1
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Salihovic A, Ascham A, Taladriz-Sender A, Bryson S, Withers JM, McKean IJW, Hoskisson PA, Grogan G, Burley GA. Gram-scale enzymatic synthesis of 2'-deoxyribonucleoside analogues using nucleoside transglycosylase-2. Chem Sci 2024:d4sc04938a. [PMID: 39234214 PMCID: PMC11368039 DOI: 10.1039/d4sc04938a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024] Open
Abstract
Nucleosides are pervasive building blocks that are found throughout nature and used extensively in medicinal chemistry and biotechnology. However, the preparation of base-modified analogues using conventional synthetic methodology poses challenges in scale-up and purification. In this work, an integrated approach involving structural analysis, screening and reaction optimization, is established to prepare 2'-deoxyribonucleoside analogues catalysed by the type II nucleoside 2'-deoxyribosyltransferase from Lactobacillus leichmannii (LlNDT-2). Structural analysis in combination with substrate profiling, identified the constraints on pyrimidine and purine acceptor bases by LlNDT2. A solvent screen identifies pure water as a suitable solvent for the preparation of high value purine and pyrimidine 2'-deoxyribonucleoside analogues on a gram scale under optimized reaction conditions. This approach provides the basis to establish a convergent, step-efficient chemoenzymatic platform for the preparation of high value 2'-deoxyribonucleosides.
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Affiliation(s)
- Admir Salihovic
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| | - Alex Ascham
- Department of Chemistry, University of York, Heslington York YO10 5DD UK
| | - Andrea Taladriz-Sender
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| | - Samantha Bryson
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| | - Jamie M Withers
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| | - Iain J W McKean
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde 161 Cathedral Street Glasgow G4 0RE UK
| | - Gideon Grogan
- Department of Chemistry, University of York, Heslington York YO10 5DD UK
| | - Glenn A Burley
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow UK G1 1XL
- Strathclyde Centre for Molecular Bioscience, University of Strathclyde UK
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2
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Cui X, Dong X, Hu M, Zhou W, Shi W. Large field of view and spatial region of interest transcriptomics in fixed tissue. Commun Biol 2024; 7:1020. [PMID: 39164496 PMCID: PMC11335973 DOI: 10.1038/s42003-024-06694-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
Expression profiling in spatially defined regions is crucial for systematically understanding tissue complexity. Here, we report a method of photo-irradiation for in-situ barcoding hybridization and ligation sequencing, named PBHL-seq, which allows targeted expression profiling from the photo-irradiated region of interest in intact fresh frozen and formalin fixation and paraffin embedding (FFPE) tissue samples. PBHL-seq uses photo-caged oligodeoxynucleotides for in situ reverse transcription followed by spatially targeted barcoding of cDNAs to create spatially indexed transcriptomes of photo-illuminated regions. We recover thousands of differentially enriched transcripts from different regions by applying PBHL-seq to OCT-embedded tissue (E14.5 mouse embryo and mouse brain) and FFPE mouse embryo (E15.5). We also apply PBHL-seq to the subcellular microstructures (cytoplasm and nucleus, respectively) and detect thousands of differential expression genes. Thus, PBHL-seq provides an accessible workflow for expression profiles from the region of interest in frozen and FFPE tissue at subcellular resolution with areas expandable to centimeter scale, while preserving the sample intact for downstream analysis to promote the development of transcriptomics.
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Affiliation(s)
- Xiaonan Cui
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Xue Dong
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Mengzhu Hu
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Wenjian Zhou
- Single Cell Systems Biology Laboratory, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266100, China
| | - Weiyang Shi
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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3
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Tian H, You S, Xiong T, Ji M, Zhang K, Jiang L, Du T, Li Y, Liu W, Lin S, Chen X, Xu H. Discovery of a Novel Photocaged PI3K Inhibitor Capable of Real-Time Reporting of Drug Release. ACS Med Chem Lett 2023; 14:1100-1107. [PMID: 37583818 PMCID: PMC10424311 DOI: 10.1021/acsmedchemlett.3c00240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023] Open
Abstract
A novel photocaged PI3K inhibitor 2 was designed and synthesized by introducing a cascade photocaging group to block its key interaction with the kinase. Upon UV light irradiation, the photocaged compound released a highly potent PI3K inhibitor to recover its anticancer properties and a fluorescent dye for real-time reporting of drug release, providing a new approach for studying the PI3K signaling transduction pathway as well as developing precisely controlled cancer therapeutics.
