1
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Dolai A, Box SM, Bhunia S, Bera S, Das A, Samanta S. Photoisomerization of 2-Arylazoimidazoles under Visible Light: Identifying a Predictive Tool to Anticipate and Tune Likely Photoswitching Performance and Cis Half-Life. J Org Chem 2023. [PMID: 37368413 DOI: 10.1021/acs.joc.3c00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Azopyrazoles are an emerging class of photoswitches, whereas analogous azoimidazole-based switches are unable to draw much attention because of their short cis half-lives, poor cis-trans photoreversion yields, and toxic ultraviolet (UV) light-assisted isomerization. A series of 24 various aryl-substituted N-methyl-2-arylazoimidazoles were synthesized, and their photoswitching performances and cis-trans isomerization kinetics were thoroughly investigated experimentally and theoretically. Para-π-donor-substituted azoimidazoles with highly twisted T-shaped cis conformations showed nearly complete bidirectional photoswitching, whereas di-o-substituted switches exhibited very long cis half-lives (days-years) with nearly ideal T-shaped conformations. This study demonstrates how the electron density in the aryl ring affects cis half-life and cis-trans photoreversion via twisting of the NNAr dihedral angle that can be used as a predictive metric for envisaging and tuning the likely switching performance and half-life of any given 2-arylazoimidazole. By applying this tool, two better-performing azoimidazole photoswitches were engineered. All switches permitted irradiation by violet (400-405 nm) and orange (>585 nm) light for forward and reverse isomerization, respectively, and displayed comparatively high quantum yields and impressive resistance to photobleaching.
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Affiliation(s)
- Anirban Dolai
- Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, West Bengal, India
| | - Sk Majid Box
- Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, West Bengal, India
| | - Supriya Bhunia
- Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, West Bengal, India
| | - Satyajit Bera
- Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, West Bengal, India
| | - Arpan Das
- Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, West Bengal, India
| | - Subhas Samanta
- Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, West Bengal, India
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2
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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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3
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Darrah KE, Deiters A. Translational control of gene function through optically regulated nucleic acids. Chem Soc Rev 2021; 50:13253-13267. [PMID: 34739027 DOI: 10.1039/d1cs00257k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Translation of mRNA into protein is one of the most fundamental processes within biological systems. Gene expression is tightly regulated both in space and time, often involving complex signaling or gene regulatory networks, as most prominently observed in embryo development. Thus, studies of gene function require tools with a matching level of external control. Light is an excellent conditional trigger as it is minimally invasive, can be easily tuned in wavelength and amplitude, and can be applied with excellent spatial and temporal resolution. To this end, modification of established oligonucleotide-based technologies with optical control elements, in the form of photocaging groups and photoswitches, has rendered these tools capable of navigating the dynamic regulatory pathways of mRNA translation in cellular and in vivo models. In this review, we discuss the different optochemical approaches used to generate photoresponsive nucleic acids that activate and deactivate gene expression and function at the translational level.
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Affiliation(s)
- Kristie E Darrah
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA.
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA.
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4
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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5
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Yang L, Trentini D, Kim H, Sul J, Eberwine JH, Dmochowski IJ. Photoactivatable Circular Caged Oligonucleotides for Transcriptome In Vivo Analysis (TIVA). CHEMPHOTOCHEM 2021; 5:940-946. [DOI: 10.1002/cptc.202100098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Linlin Yang
- Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
| | - Dora Trentini
- Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
| | - HyunBum Kim
- Department of Pharmacology University of Pennsylvania 38 John Morgan Building 3620 Hamilton Walk Philadelphia PA 19104-6084 USA
| | - Jai‐Yoon Sul
- Department of Pharmacology University of Pennsylvania 38 John Morgan Building 3620 Hamilton Walk Philadelphia PA 19104-6084 USA
| | - James H. Eberwine
- Department of Pharmacology University of Pennsylvania 38 John Morgan Building 3620 Hamilton Walk Philadelphia PA 19104-6084 USA
| | - Ivan J. Dmochowski
- Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia PA 19104-6323 USA
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6
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Yang L, Dmochowski IJ. Conditionally Activated ("Caged") Oligonucleotides. Molecules 2021; 26:1481. [PMID: 33803234 PMCID: PMC7963183 DOI: 10.3390/molecules26051481] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 01/09/2023] Open
Abstract
Conditionally activated ("caged") oligonucleotides provide useful spatiotemporal control for studying dynamic biological processes, e.g., regulating in vivo gene expression or probing specific oligonucleotide targets. This review summarizes recent advances in caging strategies, which involve different stimuli in the activation step. Oligo cyclization is a particularly attractive caging strategy, which simplifies the probe design and affords oligo stabilization. Our laboratory developed an efficient synthesis for circular caged oligos, and a circular caged antisense DNA oligo was successfully applied in gene regulation. A second technology is Transcriptome In Vivo Analysis (TIVA), where caged oligos enable mRNA isolation from single cells in living tissue. We highlight our development of TIVA probes with improved caging stability. Finally, we illustrate the first protease-activated oligo probe, which was designed for caspase-3. This expands the toolkit for investigating the transcriptome under a specific physiologic condition (e.g., apoptosis), particularly in specimens where light activation is impractical.
