchable molecular glue, NCTA, is an RNA-binding ligand possessing a photoisomerizable azobenzene moiety. Z-NCTA is an active ligand for the target RNA containing 5'-WGG-3'/5'-WGG-3' (W = U or A) site and stabilizes its hybridized state, while its isomer E-NCTA is not. Photoreversible isomerization of NCTA enabled control of the secondary and tertiary structure of the target RNA. The RNA-cleaving activity of hammerhead ribozyme, where appropriate RNA folding is necessary, could be reversibly regulated by photoirradiation in cells treated with NCTA, demonstrating precise photocontrol of RNA structure and function by the photoswitchable molecular glue.
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Affiliation(s)
- Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Maki Kimura
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yusuke Fujiwara
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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2
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Volarić J, Szymanski W, Simeth NA, Feringa BL. Molecular photoswitches in aqueous environments. Chem Soc Rev 2021; 50:12377-12449. [PMID: 34590636 PMCID: PMC8591629 DOI: 10.1039/d0cs00547a] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 12/17/2022]
Abstract
Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.
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Affiliation(s)
- Jana Volarić
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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3
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Berdnikova DV. Photoswitches for controllable RNA binding: a future approach in the RNA-targeting therapy. Chem Commun (Camb) 2021; 57:10819-10826. [PMID: 34585681 DOI: 10.1039/d1cc04241f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA is an emerging drug target that opens new perspectives in the treatment of viral and bacterial infections, cancer and a range of so far incurable genetic diseases. Among the various strategies towards the design and development of selective and efficient ligands for targeting and detection of therapeutically relevant RNA, photoswitchable RNA binders represent a very promising approach due to the possibility to control the ligand-RNA and protein-RNA interactions by light with high spatiotemporal resolution. However, the field of photoswitchable RNA binders still remains underexplored due to challenging design of lead structures that should combine high RNA binding selectivity with efficient photochemical performance. The aim of this highlight article is to describe the development of photoswitchable noncovalent RNA binders and to outline the current situation and perspectives of this emerging interdisciplinary field.
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Affiliation(s)
- Daria V Berdnikova
- Universität Siegen, Organische Chemie II, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany.
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4
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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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5
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Yu Q, Ren K, You M. Genetically encoded RNA nanodevices for cellular imaging and regulation. NANOSCALE 2021; 13:7988-8003. [PMID: 33885099 PMCID: PMC8122502 DOI: 10.1039/d0nr08301a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nucleic acid-based nanodevices have been widely used in the fields of biosensing and nanomedicine. Traditionally, the majority of these nanodevices were first constructed in vitro using synthetic DNA or RNA oligonucleotides and then delivered into cells. Nowadays, the emergence of genetically encoded RNA nanodevices has provided a promising alternative approach for intracellular analysis and regulation. These genetically encoded RNA-based nanodevices can be directly transcribed and continuously produced inside living cells. A variety of highly precise and programmable nanodevices have been constructed in this way during the last decade. In this review, we will summarize the recent advances in the design and function of these artificial genetically encoded RNA nanodevices. In particular, we will focus on their applications in regulating cellular gene expression, imaging, logic operation, structural biology, and optogenetics. We believe these versatile RNA-based nanodevices will be broadly used in the near future to probe and program cells and other biological systems.
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Affiliation(s)
- Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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6
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Ren K, Keshri P, Wu R, Sun Z, Yu Q, Tian Q, Zhao B, Bagheri Y, Xie Y, You M. A Genetically Encoded RNA Photosensitizer for Targeted Cell Regulation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kewei Ren
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Puspam Keshri
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Rigumula Wu
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Zhining Sun
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Qikun Yu
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Qian Tian
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Bin Zhao
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Yousef Bagheri
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Yiwen Xie
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
| | - Mingxu You
- Department of Chemistry University of Massachusetts Amherst MA 01003 USA
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7
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Ren K, Keshri P, Wu R, Sun Z, Yu Q, Tian Q, Zhao B, Bagheri Y, Xie Y, You M. A Genetically Encoded RNA Photosensitizer for Targeted Cell Regulation. Angew Chem Int Ed Engl 2020; 59:21986-21990. [PMID: 32797667 PMCID: PMC7747015 DOI: 10.1002/anie.202010106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/13/2020] [Indexed: 12/12/2022]
Abstract
Genetically encoded RNA devices have emerged for various cellular applications in imaging and biosensing, but their functions as precise regulators in living systems are still limited. Inspired by protein photosensitizers, we propose here a genetically encoded RNA aptamer based photosensitizer (GRAP). Upon illumination, the RNA photosensitizer can controllably generate reactive oxygen species for targeted cell regulation. The GRAP system can be selectively activated by endogenous stimuli and light of different wavelengths. Compared with their protein analogues, GRAP is highly programmable and exhibits reduced off-target effects. These results indicate that GRAP enables efficient noninvasive target cell ablation with high temporal and spatial precision. This new RNA regulator system will be widely used for optogenetics, targeted cell ablation, subcellular manipulation, and imaging.