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Affiliation(s)
- Hua Tian
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing
Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Shen You
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Tianning Xiong
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing
Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Ming Ji
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Kehui Zhang
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing
Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Lin Jiang
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing
Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Tingting Du
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Ying Li
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing
Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Wenqian Liu
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing
Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Songwen Lin
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing
Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Xiaoguang Chen
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
| | - Heng Xu
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing
Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical
Sciences and Peking Union Medical College, Beijing 100050, China
- Key
Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences and Peking Union
Medical College, Beijing 100050, China
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4
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Eyberg J, Ringenberg M, Richert C. Caging of a Strongly Pairing Fluorescent Thymidine Analog with Soft Nucleophiles. Chemistry 2023; 29:e202203289. [PMID: 36395348 PMCID: PMC10107337 DOI: 10.1002/chem.202203289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022]
Abstract
Controlling the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell is a formidable challenge. Here we report how a thiazolyl substituent turns a strongly pairing ethynylpyridone C-nucleoside into a reactive residue in oligonucleotides. The thiazolyl-bearing pyridone reacts with soft nucleophiles, such as glutathione, but not with hard nucleophiles like hydroxide or carbonate. The addition products pair much more weakly with adenine in a complementary strand than the starting material, and also change their fluorescence. This makes oligonucleotides containing the new deoxynucleoside interesting for controlled release. Due to its reactivity toward N, P, S, and Se-nucleophiles, and the visual signal accompanying chemical conversion, the fluorescent nucleotide reported here may also have applications in chemical biology, sensing and diagnostics.
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Affiliation(s)
- Juri Eyberg
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Mark Ringenberg
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
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5
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Jin X, Kim YT, Jo K. DNA Visualization Using Fluorescent Proteins. Methods Mol Biol 2023; 2564:223-246. [PMID: 36107345 DOI: 10.1007/978-1-0716-2667-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA binding fluorescent proteins are a powerful tool for single-molecule visualization. In this chapter, we discuss a protocol for the synthesis of DNA binding fluorescent proteins and visualization of single DNA molecules. This chapter includes stepwise methods for molecular cloning, reversible staining, two-color staining, sequence-specific staining, and microscopic visualization of single DNA molecules in a microfluidic device. This content will be useful for DNA characterization using DNA binding fluorescent proteins and its visualization at the single-molecule level.
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Affiliation(s)
- Xuelin Jin
- College of Agriculture, Yanbian University, Yanji, Jilin Province, China.
| | - Y Tehee Kim
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul, Korea
| | - Kyubong Jo
- Department of Chemistry and Program of Integrated Biotechnology, Sogang University, Seoul, Korea.
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6
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White LJ, Boles JE, Clifford M, Patenall BL, Hilton KHLF, Ng KKL, Ellaby RJ, Hind CK, Mulvihill DP, Hiscock JR. Di-anionic self-associating supramolecular amphiphiles (SSAs) as antimicrobial agents against MRSA and Escherichia coli. Chem Commun (Camb) 2021; 57:11839-11842. [PMID: 34698738 DOI: 10.1039/d1cc05455d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report a series of di-anionic supramolecular self-associating amphiphiles (SSAs). We elucidate the antimicrobial properties of these SSAs against both methicillin resistant Staphylococcus aureus and Escherichia coli. In addition, we show this class of compound to form both intra- and intermolecular hydrogen bonded macrocyclic structures in the solid state.