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Affiliation(s)
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA;
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7
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Wang S, Zhao J, Wang L, Zhang J, Hu H, Yu P, Wang R. Inducible DNA Polymerase Chain Reaction Triggered by Oxidative Species. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202000377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sheng Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Jizhong Zhao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Li Wang
- Wuhan No.1 Hospital 215 Zhongshan Avenue Wuhan Hubei 430022 P. R. China
| | - Jingwen Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Hongmei Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Ping Yu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
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8
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Zhang D, Jin S, Piao X, Devaraj NK. Multiplexed Photoactivation of mRNA with Single-Cell Resolution. ACS Chem Biol 2020; 15:1773-1779. [PMID: 32484653 DOI: 10.1021/acschembio.0c00205] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We demonstrate sequential optical activation of two types of mRNAs in the same mammalian cell through the sequential photocleavage of small molecule caging groups ("photocages") tethered to the 5'-untranslated region (5'-UTR) of mRNAs. Synthetic photocages were conjugated onto target mRNA using RNA-TAG, an enzymatic site-specific RNA modification technique. Translation of mRNA was severely reduced upon conjugation of the photocages onto the 5'-UTR. However, subsequent photorelease of the cages from the mRNA transcript triggered activation of translation with single-cell spatiotemporal resolution. To achieve sequential photoactivation of two mRNAs in the same cell, we synthesized a pair of photocages that can be selectively cleaved from mRNA upon photoirradiation with different wavelengths of light. Sequential photoactivation of two mRNAs enabled precise optical control of translation of two unique transcripts. We believe that this modular approach to precisely and rapidly control gene expression will serve as a powerful tool in future biological studies that require controlling translation of multiple transcripts with high spatiotemporal resolution.
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Affiliation(s)
- Dongyang Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Shuaijiang Jin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Xijun Piao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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9
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Xu J, Miyamoto S, Tojo S, Kawai K. Sulfonated Pyrene as a Photoregulator for Single‐Stranded DNA Looping. Chemistry 2020; 26:5075-5084. [DOI: 10.1002/chem.202000184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/14/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Jie Xu
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Shunichi Miyamoto
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Sachiko Tojo
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN)Osaka University Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
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10
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11
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Bhunia S, Dolai A, Samanta S. Robust bi-directional photoswitching of thiomethyl substituted arylazopyrazoles under visible light. Chem Commun (Camb) 2020; 56:10247-10250. [DOI: 10.1039/d0cc04098c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mono-ortho- and para-thiomethyl substituted arylazopyrazoles display excellent isomerization in both directions under visible light, and show long cis half-lives. These switches are also resistant to photobleaching and reduction by glutathione.
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Affiliation(s)
- Supriya Bhunia
- Department of Chemistry
- University of Calcutta
- Kolkata 700009
- India
| | - Anirban Dolai
- Department of Chemistry
- University of Calcutta
- Kolkata 700009
- India
| | - Subhas Samanta
- Department of Chemistry
- University of Calcutta
- Kolkata 700009
- India
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12
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Wu Z, Zhang L. Photoregulation between small DNAs and reversible photochromic molecules. Biomater Sci 2019; 7:4944-4962. [PMID: 31650136 DOI: 10.1039/c9bm01305a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.
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Affiliation(s)
- Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
| | - Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
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13
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Zhang L, Linden G, Vázquez O. In search of visible-light photoresponsive peptide nucleic acids (PNAs) for reversible control of DNA hybridization. Beilstein J Org Chem 2019; 15:2500-2508. [PMID: 31728164 PMCID: PMC6839558 DOI: 10.3762/bjoc.15.243] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
Photoswitchable oligonucleotides can determine specific biological outcomes by light-induced conformational changes. In particular, artificial probes activated by visible-light irradiation are highly desired in biological applications. Here, we report two novel types of visible-light photoswitchable peptide nucleic acids (PNAs) based on the molecular transducers: hemithioindigo and tetra-ortho-fluoroazobenzene. Our study reveals that the tetra-ortho-fluoroazobenzene-PNA conjugates have promising properties (fast reversible isomerization, exceptional thermal stability, high isomer conversions and sensitivity to visible-light irradiation) as reversible modulators to control oligonucleotide hybridization in biological contexts. Furthermore, we verified that this switchable modification delivers a slightly different hybridization behavior in the PNA. Thus, both melting experiments and strand-displacement assays showed that in all the cases the trans-isomer is the one with superior binding affinities. Alternative versions, inspired by our first compounds here reported, may find applications in different fields such as chemical biology, nanotechnology and materials science.
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Affiliation(s)
- Lei Zhang
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein Straße 4, 35043 Marburg, Germany
| | - Greta Linden
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein Straße 4, 35043 Marburg, Germany
| | - Olalla Vázquez
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein Straße 4, 35043 Marburg, Germany
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14
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Zhang L, Deng Y, Tang Z, Zheng N, Zhang C, Xie C, Wu Z. One‐Pot Synthesis of Spiropyrans. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; College of Chemistry and Molecular EngineeringQingdao University of Science and Technology Qingdao 266042 P.R. China
| | - Yawen Deng
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; College of Chemistry and Molecular EngineeringQingdao University of Science and Technology Qingdao 266042 P.R. China
| | - Zhenyu Tang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; College of Chemistry and Molecular EngineeringQingdao University of Science and Technology Qingdao 266042 P.R. China
| | - Ning Zheng
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; College of Chemistry and Molecular EngineeringQingdao University of Science and Technology Qingdao 266042 P.R. China
| | - Chenghao Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; College of Chemistry and Molecular EngineeringQingdao University of Science and Technology Qingdao 266042 P.R. China
| | - Congxia Xie
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; College of Chemistry and Molecular EngineeringQingdao University of Science and Technology Qingdao 266042 P.R. China
| | - Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE; Shandong Key Laboratory of Biochemical Analysis; College of Chemistry and Molecular EngineeringQingdao University of Science and Technology Qingdao 266042 P.R. China
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15
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Chen C, Wang Z, Zhang J, Fan X, Xu L, Tang X. Dextran-Conjugated Caged siRNA Nanoparticles for Photochemical Regulation of RNAi-Induced Gene Silencing in Cells and Mice. Bioconjug Chem 2019; 30:1459-1465. [DOI: 10.1021/acs.bioconjchem.9b00204] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Changmai Chen
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Zhongyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Jinhao Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Xinli Fan
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Luzheng Xu
- Medical and Health Analytical Center, Peking University, Beijing, 100191, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery Systems, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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16
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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: 92] [Impact Index Per Article: 18.4] [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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17
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O’Connor MJ, Beebe LL, Deodato D, Ball RE, Page AT, VanLeuven AJ, Harris KT, Park S, Hariharan V, Lauderdale JD, Dore TM. Bypassing Glutamic Acid Decarboxylase 1 (Gad1) Induced Craniofacial Defects with a Photoactivatable Translation Blocker Morpholino. ACS Chem Neurosci 2019; 10:266-278. [PMID: 30200754 PMCID: PMC6337688 DOI: 10.1021/acschemneuro.8b00231] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
![]()
γ-Amino
butyric acid (GABA) mediated signaling is critical
in the central and enteric nervous systems, pancreas, lungs, and other
tissues. It is associated with many neurological disorders and craniofacial
development. Glutamic acid decarboxylase (GAD) synthesizes GABA from
glutamate, and knockdown of the gad1 gene results
in craniofacial defects that are lethal in zebrafish. To bypass this
and enable observation of the neurological defects resulting from
knocking down gad1 expression, a photoactivatable
morpholino oligonucleotide (MO) against gad1 was
prepared by cyclization with a photocleavable linker rendering the
MO inactive. The cyclized MO was stable in the dark and toward degradative
enzymes and was completely linearized upon brief exposure to 405 nm
light. In the course of investigating the function of the ccMOs in
zebrafish, we discovered that zebrafish possess paralogous gad1 genes, gad1a and gad1b. A gad1b MO injected at the 1–4 cell stage
caused severe morphological defects in head development, which could
be bypassed, enabling the fish to develop normally, if the fish were
injected with a photoactivatable, cyclized gad1b MO
and grown in the dark. At 1 day post fertilization (dpf), light activation
of the gad1b MO followed by observation at 3 and
7 dpf led to increased and abnormal electrophysiological brain activity
compared to wild type animals. The photocleavable linker can be used
to cyclize and inactivate any MO, and represents a general strategy
to parse the function of developmentally important genes in a spatiotemporal
manner.