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Affiliation(s)
- Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Qian Tian
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Bin Zhao
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Yousef Bagheri
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Yiwen Xie
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
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8
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Chemo- and biosensing applications of spiropyran and its derivatives - A review. Anal Chim Acta 2020; 1110:199-223. [DOI: 10.1016/j.aca.2020.01.057] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/24/2020] [Accepted: 01/24/2020] [Indexed: 12/20/2022]
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9
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Rotstan KA, Abdelsayed MM, Passalacqua LFM, Chizzolini F, Sudarshan K, Chamberlin AR, Míšek J, Luptak A. Regulation of mRNA translation by a photoriboswitch. eLife 2020; 9:e51737. [PMID: 32053109 PMCID: PMC7051177 DOI: 10.7554/elife.51737] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Optogenetic tools have revolutionized the study of receptor-mediated processes, but such tools are lacking for RNA-controlled systems. In particular, light-activated regulatory RNAs are needed for spatiotemporal control of gene expression. To fill this gap, we used in vitro selection to isolate a novel riboswitch that selectively binds the trans isoform of a stiff-stilbene (amino-tSS)-a rapidly and reversibly photoisomerizing small molecule. Structural probing revealed that the RNA binds amino-tSS about 100-times stronger than the cis photoisoform (amino-cSS). In vitro and in vivo functional analysis showed that the riboswitch, termed Werewolf-1 (Were-1), inhibits translation of a downstream open reading frame when bound to amino-tSS. Photoisomerization of the ligand with a sub-millisecond pulse of light induced the protein expression. In contrast, amino-cSS supported protein expression, which was inhibited upon photoisomerization to amino-tSS. Reversible photoregulation of gene expression using a genetically encoded RNA will likely facilitate high-resolution spatiotemporal analysis of complex RNA processes.
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Affiliation(s)
- Kelly A Rotstan
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
| | - Michael M Abdelsayed
- Department of Molecular Biology and Biochemistry, University of CaliforniaIrvineUnited States
| | - Luiz FM Passalacqua
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
| | - Fabio Chizzolini
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
| | | | - A Richard Chamberlin
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
- Department of Chemistry, University of CaliforniaIrvineUnited States
| | - Jiří Míšek
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
- Department of Organic Chemistry, Charles UniversityPragueCzech Republic
| | - Andrej Luptak
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
- Department of Molecular Biology and Biochemistry, University of CaliforniaIrvineUnited States
- Department of Chemistry, University of CaliforniaIrvineUnited States
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10
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Lotz TS, Halbritter T, Kaiser C, Rudolph MM, Kraus L, Groher F, Steinwand S, Wachtveitl J, Heckel A, Suess B. A light-responsive RNA aptamer for an azobenzene derivative. Nucleic Acids Res 2019; 47:2029-2040. [PMID: 30517682 PMCID: PMC6393235 DOI: 10.1093/nar/gky1225] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/20/2022] Open
Abstract
Regulation of complex biological networks has proven to be a key bottleneck in synthetic biology. Interactions between the structurally flexible RNA and various other molecules in the form of riboswitches have shown a high-regulation specificity and efficiency and synthetic riboswitches have filled the toolbox of devices in many synthetic biology applications. Here we report the development of a novel, small molecule binding RNA aptamer, whose binding is dependent on light-induced change of conformation of its small molecule ligand. As ligand we chose an azobenzene because of its reliable photoswitchability and modified it with chloramphenicol for a better interaction with RNA. The synthesis of the ligand 'azoCm' was followed by extensive biophysical analysis regarding its stability and photoswitchability. RNA aptamers were identified after several cycles of in vitro selection and then studied regarding their binding specificity and affinity toward the ligand. We show the successful development of an RNA aptamer that selectively binds to only the trans photoisomer of azoCm with a KD of 545 nM. As the aptamer cannot bind to the irradiated ligand (λ = 365 nm), a light-selective RNA binding system is provided. Further studies may now result in the engineering of a reliable, light-responsible riboswitch.
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Affiliation(s)
- Thea S Lotz
- Technische Universität Darmstadt, Department of Biology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Thomas Halbritter
- Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 9, 60438 Frankfurt (M), Germany
| | - Christoph Kaiser
- Goethe-University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Strasse 7, 60438 Frankfurt (M), Germany
| | - Martin M Rudolph
- Technische Universität Darmstadt, Department of Biology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Leon Kraus
- Technische Universität Darmstadt, Department of Biology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian Groher
- Technische Universität Darmstadt, Department of Biology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sabrina Steinwand
- Goethe-University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Strasse 7, 60438 Frankfurt (M), Germany
| | - Josef Wachtveitl
- Goethe-University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Strasse 7, 60438 Frankfurt (M), Germany
| | - Alexander Heckel
- Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 9, 60438 Frankfurt (M), Germany
| | - Beatrix Suess
- Technische Universität Darmstadt, Department of Biology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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11
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Berdnikova DV. Visible-range hemi-indigo photoswitch: ON-OFF fluorescent binder for HIV-1 RNA. Chem Commun (Camb) 2019; 55:8402-8405. [PMID: 31257385 DOI: 10.1039/c9cc04270a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A proof-of-principle for the application of hemi-indigo derivatives as RNA binders with photocontrollable fluorescence is presented. The photoswitch binds to the human immunodeficiency virus type 1 (HIV-1) RNA with a significant light-up effect. The fluorescence of the RNA-bound ligand can be reversibly switched ON and OFF by light without destroying the ligand-RNA associates.