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Affiliation(s)
- Lisa J White
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Jessica E Boles
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK. .,School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
| | - Melanie Clifford
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | - Bethany L Patenall
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | - Kira H L F Hilton
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Kendrick K L Ng
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Rebecca J Ellaby
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.
| | - Charlotte K Hind
- National Infection Service, Public Health England, Porton Down, Salisbury SP4 0JG, UK.
| | - Daniel P Mulvihill
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK.
| | - Jennifer R Hiscock
- School of Physical Sciences, University of Kent, Canterbury, Kent, CT2 7NH, UK.
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7
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High-depth spatial transcriptome analysis by photo-isolation chemistry. Nat Commun 2021; 12:4416. [PMID: 34285220 PMCID: PMC8292322 DOI: 10.1038/s41467-021-24691-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/24/2021] [Indexed: 12/18/2022] Open
Abstract
In multicellular organisms, expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we establish a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. PIC transcriptome analysis detects genes specifically expressed in small distinct areas of the mouse embryo. Photo-irradiation of single cells demonstrated that approximately 8,000 genes were detected with 7 × 104 unique read counts. Furthermore, PIC transcriptome analysis is applicable to the subcellular and subnuclear microstructures (stress granules and nuclear speckles, respectively), where hundreds of genes can be detected as being specifically localised. The spatial density of the read counts is higher than 100 per square micrometre. Thus, PIC enables high-depth transcriptome profiles to be determined from limited regions up to subcellular and subnuclear resolutions. Spatial analysis of RNAseq data is important. Here the authors report a method for transcriptome profiling combined with photo-isolation chemistry to allow determination of expression profiles specifically from photo-irradiated regions of interest which they use in mouse brains and embryonic tissues.
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8
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Shieh P, Hill MR, Zhang W, Kristufek SL, Johnson JA. Clip Chemistry: Diverse (Bio)(macro)molecular and Material Function through Breaking Covalent Bonds. Chem Rev 2021; 121:7059-7121. [PMID: 33823111 DOI: 10.1021/acs.chemrev.0c01282] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the two decades since the introduction of the "click chemistry" concept, the toolbox of "click reactions" has continually expanded, enabling chemists, materials scientists, and biologists to rapidly and selectively build complexity for their applications of interest. Similarly, selective and efficient covalent bond breaking reactions have provided and will continue to provide transformative advances. Here, we review key examples and applications of efficient, selective covalent bond cleavage reactions, which we refer to herein as "clip reactions." The strategic application of clip reactions offers opportunities to tailor the compositions and structures of complex (bio)(macro)molecular systems with exquisite control. Working in concert, click chemistry and clip chemistry offer scientists and engineers powerful methods to address next-generation challenges across the chemical sciences.
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Affiliation(s)
- Peyton Shieh
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Megan R Hill
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wenxu Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Samantha L Kristufek
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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9
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Hammers MD, Hodny MH, Bader TK, Mahmoodi MM, Fang S, Fenton AD, Nurie K, Trial HO, Xu F, Healy AT, Ball ZT, Blank DA, Distefano MD. Two-photon uncaging of bioactive thiols in live cells at wavelengths above 800 nm. Org Biomol Chem 2021; 19:2213-2223. [PMID: 33349821 PMCID: PMC8437107 DOI: 10.1039/d0ob01986k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Photoactivatable protecting groups (PPGs) are useful for a broad range of applications ranging from biology to materials science. In chemical biology, induction of biological processes via photoactivation is a powerful strategy for achieving spatiotemporal control. The importance of cysteine, glutathione, and other bioactive thiols in regulating protein structure/activity and cell redox homeostasis makes modulation of thiol activity particularly useful. One major objective for enhancing the utility of photoactivatable protecting groups (PPGs) in living systems is creating PPGs with longer wavelength absorption maxima and efficient two-photon (TP) absorption. Toward these objectives, we developed a carboxyl- and dimethylamine-functionalized nitrodibenzofuran PPG scaffold (cDMA-NDBF) for thiol photoactivation, which has a bathochromic shift in the one-photon absorption maximum from λmax = 315 nm with the unfunctionalized NDBF scaffold to λmax = 445 nm. While cDMA-NDBF-protected thiols are stable in the presence of UV irradiation, they undergo efficient broad-spectrum TP photolysis at wavelengths as long as 900 nm. To demonstrate the wavelength orthogonality of cDMA-NDBF and NDBF photolysis in a biological setting, caged farnesyltransferase enzyme inhibitors (FTI) were prepared and selectively photoactivated in live cells using 850-900 nm TP light for cDMA-NDBF-FTI and 300 nm UV light for NDBF-FTI. These experiments represent the first demonstration of thiol photoactivation at wavelengths above 800 nm. Consequently, cDMA-NDBF-caged thiols should have broad applicability in a wide range of experiments in chemical biology and materials science.