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Affiliation(s)
- Matthew J. O’Connor
- New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Lindsey L. Beebe
- Department of Genetics, University of Georgia, Athens, Georgia 30602, United States
| | - Davide Deodato
- New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Rebecca E. Ball
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - A. Tyler Page
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Ariel J. VanLeuven
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Kyle T. Harris
- Department of Chemistry, University of Georgia, Athens, Georgia 30602 United States
| | - Sungdae Park
- Department of Genetics, University of Georgia, Athens, Georgia 30602, United States
| | - Vani Hariharan
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - James D. Lauderdale
- Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
- Neuroscience
Division
of the Biomedical and Health Sciences Institute, Athens, Georgia 30602, United States
| | - Timothy M. Dore
- New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
- Department of Chemistry, University of Georgia, Athens, Georgia 30602 United States
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18
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Hayakawa Y, Banno A, Kitagawa H, Higashi S, Kitade Y, Shibata A, Ikeda M. Reduction-Responsive DNA Duplex Containing O 6-Nitrobenzyl-Guanine. ACS OMEGA 2018; 3:9267-9275. [PMID: 31459058 PMCID: PMC6645092 DOI: 10.1021/acsomega.8b01177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/01/2018] [Indexed: 05/27/2023]
Abstract
Stimuli-controlled structural transitions of nucleic acids have received growing attentions owing to their potential applications in the fields of chemical and synthetic biology. Here, we describe the development of reduction-responsive deoxyribonucleic acid (DNA) duplexes, in which guanine rings bearing a reduction-responsive cleavable nitrobenzyl (NB) group at the O 6 position (GNB) are introduced at defined positions. We demonstrate that the artificial NB group can be removed in response to reduction stimulus without the dissociation of the intermolecular duplex structure, which comprises a G-quadruplex forming nucleic acid strand with one GNB and its complementary sequence with one mismatch pair. Meanwhile, another duplex that comprised a G-quadruplex forming nucleic acid strand with two GNB and its complementary sequence with three mismatch pairs exhibited reduction-responsive structural transitions from intermolecular duplex to intramolecular quadruplex. These findings might be useful for the development of DNA architectures endowed with reduction-responsive functions.
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Affiliation(s)
- Yukiko Hayakawa
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Ayaka Banno
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hiroaki Kitagawa
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Sayuri Higashi
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yukio Kitade
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Aya Shibata
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Masato Ikeda
- Department
of Life Science and Chemistry, Graduate School of Natural
Science and Technology and United Graduate School of Drug Discovery and Medical
Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Center
for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu 501-1193, Japan
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19
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Jun M, Joshi DK, Yalagala RS, Vanloon J, Simionescu R, Lough AJ, Gordon HL, Yan H. Confirmation of the Structure of Trans
-Cyclic Azobenzene by X-Ray Crystallography and Spectroscopic Characterization of Cyclic Azobenzene Analogs. ChemistrySelect 2018. [DOI: 10.1002/slct.201703126] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Meesook Jun
- Department of Chemistry and Centre for Biotechnology; Brock University; 1812 Sir Isaac Brock Way, St. Catharines Ontario L2S 3 A1 Canada
| | - Dhruval K. Joshi
- Department of Chemistry and Centre for Biotechnology; Brock University; 1812 Sir Isaac Brock Way, St. Catharines Ontario L2S 3 A1 Canada
| | - Ravi S. Yalagala
- Department of Chemistry and Centre for Biotechnology; Brock University; 1812 Sir Isaac Brock Way, St. Catharines Ontario L2S 3 A1 Canada
| | - Jesse Vanloon
- Department of Chemistry and Centre for Biotechnology; Brock University; 1812 Sir Isaac Brock Way, St. Catharines Ontario L2S 3 A1 Canada
| | - Razvan Simionescu
- Department of Chemistry and Centre for Biotechnology; Brock University; 1812 Sir Isaac Brock Way, St. Catharines Ontario L2S 3 A1 Canada
| | - Alan J. Lough
- Department of Chemistry; University of Toronto; 80 St. George Street Toronto Ontario M5S 3H6 Canada
| | - Heather L. Gordon
- Department of Chemistry and Centre for Biotechnology; Brock University; 1812 Sir Isaac Brock Way, St. Catharines Ontario L2S 3 A1 Canada
| | - Hongbin Yan
- Department of Chemistry and Centre for Biotechnology; Brock University; 1812 Sir Isaac Brock Way, St. Catharines Ontario L2S 3 A1 Canada
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20
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Zhang L, Chen C, Fan X, Tang X. Photomodulating Gene Expression by Using Caged siRNAs with Single-Aptamer Modification. Chembiochem 2018; 19:1259-1263. [PMID: 29488297 DOI: 10.1002/cbic.201700623] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Indexed: 12/21/2022]
Abstract
Caged siRNAs incorporating terminal modification were rationally designed for photochemical regulation of gene silencing induced by RNA interference (RNAi). Through the conjugation of a single oligonucleotide aptamer at the 5' terminus of the antisense RNA strand, enhancement of the blocking effect for RNA-induced silencing complex (RISC) formation/processing was expected, due both/either to the aptamers themselves and/or to their interaction with large binding proteins. Two oligonucleotide aptamers (AS1411 and MUC-1) were chosen for aptamer-siRNA conjugation through a photolabile linker. This caging strategy was successfully used to photoregulate gene expression both of firefly luciferase and of green fluorescent protein (GFP) in cells. Further patterning experiments revealed that spatial regulation of GFP expression was successfully achieved by using the aptamer-modified caged siRNA and light activation. We expect that further optimized caged siRNAs featuring aptamer conjugation will be promising for practical applications to spatiotemporal photoregulation of gene expression in the future.