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Affiliation(s)
- Daria V Berdnikova
- Universität Siegen, Organische Chemie II, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany.
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12
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Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection. BMC Biomed Eng 2019; 1:6. [PMID: 32903305 PMCID: PMC7421392 DOI: 10.1186/s42490-019-0008-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
Background Long double-stranded RNAs (dsRNAs) are duplex RNAs that can induce immune response when present in mammalian cells. These RNAs are historically associated with viral replication, but recent evidence suggests that human cells naturally encode endogenous dsRNAs that can regulate antiviral machineries in cellular contexts beyond immune response. Results In this study, we use photochromic organic compound spiropyran to profile and quantitate dsRNA expression. We show that the open form of spiropyran, merocyanine, can intercalate between RNA base pairs, which leads to protonation and alteration in the spectral property of the compound. By quantifying the spectral change, we can detect and quantify dsRNA expression level, both synthetic and cellular. We further demonstrate that spiropyrans can be used as a molecular diagnostic tool to profile endogenously expressed dsRNAs. Particularly, we show that spiropyrans can robustly detect elevated dsRNA levels when colorectal cancer cells are treated with 5-aza-2'-deoxycytidine, an FDA-approved DNA-demethylating agent used for chemotherapy, thus demonstrating the use of spiropyran for predicting responsiveness to the drug treatment. Conclusion As dsRNAs are signature of virus and accumulation of dsRNAs is implicated in various degenerative disease, our work establishes potential application of spiropyrans as a simple spectral tool to diagnose human disease based on dsRNA expression.
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13
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Fleming CL, Li S, Grøtli M, Andréasson J. Shining New Light on the Spiropyran Photoswitch: A Photocage Decides between cis–trans or Spiro-Merocyanine Isomerization. J Am Chem Soc 2018; 140:14069-14072. [DOI: 10.1021/jacs.8b09523] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Cassandra L. Fleming
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Göteborg, Sweden
| | - Shiming Li
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Göteborg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296 Göteborg, Sweden
| | - Joakim Andréasson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Göteborg, Sweden
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14
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Cao C, Long YT. Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis. Acc Chem Res 2018; 51:331-341. [PMID: 29364650 DOI: 10.1021/acs.accounts.7b00143] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis, we develop an integrated current measurement system and an accurate data processing method for nanopore sensing. The unique geometric structure of a biological nanopore offers a distinct advantage as a nanosensor for single-molecule sensing. The construction of the pore entrance is responsible for capturing the target molecule, while the lumen region determines the translocation process of the single molecule. Since the capture of the target molecule is predominantly diffusion-limited, it is expected that the capture ability of the nanopore toward the target analyte could be effectively enhanced by site-directed mutations of key amino acids with desirable groups. Additionally, changing the side chains inside the wall of the biological nanopore could optimize the geometry of the pore and realize an optimal interaction between the single-molecule interface and the analyte. These improvements would allow for high spatial and current resolution of nanopore sensors, which would ensure the possibility of dynamic study of single biomolecules, including their metastable conformations, charge distributions, and interactions. In the future, data analysis with powerful algorithms will make it possible to automatically and statistically extract detailed information while an analyte translocates through the pore. We conclude that these improvements could have tremendous potential applications for nanopore sensing in the near future.
