1
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Yang G, Li Y, Wang B, Zhang Y. Lighting Up Fluorescence: Precise Recognition of Halogenated Solvents Through Effective Fluorescence Detection Using Chalcone Derivatives as a D-A-D-A-type Fluorescent Chemosensor. J Fluoresc 2023:10.1007/s10895-023-03527-2. [PMID: 38055140 DOI: 10.1007/s10895-023-03527-2] [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: 11/06/2023] [Accepted: 11/24/2023] [Indexed: 12/07/2023]
Abstract
In this paper, we report a D-A-D-A-type fluorescence sensor, FX, composed of triphenylamine and pyrazine units as electron donors, pyridine units, and α-β unsaturated carbon-based structures as electron acceptors. FX exhibits typical ICT characteristics. As a dual-emission material, FX undergoes acid-base-induced color changes and displays mechanofluorochromic properties in the solid state. In solution, FX, as an AIE material, shows significant fluorescence enhancement behavior in most halogenated solvents. Notably, it achieves a high quantum yield of 0.672 in a chloroform solution. We utilized this phenomenon to quantitatively detect chloroform through fluorescence titration analysis, with a detection limit of 0.061%. Additionally, we developed a test paper to verify the practical applicability of the sensor for detecting halogenated solvents. The fluorescence enhancement behavior was confirmed through DFT calculations. The results indicate that FX is not only a multifunctional dual-state emission material but also provides valuable references for the fluorescence detection of halogenated solvents.
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Affiliation(s)
- Guo Yang
- College of Chemistry and Chemical Engineering, China West Normal University, Nanchong, 637000, China
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province of China, Nanchong, 637000, China
| | - Yuanwei Li
- College of Chemistry and Chemical Engineering, China West Normal University, Nanchong, 637000, China
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province of China, Nanchong, 637000, China
| | - Bin Wang
- College of Chemistry and Chemical Engineering, China West Normal University, Nanchong, 637000, China.
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province of China, Nanchong, 637000, China.
| | - Ying Zhang
- Sichuan University of Science & Engineering, GongZi, 634002, China
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2
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Abstract
Many RNA delivery strategies require efficient endosomal uptake and release. To monitor this process, we developed a 2'-OMe RNA-based ratiometric pH probe with a pH-invariant 3'-Cy5 and 5'-FAM whose pH sensitivity is enhanced by proximal guanines. The probe, in duplex with a DNA complement, exhibits a 48.9-fold FAM fluorescence enhancement going from pH 4.5 to pH 8.0 and reports on both endosomal entrapment and release when delivered to HeLa cells. In complex with an antisense RNA complement, the probe constitutes an siRNA mimic capable of protein knockdown in HEK293T cells. This illustrates a general approach for measuring the localization and pH microenvironment of any oligonucleotide.
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Affiliation(s)
- Madison R. Herling
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104-6323, U.S.A
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104-6323, U.S.A
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3
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Geng J, Xia X, Teng L, Wang L, Chen L, Guo X, Belingon B, Li J, Feng X, Li X, Shang W, Wan Y, Wang H. Emerging landscape of cell-penetrating peptide-mediated nucleic acid delivery and their utility in imaging, gene-editing, and RNA-sequencing. J Control Release 2022; 341:166-183. [PMID: 34822907 DOI: 10.1016/j.jconrel.2021.11.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022]
Abstract
The safety issues like immunogenicity and unacceptable cancer risk of viral vectors for DNA/mRNA vaccine delivery necessitate the development of non-viral vectors with no toxicity. Among the non-viral strategies, cell-penetrating peptides (CPPs) have been a topic of interest recently because of their ability to cross plasma membranes and facilitate nucleic acids delivery both in vivo and in vitro. In addition to the application in the field of gene vaccine and gene therapy, CPPs based nucleic acids delivery have been proved by its potential application like gene editing, RNA-sequencing, and imaging. Here, we focus on summarizing the recent applications and progress of CPPs-mediated nucleic acids delivery and discuss the current problems and solutions in this field.
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Affiliation(s)
- Jingping Geng
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Xuan Xia
- Department of Physiology and Pathophysiology, Medical School, China Three Gorges University, Yichang 443002, China
| | - Lin Teng
- Department of Cardiovascular Medicine, The First Clinical Medical College of China Three Gorges University, Yichang 443002, China
| | - Lidan Wang
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Linlin Chen
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China; Affiliated Ren He Hospital of China Three Gorges University, Yichang 443002, China
| | - Xiangli Guo
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Bonn Belingon
- Institute of Cell Engineering, Johns Hopkins University, Baltimore, MD 21210, USA
| | - Jason Li
- Department of Biology, Johns Hopkins University, Baltimore, MD 21210, USA
| | - Xuemei Feng
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Xianghui Li
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Wendou Shang
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Yingying Wan
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
| | - Hu Wang
- Department of Microbiology and Immunology, Medical School, China Three Gorges University, Yichang 443002, China.