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Affiliation(s)
- Liangliang Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
| | - Changmai Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
| | - Xinli Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, P.R. China
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21
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Debart F, Dupouy C, Vasseur JJ. Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing. Beilstein J Org Chem 2018; 14:436-469. [PMID: 29520308 PMCID: PMC5827813 DOI: 10.3762/bjoc.14.32] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
Oligonucleotides (ONs) have been envisaged for therapeutic applications for more than thirty years. However, their broad use requires overcoming several hurdles such as instability in biological fluids, low cell penetration, limited tissue distribution, and off-target effects. With this aim, many chemical modifications have been introduced into ONs definitively as a means of modifying and better improving their properties as gene silencing agents and some of them have been successful. Moreover, in the search for an alternative way to make efficient ON-based drugs, the general concept of prodrugs was applied to the oligonucleotide field. A prodrug is defined as a compound that undergoes transformations in vivo to yield the parent active drug under different stimuli. The interest in stimuli-responsive ONs for gene silencing functions has been notable in recent years. The ON prodrug strategies usually help to overcome limitations of natural ONs due to their low metabolic stability and poor delivery. Nevertheless, compared to permanent ON modifications, transient modifications in prodrugs offer the opportunity to regulate ON activity as a function of stimuli acting as switches. Generally, the ON prodrug is not active until it is triggered to release an unmodified ON. However, as it will be described in some examples, the opposite effect can be sought. This review examines ON modifications in response to various stimuli. These stimuli may be internal or external to the cell, chemical (glutathione), biochemical (enzymes), or physical (heat, light). For each stimulus, the discussion has been separated into sections corresponding to the site of the modification in the nucleotide: the internucleosidic phosphate, the nucleobase, the sugar or the extremities of ONs. Moreover, the review provides a current and detailed account of stimuli-responsive ONs with the main goal of gene silencing. However, for some stimuli-responsive ONs reported in this review, no application for controlling gene expression has been shown, but a certain potential in this field could be demonstrated. Additionally, other applications in different domains have been mentioned to extend the interest in such molecules.
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Affiliation(s)
- Françoise Debart
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, France
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22
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Heimes M, Kolmar L, Brieke C. Efficient cosubstrate enzyme pairs for sequence-specific methyltransferase-directed photolabile caging of DNA. Chem Commun (Camb) 2018; 54:12718-12721. [DOI: 10.1039/c8cc05913f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Efficient and selective methyltransferase-catalyzed transfer of photolabile groups onto DNA enables photoregulation of gene expression and can be performed even in the presence of AdoMet.
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Affiliation(s)
- Michael Heimes
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- D-69120 Heidelberg
- Germany
| | - Leonie Kolmar
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- D-69120 Heidelberg
- Germany
| | - Clara Brieke
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- D-69120 Heidelberg
- Germany
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23
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Photomodulation of DNA-Templated Supramolecular Assemblies. Chemistry 2017; 24:706-714. [DOI: 10.1002/chem.201704538] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 12/22/2022]
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24
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Abstract
This review highlights relevant studies of light-controlled molecular containers able to catch and release small molecules.
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Affiliation(s)
- Alejandro Díaz-Moscoso
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- Tarragona
- Spain
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ)
- The Barcelona Institute of Science and Technology
- Tarragona
- Spain
- ICREA
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25
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Zhang CC, Li SH, Zhang CF, Liu Y. Size Switchable Supramolecular Nanoparticle Based on Azobenzene Derivative within Anionic Pillar[5]arene. Sci Rep 2016; 6:37014. [PMID: 27849055 PMCID: PMC5111115 DOI: 10.1038/srep37014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/21/2016] [Indexed: 12/15/2022] Open
Abstract
A photo/thermal-switchable supramolecular nanoparticles assembly has been constructed based on an inclusion complex between anionic pillar[5]arene 2C-WP5A and azobenzene derivative Azo-py-OMe (G). The novel anionic pillar[5]arene-based host-guest inclusion complexation was investigated by the 1H NMR titration, 2D ROESY and isothermal titration microcalorimetry (ITC) showing high association constant (Ka) of (2.60 ± 0.06) × 104 M−1 with 1:1 binding stoichiometry. Furthermore, the supramolecular nanoparticles assembly can be conveniently obtained from G and a small amount of 2C-WP5A in aqueous solution, which was so-called “host induced aggregating (HIA)”. The size and morphology of the supramolecular nanoparticles assembly were characterized by TEM and DLS. As a result of the photo/thermal-isomerization of G included in the cavity of 2C-WP5A, the size of these nanoparticles could reversibly change from ~800 nm to ~250 nm, which could switch the solution of this assembly from turbid to clear.