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Affiliation(s)
- Chan Cao
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
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15
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Halbritter T, Kaiser C, Wachtveitl J, Heckel A. Pyridine–Spiropyran Derivative as a Persistent, Reversible Photoacid in Water. J Org Chem 2017; 82:8040-8047. [DOI: 10.1021/acs.joc.7b01268] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Halbritter
- Institute for Organic Chemistry and Chemical Biology and ‡Institute for Physical
and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse
7, 60438 Frankfurt
(M), Germany
| | - Christoph Kaiser
- Institute for Organic Chemistry and Chemical Biology and ‡Institute for Physical
and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse
7, 60438 Frankfurt
(M), Germany
| | - Josef Wachtveitl
- Institute for Organic Chemistry and Chemical Biology and ‡Institute for Physical
and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse
7, 60438 Frankfurt
(M), Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology and ‡Institute for Physical
and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse
7, 60438 Frankfurt
(M), Germany
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16
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Kaiser C, Halbritter T, Heckel A, Wachtveitl J. Thermal, Photochromic and Dynamic Properties of Water-Soluble Spiropyrans. ChemistrySelect 2017. [DOI: 10.1002/slct.201700868] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christoph Kaiser
- Institute of Physical and Theoretical Chemistry; Goethe-University Frankfurt; Max-von-Laure-Str. 7 60438 Frankfurt Germany
| | - Thomas Halbritter
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laure-Str. 7 60438 Frankfurt Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology; Goethe-University Frankfurt; Max-von-Laure-Str. 7 60438 Frankfurt Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry; Goethe-University Frankfurt; Max-von-Laure-Str. 7 60438 Frankfurt Germany
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17
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Pfeiffer F, Mayer G. Selection and Biosensor Application of Aptamers for Small Molecules. Front Chem 2016; 4:25. [PMID: 27379229 PMCID: PMC4908669 DOI: 10.3389/fchem.2016.00025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
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Affiliation(s)
- Franziska Pfeiffer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| | - Günter Mayer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
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18
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Wang X, Feng M, Xiao L, Tong A, Xiang Y. Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme. ACS Chem Biol 2016; 11:444-51. [PMID: 26669486 DOI: 10.1021/acschembio.5b00867] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photocaged (photoactivatable) biomolecules are powerful tools for noninvasive control of biochemical activities by light irradiation. DNAzymes (deoxyribozymes) are single-stranded oligonucleotides with a broad range of enzymatic activities. In this work, to construct photocaged DNAzymes, we developed a facile and mild postsynthetic method to incorporate an interesting photolabile modification (thioether-enol phosphate, phenol substituted, TEEP-OH) into readily available phosphorothioate DNA. Upon light irradiation, TEEP-OH transformed into a native DNA phosphodiester, and accordingly the DNAzymes with RNA-cleaving activities were turned "on" from its inactive and caged form. Activation of the TEEP-OH-caged DNAzyme by light was also successful inside live cells.
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Affiliation(s)
- Xiaoyan Wang
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Mengli Feng
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Lu Xiao
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry,
Beijing Key Laboratory for Microanalytical Methods and Instrumentation,
Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology
(Ministry of Education), Tsinghua University, Beijing 100084, China
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19
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Lokshin V, Paramonov SV, Fedorova OA. New photochromes equipped with positively charged ammonium fragments. MENDELEEV COMMUNICATIONS 2015. [DOI: 10.1016/j.mencom.2015.09.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Kamiya Y, Takagi T, Ooi H, Ito H, Liang X, Asanuma H. Synthetic gene involving azobenzene-tethered T7 promoter for the photocontrol of gene expression by visible light. ACS Synth Biol 2015; 4:365-70. [PMID: 25144622 DOI: 10.1021/sb5001092] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the present study, we demonstrate photoregulation of gene expression in a cell-free translation system from a T7 promoter containing two azobenzene derivatives at specific positions. As photoswitches, we prepared azobenzene-4'-carboxlyic acid (Azo) and 2,6-dimethylazobenzene-4'-carboxylic acid (DM-Azo), which were isomerized from trans to cis upon irradiation with UV light (λ < 370 nm), and 4-methylthioazobenzene-4'-carboxylic acid (S-Azo) and 2,6-dimethyl-4-(methylthio)azobenzene-4'-carobxylic acid (S-DM-Azo), which were cis-isomerized by irradiation with 400 nm visible light. Expression of green fluorescent protein from a promoter modified with S-Azo or S-DM-Azo could be induced by harmless visible light whereas that from a promoter modified with Azo or DM-Azo was induced only by UV light (340-360 nm). Thus, efficient photoregulation of green fluorescent protein production was achieved in a cell-free translation system with visible light without photodamage.
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Affiliation(s)
| | | | | | | | - Xingguo Liang
- School
of Food Science and Engineering, Ocean University of China, Yushan-lu 5, Shinanqu, Qingdao 266003, China
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21
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Özçoban C, Halbritter T, Steinwand S, Herzig LM, Kohl-Landgraf J, Askari N, Groher F, Fürtig B, Richter C, Schwalbe H, Suess B, Wachtveitl J, Heckel A. Water-soluble Py-BIPS spiropyrans as photoswitches for biological applications. Org Lett 2015; 17:1517-20. [PMID: 25760939 DOI: 10.1021/acs.orglett.5b00397] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The ultrafast photochemistry of a new spiropyran photoswitch (Py-BIPS) has been investigated, revealing many advantages in the application in water over the previously studied spiropyrans. Functionalized Py-BIPS derivatives are presented for the study of pH dependence, stability, toxicity, and the thermal and photochemical behavior on longer time scales in aqueous media using several spectroscopic methods. These investigations pave the way for the practical use of Py-BIPS derivatives as photoswitchable ligands of biomolecules.