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4
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He L, Zhu Y, Xu Y. Copper‐Catalyzed Ligand‐Free Remote C−H Bond Amidation of 8‐Amidoquinolines with
N
‐Fluorobenzenesulfonimide. ChemistrySelect 2021. [DOI: 10.1002/slct.202102981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Li He
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Yihang Zhu
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Yongjun Xu
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
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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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Yeldell SB, Yang L, Lee J, Eberwine JH, Dmochowski IJ. Oligonucleotide Probe for Transcriptome in Vivo Analysis (TIVA) of Single Neurons with Minimal Background. ACS Chem Biol 2020; 15:2714-2721. [PMID: 32902259 DOI: 10.1021/acschembio.0c00499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Messenger RNA (mRNA) isolated from single cells can generate powerful biological insights, including the discovery of new cell types with unique functions as well as markers potentially predicting a cell's response to various therapeutic agents. We previously introduced an oligonucleotide-based technique for site-selective, photoinduced biotinylation and capture of mRNA within a living cell called transcriptome in vivo analysis (TIVA). Successful application of the TIVA technique hinges upon its oligonucleotide probe remaining completely inert (or "caged") to mRNA unless photoactivated. To improve the reliability of TIVA probe caging in diverse and challenging biological conditions, we applied a rational design process involving iterative modifications to the oligonucleotide construct. In this work, we discuss these design motivations and present an optimized probe with minimal background binding to mRNA prior to photolysis. We assess its caging performance through multiple in vitro assays including FRET analysis, native gel comigration, and pull down with model mRNA transcripts. Finally, we demonstrate that this improved probe can also isolate mRNA from single living neurons in brain tissue slices with excellent caging control.
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Affiliation(s)
- Sean B. Yeldell
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Linlin Yang
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Jaehee Lee
- Department of Pharmacology, University of Pennsylvania, 38 John Morgan Building, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104-6084, United States
| | - James H. Eberwine
- Department of Pharmacology, University of Pennsylvania, 38 John Morgan Building, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104-6084, United States
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
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8
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Abstract
Light-activated ("caged") oligonucleotides provide a strategy for modulating the activity of antisense oligos, siRNA, miRNA, aptamers, DNAzymes, and mRNA-capturing probes with high spatiotemporal resolution. However, the near-UV and visible wavelengths that promote these bond-breaking reactions poorly penetrate living tissue, which limits some biological applications. To address this issue, we describe the first example of a protease-activated oligonucleotide probe, capable of reporting on caspase-3 during cellular apoptosis. The 2'-F RNA-peptide substrate-peptide nucleic acid (PNA) hairpin structure was generated in 30% yield in a single bioconjugation step.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - James H Eberwine
- Department of Pharmacology, University of Pennsylvania, 38 John Morgan Building, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104-6084, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
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9
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Yang L, Kim HB, Sul JY, Yeldell SB, Eberwine JH, Dmochowski IJ. Efficient Synthesis of Light-Triggered Circular Antisense Oligonucleotides Targeting Cellular Protein Expression. Chembiochem 2018; 19:1250-1254. [PMID: 29479781 PMCID: PMC6248878 DOI: 10.1002/cbic.201800012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 02/06/2023]
Abstract
Light-activated ("caged") antisense oligonucleotides are powerful molecules for regulating gene expression at submicron spatial resolution through the focal modulation of endogenous cellular processes. Cyclized caged oligos are particularly promising structures because of their inherent stability and similarity to naturally occurring circular DNA and RNA molecules. Here, we introduce an efficient route for cyclizing an antisense oligodeoxynucleotide incorporating a photocleavable linker. Oligo cyclization was achieved for several sequences in nearly quantitative yields through intramolecular copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). Caging stability and light activation were characterized by FRET efficiency, denaturing gel assay, and melting temperature measurements. Finally, a cyclized caged oligo was designed to target gfap, and it gave a tenfold reduction in glial fibrillary acidic protein upon photoactivation in astrocytes.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, USA
| | - Hyun Bum 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
| | - Sean B Yeldell
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, 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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10
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Becker Y, Unger E, Fichte MAH, Gacek DA, Dreuw A, Wachtveitl J, Walla PJ, Heckel A. A red-shifted two-photon-only caging group for three-dimensional photorelease. Chem Sci 2018; 9:2797-2802. [PMID: 29732066 PMCID: PMC5914290 DOI: 10.1039/c7sc05182d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/08/2018] [Indexed: 12/27/2022] Open
Abstract
Based on nitrodibenzofuran (NDBF) a new photocage with higher two-photon action cross section and red-shifted absorption was developed. Due to calculations, a dimethylamino functionality (DMA) was added at ring position 7. The uncaging of nucleobases after two-photon excitation (2PE) could be visualized via double-strand displacement in a hydrogel. With this assay we achieved three-dimensional photorelease of DMA-NDBF-protected DNA orthogonal to NDBF-protected strands. While being an excellent 2P-cage, DMA-NDBF is surprisingly stable under visible-light one-photon excitation (1PE). This case of excitation-specific photochemistry enhances the scope of orthogonal photoregulation.
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Affiliation(s)
- Yvonne Becker
- Goethe University Frankfurt , Institute for Organic Chemistry and Chemical Biology , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany .
| | - Erik Unger
- Goethe University Frankfurt , Institute for Organic Chemistry and Chemical Biology , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany .
| | - Manuela A H Fichte
- Goethe University Frankfurt , Institute for Organic Chemistry and Chemical Biology , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany .
| | - Daniel A Gacek
- Technical University Braunschweig , Institute for Physical and Theoretical Chemistry , Gaußstr. 17 , 38106 Braunschweig , Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing (IWR) , Theoretical and Computational Chemistry , Im Neuenheimer Feld 205A , 69120 Heidelberg , Germany
| | - Josef Wachtveitl
- Goethe University Frankfurt , Institute for Physical and Theoretical Chemistry , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany
| | - Peter J Walla
- Technical University Braunschweig , Institute for Physical and Theoretical Chemistry , Gaußstr. 17 , 38106 Braunschweig , Germany
| | - Alexander Heckel
- Goethe University Frankfurt , Institute for Organic Chemistry and Chemical Biology , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany .
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