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Affiliation(s)
- Cai-Cai Zhang
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Sheng-Hua Li
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, P. R. China
| | - Cui-Fang Zhang
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yu Liu
- Department of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, P. R. China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, P. R. China
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26
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Jain PK, Ramanan V, Schepers AG, Dalvie NS, Panda A, Fleming HE, Bhatia SN. Development of Light-Activated CRISPR Using Guide RNAs with Photocleavable Protectors. Angew Chem Int Ed Engl 2016; 55:12440-4. [PMID: 27554600 PMCID: PMC5864249 DOI: 10.1002/anie.201606123] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Indexed: 12/11/2022]
Abstract
The ability to remotely trigger CRISPR/Cas9 activity would enable new strategies to study cellular events with greater precision and complexity. In this work, we have developed a method to photocage the activity of the guide RNA called "CRISPR-plus" (CRISPR-precise light-mediated unveiling of sgRNAs). The photoactivation capability of our CRISPR-plus method is compatible with the simultaneous targeting of multiple DNA sequences and supports numerous modifications that can enable guide RNA labeling for use in imaging and mechanistic investigations.
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Affiliation(s)
- Piyush K Jain
- Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Vyas Ramanan
- Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Arnout G Schepers
- Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Nisha S Dalvie
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Apekshya Panda
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Heather E Fleming
- Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sangeeta N Bhatia
- Institute for Medical Engineering & Science, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Electrical Engineering and Computer Science, Marble Center for Cancer Nanomedicine, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
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27
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Jain PK, Ramanan V, Schepers AG, Dalvie NS, Panda A, Fleming HE, Bhatia SN. Development of Light-Activated CRISPR Using Guide RNAs with Photocleavable Protectors. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606123] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Piyush K. Jain
- Institute for Medical Engineering & Science; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Vyas Ramanan
- Institute for Medical Engineering & Science; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Arnout G. Schepers
- Institute for Medical Engineering & Science; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Nisha S. Dalvie
- Department of Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Apekshya Panda
- Department of Biological Engineering; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Heather E. Fleming
- Institute for Medical Engineering & Science; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Sangeeta N. Bhatia
- Institute for Medical Engineering & Science; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Department of Electrical Engineering and Computer Science; Marble Center for Cancer Nanomedicine; Massachusetts Institute of Technology; Cambridge MA 02139 USA
- Department of Medicine; Brigham and Women's Hospital; Boston MA 02115 USA
- Broad Institute of MIT and Harvard; Cambridge MA 02139 USA
- Howard Hughes Medical Institute; Cambridge MA 02139 USA
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28
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McGuigan AP, Javaherian S. Tissue Patterning: Translating Design Principles from In Vivo to In Vitro. Annu Rev Biomed Eng 2016; 18:1-24. [DOI: 10.1146/annurev-bioeng-083115-032943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alison P. McGuigan
- Department of Chemical Engineering and Applied Chemistry and
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E5, Canada;
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29
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Doi T, Kawai H, Murayama K, Kashida H, Asanuma H. Visible-Light-Triggered Cross-Linking of DNA Duplexes by Reversible [2+2] Photocycloaddition of Styrylpyrene. Chemistry 2016; 22:10533-8. [DOI: 10.1002/chem.201602006] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tetsuya Doi
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hayato Kawai
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hiromu Kashida
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
- PRESTO (Japan) Science and Technology Agency; 4-1-8 Honcho, Kawaguchi Saitama 332-0012 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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30
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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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31
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Ji Y, Yang J, Wu L, Yu L, Tang X. Photochemical Regulation of Gene Expression Using Caged siRNAs with Single Terminal Vitamin E Modification. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201510921] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Yuzhuo Ji
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; No. 38, Xueyuan Rd. Beijing 100191 China
| | - Jiali Yang
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; No. 38, Xueyuan Rd. Beijing 100191 China
| | - Li Wu
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; No. 38, Xueyuan Rd. Beijing 100191 China
| | - Lijia Yu
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; No. 38, Xueyuan Rd. Beijing 100191 China
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32
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Ji Y, Yang J, Wu L, Yu L, Tang X. Photochemical Regulation of Gene Expression Using Caged siRNAs with Single Terminal Vitamin E Modification. Angew Chem Int Ed Engl 2015; 55:2152-6. [DOI: 10.1002/anie.201510921] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Yuzhuo Ji
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; No. 38, Xueyuan Rd. Beijing 100191 China
| | - Jiali Yang
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; No. 38, Xueyuan Rd. Beijing 100191 China
| | - Li Wu
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; No. 38, Xueyuan Rd. Beijing 100191 China
| | - Lijia Yu
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; No. 38, Xueyuan Rd. Beijing 100191 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs; School of Pharmaceutical Sciences; Peking University; No. 38, Xueyuan Rd. Beijing 100191 China
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33
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Eljabu F, Dhruval J, Yan H. Incorporation of cyclic azobenzene into oligodeoxynucleotides for the photo-regulation of DNA hybridization. Bioorg Med Chem Lett 2015; 25:5594-6. [PMID: 26592170 DOI: 10.1016/j.bmcl.2015.10.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 10/13/2015] [Accepted: 10/15/2015] [Indexed: 11/26/2022]
Abstract
Cyclic azobenzene carboxylic acid was synthesized using a shortened route. After reaction with D-threolinol, the resulting cyclic azobenzene-D-threolinol (cAB-Thr) building block was transformed into the corresponding DMTr-protected phosphoramidite, and incorporated into oligodeoxynucleotides at various positions and frequencies by solid phase synthesis. The melting temperatures of these modified oligonucleotides were determined by UV spectrometry. Photo-regulation of cAB-Thr-modified oligonucleotides with their complementary sequence was evaluated by Fluorescence Resonance Energy Transfer experiments using a fluorescein-Black Hole Quencher pair. Results suggest that while cis-cAB destabilizes DNA duplexes, trans-cAB can be accommodated in double stranded DNA.