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Affiliation(s)
- Matthew D Hammers
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Michael H Hodny
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Taysir K Bader
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - M Mohsen Mahmoodi
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Sifei Fang
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Alexander D Fenton
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Kadiro Nurie
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Hallie O Trial
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Feng Xu
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Andrew T Healy
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Zachary T Ball
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - David A Blank
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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10
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Zhou Y, Zhang Y, Lin W, Kesseli SJ, Huang L, Zhao Y, Yao X, Huang K, Han G. Wavelength-Selective Light-Controlled Stepwise Photolysis from Single Gold Nanoparticles. Adv Healthc Mater 2021; 10:e2000321. [PMID: 33034955 DOI: 10.1002/adhm.202000321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/02/2020] [Indexed: 11/09/2022]
Abstract
Light-controlled sequential photolysis from a single nanoparticle is a challenge for controlled release. A wavelength-selective sequential photolysis from single gold nanoparticles is reported for the first time. In particular, it is also demonstrated that such nanoparticle can be used to sequentially release two payloads in living cells. In principle, this system can be extended to sequential release of multiple different types of payloads by rational design of diverse photocleavable linkers. It is expected that this work can provide a new tool for better orderly controlling cellular events that request high spatiotemporal manners.
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Affiliation(s)
- Yekui Zhou
- Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA
| | - Yuanwei Zhang
- Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA
| | - Wenhai Lin
- Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA
| | - Samuel J. Kesseli
- Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA
| | - Ling Huang
- Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA
| | - Yang Zhao
- Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA
| | - Xikuang Yao
- Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA
| | - Kai Huang
- Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA
| | - Gang Han
- Department of Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA 01605 USA
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11
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Construction of a reduction-responsive oligonucleotide via a post-modification approach utilizing 4-nitrophenyl diazomethane. Polym J 2021. [DOI: 10.1038/s41428-021-00464-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
AbstractHerein, we describe the construction of a reduction-responsive oligonucleotide by post-modification of an oligonucleotide with a diazo compound bearing a 4-nitrobenzyl group as a reduction-responsive cleavable moiety. High-performance liquid chromatography and mass spectrometry were used to reveal the introduction of a 4-nitrobenzyl group to the 5′-phosphate group of an oligonucleotide, and the subsequent reduction-triggered recovery of the original oligonucleotide. The protocol used for the preparation of this reduction-responsive oligonucleotide is simple and it will have various applications in the fields of chemical and synthetic biology.
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12
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Bollu A, Sharma NK. Biased photo cleavage of N-/N-nitrobenzyl from 2’-hydroxyethyl-adenosine and their DNA/RNA Caged-analogues. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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13
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Abstract
The specific non-invasive control of intracellular signaling events requires advanced tools that enter cells by diffusion and are controllable by light. Here, we detail the synthesis and application of membrane-permeant caged inositol pyrophosphates with respect to cell entry and cell distribution. We recently published the synthesis of these tools as well as their effect on PH-domain localization in HeLa cells and oscillations of the intracellular calcium concentration in β-cells, which are known to drive insulin secretion. In this chapter, we discuss the possibilities and limitations when using cell-penetrating inositol pyrophosphates. We provide a detailed protocol for the application in live mouse β-cells and we discuss the image analysis needed for following effects on calcium signaling.