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Affiliation(s)
- Cem Özçoban
- †Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 9, 60438 Frankfurt (M), Germany
| | - Thomas Halbritter
- †Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 9, 60438 Frankfurt (M), Germany
| | - Sabrina Steinwand
- ‡Goethe-University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt (M), Germany
| | - Lisa-Marie Herzig
- ‡Goethe-University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt (M), Germany
| | - Jörg Kohl-Landgraf
- ‡Goethe-University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt (M), Germany
| | - Noushin Askari
- †Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 9, 60438 Frankfurt (M), Germany
| | - Florian Groher
- §Technical University of Darmstadt, Department of Biology, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Boris Fürtig
- †Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 9, 60438 Frankfurt (M), Germany
| | - Christian Richter
- †Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 9, 60438 Frankfurt (M), Germany
| | - Harald Schwalbe
- †Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 9, 60438 Frankfurt (M), Germany
| | - Beatrix Suess
- §Technical University of Darmstadt, Department of Biology, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Josef Wachtveitl
- ‡Goethe-University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt (M), Germany
| | - Alexander Heckel
- †Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 9, 60438 Frankfurt (M), Germany
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22
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You M, Jaffrey SR. Designing optogenetically controlled RNA for regulating biological systems. Ann N Y Acad Sci 2015; 1352:13-9. [PMID: 25758022 DOI: 10.1111/nyas.12660] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Light-responsive proteins have been used in the field of optogenetics to control cellular functions. However, surprisingly, analogous approaches to regulate and alter the functions of RNA molecules by light remain underdeveloped. RNA aptamers and RNA devices can perform diverse intracellular functions and are important tools in synthetic biology. This report explores the challenges of and potential strategies for engineering light regulation into functional RNAs in cells. We discuss approaches for using existing light-regulated proteins and small molecules to control RNA function in living cells. In addition, applications of light-regulated RNAs for synthetic biology and for studying functions of endogenously expressed RNAs are discussed.
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Affiliation(s)
- Mingxu You
- Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, New York, New York
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23
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Pranzetti A, Davis M, Yeung CL, Preece JA, Koelsch P, Mendes PM. Direct Observation of Reversible Biomolecule Switching Controlled By Electrical Stimulus. ADVANCED MATERIALS INTERFACES 2014; 1:1-4. [PMID: 25810954 PMCID: PMC4368128 DOI: 10.1002/admi.201400026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/14/2014] [Indexed: 06/04/2023]
Affiliation(s)
- Alice Pranzetti
- School of Chemical Engineering, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Matthew Davis
- National ESCA and Surface Analysis Center for Biomedical Problems, Department of Bioengineering, University of Washington P.O. Box 351653, Seattle, Washington, 98195-1653, USA
| | - Chun L Yeung
- School of Chemical Engineering, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Jon A Preece
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Patrick Koelsch
- National ESCA and Surface Analysis Center for Biomedical Problems, Department of Bioengineering, University of Washington P.O. Box 351653, Seattle, Washington, 98195-1653, USA
| | - Paula M Mendes
- School of Chemical Engineering, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
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24
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Ying YL, Cao C, Long YT. Single molecule analysis by biological nanopore sensors. Analyst 2014; 139:3826-35. [PMID: 24991734 DOI: 10.1039/c4an00706a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nanopore sensors provide a highly innovative technique for a rapid and label-free single molecule analysis, which holds a great potential in routing applications. Biological nanopores have been used as ultra-sensitive sensors over a wide range of single molecule analysis including DNA sequencing, disease diagnosis, drug screening, environment monitoring and the construction of molecule machines. This mini review will focus on the current strategies for the identification and characterization of an individual analyte, especially based on our recent achievements in biological nanopore biosensors.
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Affiliation(s)
- Yi-Lun Ying
- Key Laboratory for Advanced Materials & Department of Chemistry, East China University of Science and Technology, P. R. China.
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25
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Yeung CL, Wang X, Lashkor M, Cantini E, Rawson FJ, Iqbal P, Preece JA, Ma J, Mendes PM. Modulation of Biointeractions by Electrically Switchable Oligopeptide Surfaces: Structural Requirements and Mechanism. ADVANCED MATERIALS INTERFACES 2014; 1:1300085. [PMID: 25793154 PMCID: PMC4358153 DOI: 10.1002/admi.201300085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/01/2013] [Indexed: 06/04/2023]
Abstract
Understanding the dynamic behavior of switchable surfaces is of paramount importance for the development of controllable and tailor-made surface materials. Herein, electrically switchable mixed self-assembled monolayers based on oligopeptides have been investigated in order to elucidate their conformational mechanism and structural requirements for the regulation of biomolecular interactions between proteins and ligands appended to the end of surface tethered oligopeptides. The interaction of the neutravidin protein to a surface appended biotin ligand was chosen as a model system. All the considerable experimental data, taken together with detailed computational work, support a switching mechanism in which biomolecular interactions are controlled by conformational changes between fully extended ("ON" state) and collapsed ("OFF" state) oligopeptide conformer structures. In the fully extended conformation, the biotin appended to the oligopeptide is largely free from steric factors allowing it to efficiently bind to the neutravidin from solution. While under a collapsed conformation, the ligand presented at the surface is partially embedded in the second component of the mixed SAM, and thus sterically shielded and inaccessible for neutravidin binding. Steric hindrances aroused from the neighboring surface-confined oligopeptide chains exert a great influence over the conformational behaviour of the oligopeptides, and as a consequence, over the switching efficiency. Our results also highlight the role of oligopeptide length in controlling binding switching efficiency. This study lays the foundation for designing and constructing dynamic surface materials with novel biological functions and capabilities, enabling their utilization in a wide variety of biological and medical applications.