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Affiliation(s)
- Fatma Eljabu
- Department of Chemistry, Brock University, 500 Glenridge Ave., St. Catharines, Ontario L2S 3A1, Canada
| | - Joshi Dhruval
- Department of Chemistry, Brock University, 500 Glenridge Ave., St. Catharines, Ontario L2S 3A1, Canada
| | - Hongbin Yan
- Department of Chemistry, Brock University, 500 Glenridge Ave., St. Catharines, Ontario L2S 3A1, Canada.
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34
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Lu J, Koo SC, Li NS, Piccirilli JA. Synthesis of 2'-O-photocaged ribonucleoside phosphoramidites. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:114-29. [PMID: 25621705 DOI: 10.1080/15257770.2014.965256] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The chemical synthesis and incorporation of the phosphoramidite derivatives of 2 '-O-photocaged ribonucleosides (A, C, G and U) with o-nitrobenzyl, α-methyl-o-nitrobenzyl or 4,5-dimethoxy-2-nitrobenzyl group into oligoribonucleotides are described. The efficiency of UV irradiated uncaging of these 2'-O-photocaged oligoribonucleotides was found in the order of α-methyl-o-nitrobenzyl < 4,5-dimethoxy-2-nitrobenzyl < 2'-O-o-nitrobenzyl.
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Affiliation(s)
- Jun Lu
- a Department of Biochemistry & Molecular Biology and Department of Chemistry , University of Chicago , Chicago , Illinois , United States
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35
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Griepenburg JC, Rapp TL, Carroll PJ, Eberwine J, Dmochowski IJ. Ruthenium-Caged Antisense Morpholinos for Regulating Gene Expression in Zebrafish Embryos. Chem Sci 2015; 6:2342-2346. [PMID: 26023327 PMCID: PMC4443914 DOI: 10.1039/c4sc03990d] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/29/2015] [Indexed: 11/25/2022] Open
Abstract
Photochemical approaches afford high spatiotemporal control over molecular structure and function, for broad applications in materials and biological science. Here, we present the first example of a visible light responsive ruthenium-based photolinker, Ru(bipyridine)2(3-ethynylpyridine)2 (RuBEP), which was reacted stoichiometrically with a 25mer DNA or morpholino (MO) oligonucleotide functionalized with 3' and 5' terminal azides, via Cu(I)-mediated [3+2] Huisgen cycloaddition reactions. RuBEP-caged circular morpholinos (Ru-MOs) targeting two early developmental zebrafish genes, chordin and notail, were synthesized and tested in vivo. One-cell-stage zebrafish embryos microinjected with Ru-MO and incubated in the dark for 24 h developed normally, consistent with caging, whereas irradiation at 450 nm dissociated one 3-ethynylpyridine ligand (ϕ = 0.33) and uncaged the MO to achieve gene knockdown. As demonstrated, Ru photolinkers provide a versatile method for controlling structure and function of biopolymers.
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Affiliation(s)
- Julianne C. Griepenburg
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , USA .
| | - Teresa L. Rapp
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , USA .
| | - Patrick J. Carroll
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , USA .
| | - James Eberwine
- Department of Systems Pharmacology and Experimental Therapeutics , Perelman School of Medicine , University of Pennsylvania , 37 John Morgan Building, 3620 Hamilton Walk , Philadelphia , Pennsylvania 19104 , USA
| | - Ivan J. Dmochowski
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , USA .
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Saneyoshi H, Shimamura K, Sagawa N, Ando Y, Tomori T, Okamoto I, Ono A. Development of a photolabile protecting group for phosphodiesters in oligonucleotides. Bioorg Med Chem Lett 2015; 25:2129-32. [PMID: 25881825 DOI: 10.1016/j.bmcl.2015.03.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/20/2015] [Accepted: 03/25/2015] [Indexed: 11/17/2022]
Abstract
A photolabile protecting group, consisting of an o-nitrobenzyl group and a 3-(2'-hydroxy-3',6'-dimethylphenyl)-2,2-dimethylpropyl moiety, was developed for phosphodiesters in oligodeoxyribonucleotides. Deprotection was triggered by photoirradiation and subsequent spontaneous cyclization to release the naked oligonucleotide.
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Affiliation(s)
- Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan.
| | - Kanami Shimamura
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Naoki Sagawa
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yuki Ando
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Takahito Tomori
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Itaru Okamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan.
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37
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Markiewicz BN, Culik RM, Gai F. Tightening up the structure, lighting up the pathway: Application of molecular constraints and light to manipulate protein folding, self-assembly and function. Sci China Chem 2014; 57:1615-1624. [PMID: 25722715 PMCID: PMC4337807 DOI: 10.1007/s11426-014-5225-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chemical cross-linking provides an effective avenue to reduce the conformational entropy of polypeptide chains and hence has become a popular method to induce or force structural formation in peptides and proteins. Recently, other types of molecular constraints, especially photoresponsive linkers and functional groups, have also found increased use in a wide variety of applications. Herein, we provide a concise review of using various forms of molecular strategies to constrain proteins, thereby stabilizing their native states, gaining insight into their folding mechanisms, and/or providing a handle to trigger a conformational process of interest with light. The applications discussed here cover a wide range of topics, ranging from delineating the details of the protein folding energy landscape to controlling protein assembly and function.
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Affiliation(s)
| | - Robert M. Culik
- Department of Biochemistry and Biophysics, University of Pennsylvania, PA, 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, PA, 19104, USA
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38
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Li J, Wang X, Liang X. Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology. Chem Asian J 2014; 9:3344-58. [DOI: 10.1002/asia.201402758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 01/29/2023]
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39
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Li NS, Tuttle N, Staley J, Piccirilli JA. Synthesis and incorporation of the phosphoramidite derivative of 2'-O-photocaged 3'-s-thioguanosine into oligoribonucleotides: substrate for probing the mechanism of RNA catalysis. J Org Chem 2014; 79:3647-52. [PMID: 24635216 PMCID: PMC4203407 DOI: 10.1021/jo4028374] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 11/30/2022]
Abstract
Oligoribonucleotides containing 3'-S-phosphorothiolate linkages possess properties that can reveal deep mechanistic insights into ribozyme-catalyzed reactions. "Photocaged" 3'-S- RNAs could provide a strategy to stall reactions at the chemical stage and release them after assembly steps have occurred. Toward this end, we describe here an approach for the synthesis of 2'-O-(o-nitrobenzyl)-3'-thioguanosine phosphoramidite starting from N(2)-isobutyrylguanosine in nine steps with 10.2% overall yield. Oligonucleotides containing the 2'-O-(o-nitrobenzyl)-3'-S-guanosine nucleotide were then constructed, characterized, and used in a nuclear pre-mRNA splicing reaction.