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14
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Acevedo-Jake A, Ball AT, Galli M, Kukwikila M, Denis M, Singleton DG, Tavassoli A, Goldup SM. AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides. J Am Chem Soc 2020; 142:5985-5990. [PMID: 32155338 PMCID: PMC8016193 DOI: 10.1021/jacs.0c01670] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/22/2022]
Abstract
We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.
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Affiliation(s)
- Amanda Acevedo-Jake
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Andrew T. Ball
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Marzia Galli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mikiembo Kukwikila
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Mathieu Denis
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Daniel G. Singleton
- ATDBio
Ltd, School of Chemistry, University of
Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Ali Tavassoli
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
| | - Stephen M. Goldup
- Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, U.K.
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15
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Kimura Y, Shu Z, Ito M, Abe N, Nakamoto K, Tomoike F, Shuto S, Ito Y, Abe H. Intracellular build-up RNAi with single-strand circular RNAs as siRNA precursors. Chem Commun (Camb) 2020; 56:466-469. [DOI: 10.1039/c9cc04872c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We herein report a new approach for RNA interference, so-called “build-up RNAi” approach, where single-strand circular RNAs with a photocleavable unit or disulfide moiety were used as siRNA precursors.
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Affiliation(s)
- Yasuaki Kimura
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Zhaoma Shu
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Mika Ito
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Kita-12, Nishi-6, Kita-ku
- Sapporo 060-0812
- Japan
| | - Naoko Abe
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Kosuke Nakamoto
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science
- Nagoya University
- Nagoya 464-8602
- Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences
- Hokkaido University
- Kita-12, Nishi-6, Kita-ku
- Sapporo 060-0812
- Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team
- RIKEN Center for Emergent Matter Science
- Wako-Shi
- Japan
| | - Hiroshi Abe
- Department of Chemistry
- Graduate School of Science
- Nagoya University
- Nagoya 464-8602
- Japan
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16
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Nguyen HP, Stewart S, Kukwikila MN, Jones SF, Offenbartl‐Stiegert D, Mao S, Balasubramanian S, Beck S, Howorka S. A Photo-responsive Small-Molecule Approach for the Opto-epigenetic Modulation of DNA Methylation. Angew Chem Int Ed Engl 2019; 58:6620-6624. [PMID: 30773767 PMCID: PMC7027477 DOI: 10.1002/anie.201901139] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Indexed: 12/12/2022]
Abstract
Controlling the functional dynamics of DNA within living cells is essential in biomedical research. Epigenetic modifications such as DNA methylation play a key role in this endeavour. DNA methylation can be controlled by genetic means. Yet there are few chemical tools available for the spatial and temporal modulation of this modification. Herein, we present a small-molecule approach to modulate DNA methylation with light. The strategy uses a photo-tuneable version of a clinically used drug (5-aza-2'-deoxycytidine) to alter the catalytic activity of DNA methyltransferases, the enzymes that methylate DNA. After uptake by cells, the photo-regulated molecule can be light-controlled to reduce genome-wide DNA methylation levels in proliferating cells. The chemical tool complements genetic, biochemical, and pharmacological approaches to study the role of DNA methylation in biology and medicine.