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Affiliation(s)
- Chun L Yeung
- School of Chemical Engineering, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK E-mail:
| | - Xingyong Wang
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Minhaj Lashkor
- School of Chemical Engineering, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK E-mail:
| | - Eleonora Cantini
- School of Chemical Engineering, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK E-mail:
| | - Frankie J Rawson
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham University Park, Nottingham, NG7 2RD, UK
| | - Parvez Iqbal
- School of Chemical Engineering, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK E-mail: ; School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Jon A Preece
- School of Chemistry, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Nanjing University Nanjing, 210093, P. R. China E-mail:
| | - Paula M Mendes
- School of Chemical Engineering, University of Birmingham Edgbaston, Birmingham, B15 2TT, UK E-mail:
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26
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Zhang X, Zhang J, Ying YL, Tian H, Long YT. Single molecule analysis of light-regulated RNA:spiropyran interactions. Chem Sci 2014. [DOI: 10.1039/c4sc00134f] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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27
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Hammarson M, Nilsson J, Li S, Beke-Somfai T, Andréasson J. Characterization of the thermal and photoinduced reactions of photochromic spiropyrans in aqueous solution. J Phys Chem B 2013; 117:13561-71. [PMID: 24143951 PMCID: PMC3814652 DOI: 10.1021/jp408781p] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 09/30/2013] [Indexed: 12/25/2022]
Abstract
Six water-soluble spiropyran derivatives have been characterized with respect to the thermal and photoinduced reactions over a broad pH-interval. A comprehensive kinetic model was formulated including the spiro- and the merocyanine isomers, the respective protonated forms, and the hydrolysis products. The experimental studies on the hydrolysis reaction mechanism were supplemented by calculations using quantum mechanical (QM) models employing density functional theory. The results show that (1) the substitution pattern dramatically influences the pKa-values of the protonated forms as well as the rates of the thermal isomerization reactions, (2) water is the nucleophile in the hydrolysis reaction around neutral pH, (3) the phenolate oxygen of the merocyanine form plays a key role in the hydrolysis reaction. Hence, the nonprotonated merocyanine isomer is susceptible to hydrolysis, whereas the corresponding protonated form is stable toward hydrolytic degradation.
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Affiliation(s)
- Martin Hammarson
- Department of Chemical and
Biological Engineering, Physical Chemistry, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Jesper
R. Nilsson
- Department of Chemical and
Biological Engineering, Physical Chemistry, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Shiming Li
- Department of Chemical and
Biological Engineering, Physical Chemistry, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Tamás Beke-Somfai
- Department of Chemical and
Biological Engineering, Physical Chemistry, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Joakim Andréasson
- Department of Chemical and
Biological Engineering, Physical Chemistry, Chalmers University of Technology, 412 96 Göteborg, Sweden
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28
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Brieke C, Heckel A. Spiropyran Photoswitches in the Context of DNA: Synthesis and Photochromic Properties. Chemistry 2013; 19:15726-34. [DOI: 10.1002/chem.201302640] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Indexed: 01/24/2023]
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29
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Kohl-Landgraf J, Braun M, Özçoban C, Goncalves D, Heckel A, Wachtveitl J. Dynamics of a photochromic spiropyran under aqueous conditions. EPJ WEB OF CONFERENCES 2013. [DOI: 10.1051/epjconf/20134105009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Miskolczy Z, Biczók L. Photochromism of a Merocyanine Dye Bound to Sulfonatocalixarenes: Effect of pH and the Size of Macrocycle on the Kinetics. J Phys Chem B 2013; 117:648-53. [DOI: 10.1021/jp310167j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Zsombor Miskolczy
- Institute
of Molecular Pharmacology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P.O. Box 17, 1525 Budapest, Hungary
| | - László Biczók
- Institute
of Molecular Pharmacology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P.O. Box 17, 1525 Budapest, Hungary
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31
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Wang P, Querard J, Maurin S, Nath SS, Le Saux T, Gautier A, Jullien L. Photochemical properties of Spinach and its use in selective imaging. Chem Sci 2013. [DOI: 10.1039/c3sc50729g] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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32
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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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33
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Nilsson JR, Parente Carvalho C, Li S, Da Silva JP, Andréasson J, Pischel U. Switching Properties of a Spiropyran-Cucurbit[7]uril Supramolecular Assembly: Usefulness of the Anchor Approach. Chemphyschem 2012; 13:3691-9. [DOI: 10.1002/cphc.201200468] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Indexed: 12/31/2022]
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34
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Kohl-Landgraf J, Braun M, Özçoban C, Gonçalves DPN, Heckel A, Wachtveitl J. Ultrafast Dynamics of a Spiropyran in Water. J Am Chem Soc 2012; 134:14070-7. [DOI: 10.1021/ja304395k] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jörg Kohl-Landgraf
- Institute for Physical und Theoretical
Chemistry, Goethe University Frankfurt,
Max-von-Laue-Straße 7, Frankfurt/Main, Germany