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Affiliation(s)
- Nan-Sheng Li
- Department of Biochemistry &
Molecular Biology, Department of Chemistry, and Department of
Molecular Genetics & Cell Biology, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Nicole Tuttle
- Department of Biochemistry &
Molecular Biology, Department of Chemistry, and Department of
Molecular Genetics & Cell Biology, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Jonathan
P. Staley
- Department of Biochemistry &
Molecular Biology, Department of Chemistry, and Department of
Molecular Genetics & Cell Biology, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Joseph A. Piccirilli
- Department of Biochemistry &
Molecular Biology, Department of Chemistry, and Department of
Molecular Genetics & Cell Biology, University
of Chicago, Chicago, Illinois 60637, United
States
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40
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Gatterdam V, Ramadass R, Stoess T, Fichte MAH, Wachtveitl J, Heckel A, Tampé R. Three-Dimensional Protein Networks Assembled by Two-Photon Activation. Angew Chem Int Ed Engl 2014; 53:5680-4. [DOI: 10.1002/anie.201309930] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/23/2014] [Indexed: 12/16/2022]
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41
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Gatterdam V, Ramadass R, Stoess T, Fichte MAH, Wachtveitl J, Heckel A, Tampé R. Dreidimensionale Proteinnetzwerke durch Zwei-Photonen- Aktivierung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309930] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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42
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Liu Q, Deiters A. Optochemical control of deoxyoligonucleotide function via a nucleobase-caging approach. Acc Chem Res 2014; 47:45-55. [PMID: 23981235 PMCID: PMC3946944 DOI: 10.1021/ar400036a] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Synthetic oligonucleotides have been extensively applied tocontrol a wide range of biological processes such as gene expression, gene repair, DNA replication, and protein activity. Based on well-established sequence design rules that typically rely on Watson-Crick base pairing interactions researchers can readily program the function of these oligonucleotides. Therefore oligonucleotides provide a flexible platform for targeting a wide range of biological molecules, including DNA, RNA, and proteins. In addition, oligonucleotides are commonly used research tools in cell biology and developmental biology. However, a lack of conditional control methods has hampered the precise spatial and temporal regulation of oligonucleotide activity, which limits the application of these reagents to investigate complex biological questions. Nature controls biological function with a high level of spatial and temporal resolution and in order to elucidate the molecular mechanisms of biological processes, researchers need tools that allow for the perturbation of these processes with Nature's precision. Light represents an excellent external regulatory element since irradiation can be easily controlled spatially and temporally. Thus, researchers have developed several different methods to conditionally control oligonucleotide activity with light. One of the most versatile strategies is optochemical regulation through the installation and removal of photolabile caging groups on oligonucleotides. To produce switches that can control nucleic acid function with light, chemists introduce caging groups into the oligomer backbone or on specific nucleobases to block oligonucleotide function until the caging groups are removed by light exposure. In this Account, we focus on the application of caged nucleobases to the photoregulation of DNA function. Using this approach, we have both activated and deactivated gene expression optochemically at the transcriptional and translational level with spatial and temporal control. Specifically, we have used caged triplex-forming oligomers and DNA decoys to regulate transcription, and we have regulated translation with light-activated antisense agents. Moreover, we also discuss strategies that can trigger DNA enzymatic activity, DNA amplification, and DNA mutagenesis by light illumination. More recently, we have developed light-activated DNA logic operations, an advance that may lay the foundation for the optochemical control of complex DNA calculations.
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Affiliation(s)
- Qingyang Liu
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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43
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Abstract
Manipulation of protein kinase activity is widely used to dissect signaling pathways controlling physiological and pathological processes. Common methods often cannot provide the desired spatial and temporal resolution in control of kinase activity. Regulation of kinase activity by photocaged kinase inhibitors has been successfully used to achieve tight temporal and local control, but inhibitors are limited to inactivation of kinases and often do not provide the desired specificity. Here we report detailed methods for light-mediated activation of kinases in living cells using engineered rapamycin-regulated kinases in conjunction with a photocaged analog of rapamycin.
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44
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Tang X, Zhang J, Sun J, Wang Y, Wu J, Zhang L. Caged nucleotides/nucleosides and their photochemical biology. Org Biomol Chem 2013; 11:7814-24. [PMID: 24132515 DOI: 10.1039/c3ob41735b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleotides and nucleosides are not only key units of DNA/RNA that store genetic information, but are also the regulators of many biological events of our lives. By caging the key functional groups or key residues of nucleotides with photosensitive moieties, it will be possible to trigger biological events of target nucleotides with spatiotemporal resolution and amplitude upon light activation or photomodulate polymerase reactions with the caged nucleotide analogues for next-generation sequencing (NGS) and bioorthogonal labeling. This review highlights three different caging strategies for nucleotides and demonstrates the photochemical biology of these caged nucleotides.
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Affiliation(s)
- Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing 100191, China.
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45
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Griepenburg JC, Ruble BK, Dmochowski IJ. Caged oligonucleotides for bidirectional photomodulation of let-7 miRNA in zebrafish embryos. Bioorg Med Chem 2013; 21:6198-204. [PMID: 23721917 PMCID: PMC3789856 DOI: 10.1016/j.bmc.2013.04.082] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/20/2013] [Accepted: 04/30/2013] [Indexed: 12/17/2022]
Abstract
Many biological functions of microRNA (miRNA) have been identified in the past decade. However, a single miRNA can regulate multiple gene targets, thus it has been a challenge to elucidate the specific functions of each miRNA in different locations and times. New chemical tools make it possible to modulate miRNA activity with higher spatiotemporal resolution. Here, we describe light-activated (caged) constructs for switching let-7 miRNA 'on' or 'off' with 365 nm light in developing zebrafish embryos.