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Affiliation(s)
- Ha Phuong Nguyen
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | | | - Mikiembo N. Kukwikila
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - Sioned Fôn Jones
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - Daniel Offenbartl‐Stiegert
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - Shiqing Mao
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeUK
- Cancer Research (UK) Cambridge InstituteUniversity of CambridgeRobinson WayCambridgeUK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeUK
- Cancer Research (UK) Cambridge InstituteUniversity of CambridgeRobinson WayCambridgeUK
| | | | - Stefan Howorka
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London20 Gordon StreetLondonWC1H 0AJUK
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17
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Nguyen HP, Stewart S, Kukwikila MN, Jones SF, Offenbartl‐Stiegert D, Mao S, Balasubramanian S, Beck S, Howorka S. A Photo‐responsive Small‐Molecule Approach for the Opto‐epigenetic Modulation of DNA Methylation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ha Phuong Nguyen
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London 20 Gordon Street London WC1H 0AJ UK
| | | | - Mikiembo N. Kukwikila
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London 20 Gordon Street London WC1H 0AJ UK
| | - Sioned Fôn Jones
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London 20 Gordon Street London WC1H 0AJ UK
| | - Daniel Offenbartl‐Stiegert
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London 20 Gordon Street London WC1H 0AJ UK
| | - Shiqing Mao
- Department of ChemistryUniversity of Cambridge Lensfield Road Cambridge UK
- Cancer Research (UK) Cambridge InstituteUniversity of Cambridge Robinson Way Cambridge UK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of Cambridge Lensfield Road Cambridge UK
- Cancer Research (UK) Cambridge InstituteUniversity of Cambridge Robinson Way Cambridge UK
| | | | - Stefan Howorka
- Department of ChemistryInstitute for Structural and Molecular BiologyUniversity College London 20 Gordon Street London WC1H 0AJ UK
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18
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Boháčová S, Ludvíková L, Poštová Slavětínská L, Vaníková Z, Klán P, Hocek M. Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA. Org Biomol Chem 2019; 16:1527-1535. [PMID: 29431832 DOI: 10.1039/c8ob00160j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleosides, nucleotides and 2'-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleotides and DNA. Photodeprotection (photorelease) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined. Photocaged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR. DNA probes containing photocaged or free 5-hydroxymethylU in the recognition sequence of restriction endonucleases were prepared and used for the study of photorelease of caged DNA by UV or visible light at different wavelengths. The nitropiperonyl-protected nucleotide was found to be a superior building block because the corresponding dNTP is a good substrate for DNA polymerases, and the protecting group is efficiently cleavable by irradiation by UV or visible light (up to 425 nm).
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Affiliation(s)
- Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
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19
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Light-triggered release of photocaged therapeutics - Where are we now? J Control Release 2019; 298:154-176. [PMID: 30742854 DOI: 10.1016/j.jconrel.2019.02.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/02/2023]
Abstract
The current available therapeutics face several challenges such as the development of ideal drug delivery systems towards the goal of personalized treatments for patients benefit. The application of light as an exogenous activation mechanism has shown promising outcomes, owning to the spatiotemporal confinement of the treatment in the vicinity of the diseased tissue, which offers many intriguing possibilities. Engineering therapeutics with light responsive moieties have been explored to enhance the bioavailability, and drug efficacy either in vitro or in vivo. The tailor-made character turns the so-called photocaged compounds highly desirable to reduce the side effects of drugs and, therefore, have received wide research attention. Herein, we seek to highlight the potential of photocaged compounds to obtain a clear understanding of the mechanisms behind its use in therapeutic delivery. A deep overview on the progress achieved in the design, fabrication as well as current and possible future applications in therapeutics of photocaged compounds is provided, so that novel formulations for biomedical field can be designed.
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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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Boháčová S, Vaníková Z, Poštová Slavětínská L, Hocek M. Protected 2′-deoxyribonucleoside triphosphate building blocks for the photocaging of epigenetic 5-(hydroxymethyl)cytosine in DNA. Org Biomol Chem 2018; 16:5427-5432. [DOI: 10.1039/c8ob01106k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
2′-Deoxyribonucleoside triphosphates containing 5-(hydroxymethyl)cytosine protected with photocleavable groups were prepared and studied as substrates for the enzymatic synthesis of DNA containing a photocaged epigenetic 5hmC base.