| | - Markus Braun
- Institute for Physical und Theoretical
Chemistry, Goethe University Frankfurt,
Max-von-Laue-Straße 7, Frankfurt/Main, Germany
| | - Cem Özçoban
- Institute for Organic Chemistry
and Chemical Biology, Buchmann Institute for Molecular Life Sciences,
Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt/Main,
Germany
| | - Diana P. N. Gonçalves
- Institute for Organic Chemistry
and Chemical Biology, Buchmann Institute for Molecular Life Sciences,
Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt/Main,
Germany
| | - Alexander Heckel
- Institute for Organic Chemistry
and Chemical Biology, Buchmann Institute for Molecular Life Sciences,
Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Straße 9, Frankfurt/Main,
Germany
| | - Josef Wachtveitl
- Institute for Physical und Theoretical
Chemistry, Goethe University Frankfurt,
Max-von-Laue-Straße 7, Frankfurt/Main, Germany
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35
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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: 725] [Impact Index Per Article: 60.4] [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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36
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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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37
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Barrois S, Wagenknecht HA. Diarylethene-modified nucleotides for switching optical properties in DNA. Beilstein J Org Chem 2012; 8:905-14. [PMID: 23015841 PMCID: PMC3388881 DOI: 10.3762/bjoc.8.103] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 05/09/2012] [Indexed: 01/03/2023] Open
Abstract
Diarylethenes were attached to the 5-position of 2’-deoxyuridine in order to yield three different photochromic nucleosides. All nucleosides were characterized with respect to their absorption and photochromic properties. Based on these results, the most promising photochromic DNA base modification was incorporated into representative oligonucleotides by using automated phosphoramidite chemistry. The switching of optical properties in DNA can be achieved selectively at 310 nm (forward) and 450 nm (backward); both wavelengths are outside the normal nucleic acid absorption range. Moreover, this nucleoside was proven to be photochemically stable and allows switching back and forth several times. These results open the way for the use of diarylethenes as photochromic compounds in DNA-based architectures.
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Affiliation(s)
- Sebastian Barrois
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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38
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Genetically encoded RNA photoswitches as tools for the control of gene expression. FEBS Lett 2012; 586:2106-11. [PMID: 22659185 DOI: 10.1016/j.febslet.2012.05.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 05/22/2012] [Accepted: 05/22/2012] [Indexed: 11/22/2022]
Abstract
An important goal in chemical and synthetic biology is controlling the expression of defined sets of genes by external stimuli, and one of the most attractive stimuli is light. Current approaches to the photocontrol of biological processes utilize photoresponsive proteins. In this article, I will illustrate the prospects of synthetic systems in which the receptor is a photoresponsive nucleic acid, and will review the different tools already in place to develop photoresponsive systems based on RNA. A particular focus is on genetically encoded photoswitches that can be expressed in prokaryotic or eukaryotic cells, and respond to photoisomerizable, cell-permeable small molecules.
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Ceo LM, Koh JT. Photocaged DNA provides new levels of transcription control. Chembiochem 2012; 13:511-3. [PMID: 22271631 DOI: 10.1002/cbic.201100683] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Indexed: 12/24/2022]
Abstract
Spot lit: photocaged nucleic acids have been used to regulate gene expression through the action of light. Whereas most methods target mRNAs, DNA decoys have recently been used to target DNA transcription by targeting specific DNA-transcription-factor interactions. This has allowed researchers to "turn-off" transcription through the action of light on caged nucleic acids for the first time.
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Affiliation(s)
- Luke M Ceo
- Department of Chemistry and Biochemistry, University of Delaware, Brown Laboratories, USA
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Nilsson JR, Li S, Önfelt B, Andréasson J. Light-induced cytotoxicity of a photochromic spiropyran. Chem Commun (Camb) 2011; 47:11020-2. [PMID: 21909522 DOI: 10.1039/c1cc13561a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work we present a novel water soluble spiropyran photoswitch that can be photonically activated inside live cells from a form that has no significant effect on the cellular survival to a form that induces a dramatic toxic response.
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Affiliation(s)
- Jesper R Nilsson
- Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, Göteborg, 412 96, Sweden
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41
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Paramonov SV, Lokshin V, Ihmels H, Fedorova OA. Influence of DNA-binding on the photochromic equilibrium of a chromene derivative. Photochem Photobiol Sci 2011; 10:1279-82. [DOI: 10.1039/c1pp05094j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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42
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In vitro selection of a photoresponsive RNA aptamer to hemin. Bioorg Med Chem Lett 2010; 20:2964-7. [PMID: 20347300 DOI: 10.1016/j.bmcl.2010.02.109] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 02/24/2010] [Accepted: 02/27/2010] [Indexed: 01/06/2023]
Abstract
A photoresponsive RNA aptamer to hemin was selected in vitro from a random sequence library of RNAs with azobenzene residues. The aptamer bound to hemin under visible light irradiation and was released by ultraviolet light.