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Affiliation(s)
- Julianne C. Griepenburg
- Department of Chemistry, University of Pennsylvania, 231 S.34th Street, Philadelphia, PA 19104 USA
| | - Brittani K. Ruble
- Department of Chemistry, University of Pennsylvania, 231 S.34th Street, Philadelphia, PA 19104 USA
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 S.34th Street, Philadelphia, PA 19104 USA
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46
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Yang Y, Velmurugan B, Liu X, Xing B. NIR photoresponsive crosslinked upconverting nanocarriers toward selective intracellular drug release. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:2937-2944. [PMID: 23554151 DOI: 10.1002/smll.201201765] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Indexed: 06/02/2023]
Abstract
An NIR-responsive mesoporous silica coated upconverting nanoparticle (UCNP) conjugate is developed for controllable drug delivery and fluorescence imaging in living cells. In this work, antitumor drug doxorubicin (Dox) molecules are encapsulated within cross-linked photocaged mesoporous silica coated UCNPs. Upon 980 nm light irradiation, Dox could be selectively released through the photocleavage of theo-nitrobenzyl (NB) caged linker by the converted UV emission from UCNPs. This NIR light-responsive nanoparticle conjugate demonstrates high efficiency for the controlled release of the drug in cancer cells. Upon functionalization of the nanocarrier with folic acid (FA), this photocaged FA-conjugated silica-UCNP nanocarrier will also allow targeted intracellular drug delivery and selective fluorescence imaging towards the cell lines with high level expression of folate receptor (FR).
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Affiliation(s)
- Yanmei Yang
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 637371, Singapore
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47
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Szymański W, Beierle JM, Kistemaker HAV, Velema WA, Feringa BL. Reversible Photocontrol of Biological Systems by the Incorporation of Molecular Photoswitches. Chem Rev 2013; 113:6114-78. [DOI: 10.1021/cr300179f] [Citation(s) in RCA: 847] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wiktor Szymański
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - John M. Beierle
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Hans A. V. Kistemaker
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Willem A. Velema
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
| | - Ben L. Feringa
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The
Netherlands
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48
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Brown PK, Qureshi AT, Moll AN, Hayes DJ, Monroe WT. Silver nanoscale antisense drug delivery system for photoactivated gene silencing. ACS NANO 2013; 7:2948-59. [PMID: 23473419 DOI: 10.1021/nn304868y] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The unique photophysical properties of noble metal nanoparticles contribute to their potential as photoactivated drug delivery vectors. Here we demonstrate the synthesis and characterization of 60-80 nm silver nanoparticles (SNPs) decorated with thiol-terminated photolabile DNA oligonucleotides. In vitro assays and fluorescent confocal microscopy of treated cell cultures show efficient UV-wavelength photoactivation of surface-tethered caged ISIS2302 antisense oligonucleotides possessing internal photocleavable linkers. As a demonstration of the advantages of these novel nanocarriers, we investigate properties including: enhanced stability to nucleases, increased hybridization activity upon photorelease, and efficient cellular uptake as compared to commercial transfection vectors. Their potential as multicomponent delivery agents for oligonucleotide therapeutics is shown through regulation of ICAM-1 (Intracellular Adhesion Molecule-1) silencing. Our results suggest a means to achieve light-triggered, spatiotemporally controlled gene silencing via nontoxic silver nanocarriers, which hold promise as tailorable platforms for nanomedicine, gene expression studies, and genetic therapies.
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Affiliation(s)
- Paige K Brown
- Biological and Agricultural Engineering, Louisiana State University and LSU AgCenter, Baton Rouge, Louisiana 70803, United States
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49
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Liang X, Zhou M, Kato K, Asanuma H. Photoswitch nucleic acid catalytic activity by regulating topological structure with a universal supraphotoswitch. ACS Synth Biol 2013; 2:194-202. [PMID: 23656478 DOI: 10.1021/sb300120n] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We demonstrated the generality of a strategy for photoswitching the activity of functional oligonucleotides by modulating their topological structure. Our strategy was proved to be versatile because it can be used to photoregulate functional oligonucleotides, e.g., ribozymes and DNAzymes, which have two binding arms and a catalytic loop. Repeated reversible photoregulation of RNA cleavage by a ribozyme or a DNAzyme was achieved by attaching two photoresponsive strands, artificial oligomers involving azobenzene moieties and nucleobases capable of forming a duplex as the supraphotoswitch. Individual strands were attached to the 3' and 5' ends of a RNA-cleavage oligonucleotide. Thus, the topological structure of the ribozyme or DNAzyme was constrained, and RNA cleavage was greatly suppressed when the supraphotoswitch duplex formed (OFF state). In contrast, RNA cleavage resumed when the supraphotoswitch duplex dissociated (ON state). Light irradiation was used to repeatedly switch the supraphotoswitch between the ON and OFF states so that RNA cleavage activity could be efficiently photoregulated. Analysis of the regulatory mechanism showed that topological constraints suppressed the RNA cleavage by causing both structural changes at the catalytic site and lower binding affinity between the RNA substrates and the functional oligonucleotides.
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Affiliation(s)
- Xingguo Liang
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603,
Japan
- College of Food Science
and
Engineering, Ocean University of China,
Qingdao 266003, China
| | - Mengguang Zhou
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603,
Japan
| | - Kenjiro Kato
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603,
Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603,
Japan
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50
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Klán P, Šolomek T, Bochet CG, Blanc A, Givens R, Rubina M, Popik V, Kostikov A, Wirz J. Photoremovable protecting groups in chemistry and biology: reaction mechanisms and efficacy. Chem Rev 2013; 113:119-91. [PMID: 23256727 PMCID: PMC3557858 DOI: 10.1021/cr300177k] [Citation(s) in RCA: 1214] [Impact Index Per Article: 110.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Petr Klán
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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