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Affiliation(s)
- Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
| | - Zuzana Vaníková
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
- Department of Organic Chemistry
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
- Department of Organic Chemistry
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22
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Circular siRNAs for Reducing Off-Target Effects and Enhancing Long-Term Gene Silencing in Cells and Mice. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 10:237-244. [PMID: 29499936 PMCID: PMC5768153 DOI: 10.1016/j.omtn.2017.12.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 11/17/2022]
Abstract
Circular non-coding RNAs are found to play important roles in biology but are still relatively unexplored as a structural motif for chemically regulating gene function. Here, we investigated whether small interfering RNA (siRNA) with a circular structure can circumvent off-target gene silencing, a problem often observed with standard linear duplex siRNA. In the present work, we, for the first time, synthesized a series of circular siRNAs by cyclizing two ends of a single-stranded RNA (sense or antisense strand) to construct circular siRNAs that were more resistant to enzymatic degradation. Gene silencing of GFP and luciferase was successfully achieved using these circular siRNAs with circular sense strand RNAs and their complementary linear antisense strand RNAs. The off-target effect of sense strand RNAs was evaluated and no cross off-target effects were observed. In addition, we successfully achieved longer gene-silencing efficiency in mice with circular siRNAs than with linear siRNAs. These results indicate the promise of circular siRNAs for overcoming off-target effects of siRNAs and enhancing the possible long-term effect of siRNA gene silencing in basic research and drug development.
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23
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Ohno K, Sugiyama D, Takeshita L, Kanamori T, Masaki Y, Sekine M, Seio K. Synthesis of photocaged 6-O-(2-nitrobenzyl)guanosine and 4-O-(2-nitrobenzyl) uridine triphosphates for photocontrol of the RNA transcription reaction. Bioorg Med Chem 2017; 25:6007-6015. [PMID: 28986114 DOI: 10.1016/j.bmc.2017.09.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/15/2017] [Accepted: 09/20/2017] [Indexed: 11/27/2022]
Abstract
6-O-(2-Nitrobenzyl)guanosine and 4-O-(2-nitrobenzyl)uridine triphosphates (NBGTP, NBUTP) were synthesized, and their biochemical and photophysical properties were evaluated. We synthesized NBUTP using the canonical triphosphate synthesis method and NBGTP from 2',3'-O-TBDMS guanosine via a triphosphate synthesis method by utilizing mild acidic desilylation conditions. Deprotection of the nitrobenzyl group in NBGTP and NBUTP proceeded within 60s by UV irradiation at 365nm. Experiments using NBGTP or NBUTP in T7-RNA transcription reactions showed that NBGTP could be useful for the photocontrol of transcription by UV irradiation.
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Affiliation(s)
- Kentaro Ohno
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Daiki Sugiyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Leo Takeshita
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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24
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Bakshi SF, Guz N, Zakharchenko A, Deng H, Tumanov AV, Woodworth CD, Minko S, Kolpashchikov DM, Katz E. Magnetic Field-Activated Sensing of mRNA in Living Cells. J Am Chem Soc 2017; 139:12117-12120. [PMID: 28817270 PMCID: PMC5654739 DOI: 10.1021/jacs.7b06022] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Detection of specific mRNA in living cells has attracted significant attention in the past decade. Probes that can be easily delivered into cells and activated at the desired time can contribute to understanding translation, trafficking and degradation of mRNA. Here we report a new strategy termed magnetic field-activated binary deoxyribozyme (MaBiDZ) sensor that enables both efficient delivery and temporal control of mRNA sensing by magnetic field. MaBiDZ uses two species of magnetic beads conjugated with different components of a multicomponent deoxyribozyme (DZ) sensor. The DZ sensor is activated only in the presence of a specific target mRNA and when a magnetic field is applied. Here we demonstrate that MaBiDZ sensor can be internalized in live MCF-7 breast cancer cells and activated by a magnetic field to fluorescently report the presence of specific mRNA, which are cancer biomarkers.