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Rich RL, Myszka DG. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J Mol Recognit 2010; 23:1-64. [PMID: 20017116 DOI: 10.1002/jmr.1004] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Richards JL, Seward GK, Wang YH, Dmochowski IJ. Turning the 10-23 DNAzyme on and off with light. Chembiochem 2010; 11:320-4. [PMID: 20077457 PMCID: PMC2908382 DOI: 10.1002/cbic.200900702] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Indexed: 11/10/2022]
Affiliation(s)
- Julia L. Richards
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
| | - Garry K. Seward
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
| | - Yu-Hsiu Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323 (USA), Fax: (+1) 215-573-6329
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45
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Priestman MA, Lawrence DS. Light-mediated remote control of signaling pathways. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:547-58. [PMID: 19765679 DOI: 10.1016/j.bbapap.2009.09.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Accepted: 09/08/2009] [Indexed: 01/25/2023]
Abstract
Cell signaling networks display an extraordinary range of temporal and spatial plasticity. Our programmatic approach focuses on the construction of intracellular probes, including sensors, inhibitors, and functionally unique proteins that can be temporally and spatially controlled by the investigator even after they have entered the cell. We have designed and evaluated protein kinase sensors that furnish a fluorescent readout upon phosphorylation. In addition, since the sensors are inert (i.e., cannot be phosphorylated) until activated by light, they can be carried through the various stages of any given cell-based behavior without being consumed. Using this strategy, we have shown that PKCbeta is essential for nuclear envelope breakdown and thus the transition from prophase to metaphase in actively dividing cells. Photoactivatable proteins furnish the means to initiate cellular signaling pathways with a high degree of spatial and temporal control. We have used this approach to demonstrate that cofilin serves as a component of the steering apparatus of the cell. Finally, inhibitors are commonly used to assess the participation of specific enzymes in signaling pathways that control cellular behavior. We have constructed a photo-deactivatable inhibitor, an inhibitory species that can be switched off with light. In the absence of light, the target enzyme is inactive due to the presence of the potent inhibitory molecule. Upon photolysis, the inhibitory molecule is destroyed and enzymatic activity is released.
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Affiliation(s)
- Melanie A Priestman
- Department of Chemistry, The University of North Carolina at Chapel Hill, Kenan Laboratories, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
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Lee HM, Larson DR, Lawrence DS. Illuminating the chemistry of life: design, synthesis, and applications of "caged" and related photoresponsive compounds. ACS Chem Biol 2009; 4:409-27. [PMID: 19298086 DOI: 10.1021/cb900036s] [Citation(s) in RCA: 369] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biological systems are characterized by a level of spatial and temporal organization that often lies beyond the grasp of present day methods. Light-modulated bioreagents, including analogs of low molecular weight compounds, peptides, proteins, and nucleic acids, represent a compelling strategy to probe, perturb, or sample biological phenomena with the requisite control to address many of these organizational complexities. Although this technology has created considerable excitement in the chemical community, its application to biological questions has been relatively limited. We describe the challenges associated with the design, synthesis, and use of light-responsive bioreagents; the scope and limitations associated with the instrumentation required for their application; and recent chemical and biological advances in this field.
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Affiliation(s)
- Hsien-Ming Lee
- Departments of Chemistry, Medicinal Chemistry & Natural Products, and Pharmacology, The University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Daniel R. Larson
- Department of Anatomy and Structural Biology, The Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461
| | - David S. Lawrence
- Departments of Chemistry, Medicinal Chemistry & Natural Products, and Pharmacology, The University of North Carolina, Chapel Hill, North Carolina 27599-3290
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47
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Qiu Z, Yu H, Li J, Wang Y, Zhang Y. Spiropyran-linked dipeptide forms supramolecular hydrogel with dual responses to light and to ligand-receptor interaction. Chem Commun (Camb) 2009:3342-4. [PMID: 19503864 DOI: 10.1039/b822840j] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Integration of photo-sensitive spiropyran with dipeptide d-Ala-d-Ala in one small molecule resulted in a hydrogelator which can form supramolecular hydrogel with responses not only to light but to ligand-receptor interaction.
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Affiliation(s)
- Zhenjun Qiu
- School of Chemistry and Chemical Engineering, Key Lab of Analytical Chemistry for Life Science, Ministry of Education of China, Nanjing University, Nanjing, 210093, P. R. China
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Stafforst T, Hilvert D. Kinetic characterization of spiropyrans in aqueous media. Chem Commun (Camb) 2009:287-8. [DOI: 10.1039/b818050d] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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