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Affiliation(s)
- Saira F Bakshi
- Department of Chemistry and Biomolecular Science, Clarkson University , Potsdam, New York 13699-5810, United States
| | - Nataliia Guz
- Department of Chemistry and Biomolecular Science, Clarkson University , Potsdam, New York 13699-5810, United States
| | - Andrey Zakharchenko
- Nanostructured Materials Lab, University of Georgia , Athens, Georgia 30602, United States
| | - Han Deng
- Department of Biology, Clarkson University , Potsdam, New York 13699-5810, United States
| | - Alexei V Tumanov
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center at San Antonio , 7703 Floyd Curl Drive, San Antonio, Texas 78229-3900, United States
| | - Craig D Woodworth
- Department of Biology, Clarkson University , Potsdam, New York 13699-5810, United States
| | - Sergiy Minko
- Nanostructured Materials Lab, University of Georgia , Athens, Georgia 30602, United States
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida , 4000 Central Florida Boulevard, Orlando, Florida 32816-2366, United States.,Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University , Lomonosova St. 9, 191002 St. Petersburg, Russian Federation
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University , Potsdam, New York 13699-5810, United States
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25
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Abstract
Oligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2'-, 3'-, and 5'-positions of the sugar moieties, and the internucleotide phospho-linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Geeta Meher
- Spring Bank Pharmaceuticals, Inc, Milford, Massachusetts
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26
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Hikage S, Sasaki Y, Hisai T, Tanimoto H, Morimoto T, Nishiyama Y, Kakiuchi K. Synthesis of novel caged antisense oligonucleotides with fluorescence property. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2016.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Influences of alpha-substituent in 4,5-dimethoxy-2-nitrobenzyl-protected esters on both photocleavage rate and subsequent photoreaction of the generated 2-nitrosophenyl ketones: A novel photorearrangement of 2-nitrosophenyl ketones. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2016.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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28
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Lee S, Oh Y, Lee J, Choe S, Lim S, Lee HS, Jo K, Schwartz DC. DNA binding fluorescent proteins for the direct visualization of large DNA molecules. Nucleic Acids Res 2016; 44:e6. [PMID: 26264666 PMCID: PMC4705684 DOI: 10.1093/nar/gkv834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/03/2015] [Accepted: 08/06/2015] [Indexed: 12/14/2022] Open
Abstract
Fluorescent proteins that also bind DNA molecules are useful reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely 'paints' entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for intercalating between DNA bases. Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd = 14.7 μM) to confluently stain DNA molecules and such binding is reversible via pH shifts. These proteins offer useful robust advantages for single DNA molecule studies: lack of fluorophore mediated photocleavage and staining that does not perturb polymer contour lengths. Accordingly, we demonstrate confluent staining of naked DNA molecules presented within microfluidic devices, or localized within live bacterial cells.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Yeeun Oh
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Jungyoon Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Sojeong Choe
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Korea
| | - Hyun Soo Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, 1 Shinsudong, Mapogu, Seoul, 121-742, Korea
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53705, USA
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29
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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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30
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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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31
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Vaníková Z, Hocek M. Polymerase Synthesis of Photocaged DNA Resistant against Cleavage by Restriction Endonucleases. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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32
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Vaníková Z, Hocek M. Polymerase synthesis of photocaged DNA resistant against cleavage by restriction endonucleases. Angew Chem Int Ed Engl 2014; 53:6734-7. [PMID: 24850380 DOI: 10.1002/anie.201402370] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/23/2014] [Indexed: 12/12/2022]
Abstract
5-[(2-Nitrobenzyl)oxymethyl]-2'-deoxyuridine 5'-O-triphosphate was used for polymerase (primer extension or PCR) synthesis of photocaged DNA that is resistant to the cleavage by restriction endonucleases. Photodeprotection of the caged DNA released 5-hydroxymethyluracil-modified nucleic acids, which were fully recognized and cleaved by restriction enzymes.
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Affiliation(s)
- Zuzana Vaníková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic) http://www.uochb.cas.cz/hocekgroup
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Jessen HJ, Ahmed N, Hofer A. Phosphate esters and anhydrides--recent strategies targeting nature's favoured modifications. Org Biomol Chem 2014; 12:3526-30. [PMID: 24781815 DOI: 10.1039/c4ob00478g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Esters and anhydrides of phosphoric acid are essential in biology. It is very difficult to identify processes in life that do not involve these modifications and their transformation at some point. Consequently, phosphorylation chemistry is an essential methodology with significant impact on the biological sciences. This perspective gives an overview of some very recent achievements in synthetic phosphorylation chemistry and aims at identifying challenges that lie ahead.
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Affiliation(s)
- Henning J Jessen
- University of Zürich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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