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Son T, Kim M, Choi M, Nam SH, Yoo A, Lee H, Han EH, Hong KS, Park HS. Advancing fluorescence imaging: enhanced control of cyanine dye-doped silica nanoparticles. J Nanobiotechnology 2024; 22:347. [PMID: 38898529 PMCID: PMC11188253 DOI: 10.1186/s12951-024-02638-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 06/14/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Silica nanoparticles (SNPs) have immense potential in biomedical research, particularly in drug delivery and imaging applications, owing to their stability and minimal interactions with biological entities such as tissues or cells. RESULTS With synthesized and characterized cyanine-dye-doped fluorescent SNPs (CSNPs) using cyanine 3.5, 5.5, and 7 (Cy3.5, Cy5.5, and Cy7). Through systematic analysis, we discerned variations in the surface charge and fluorescence properties of the nanoparticles contingent on the encapsulated dye-(3-aminopropyl)triethoxysilane conjugate, while their size and shape remained constant. The fluorescence emission spectra exhibited a redshift correlated with increasing dye concentration, which was attributed to cascade energy transfer and self-quenching effects. Additionally, the fluorescence signal intensity showed a linear relationship with the particle concentration, particularly at lower dye equivalents, indicating a robust performance suitable for imaging applications. In vitro assessments revealed negligible cytotoxicity and efficient cellular uptake of the nanoparticles, enabling long-term tracking and imaging. Validation through in vivo imaging in mice underscored the versatility and efficacy of CSNPs, showing single-switching imaging capabilities and linear signal enhancement within subcutaneous tissue environment. CONCLUSIONS This study provides valuable insights for designing fluorescence imaging and optimizing nanoparticle-based applications in biomedical research, with potential implications for targeted drug delivery and in vivo imaging of tissue structures and organs.
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Affiliation(s)
- Taewoong Son
- Biopharmaceutical Research Center, Ochang Institute of Biological and Environmental Science, Korea Basic Science Institute (KBSI), Cheongju, 28119, Republic of Korea
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Minseo Kim
- Laboratory of Nanophotonics & Nanospectroscopic Imaging, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
- Department of Chemistry, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Minsuk Choi
- Laboratory of Nanophotonics & Nanospectroscopic Imaging, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Sang Hwan Nam
- Laboratory of Nanophotonics & Nanospectroscopic Imaging, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Ara Yoo
- Biopharmaceutical Research Center, Ochang Institute of Biological and Environmental Science, Korea Basic Science Institute (KBSI), Cheongju, 28119, Republic of Korea
| | - Hyunseung Lee
- Biopharmaceutical Research Center, Ochang Institute of Biological and Environmental Science, Korea Basic Science Institute (KBSI), Cheongju, 28119, Republic of Korea
| | - Eun Hee Han
- Biopharmaceutical Research Center, Ochang Institute of Biological and Environmental Science, Korea Basic Science Institute (KBSI), Cheongju, 28119, Republic of Korea
- Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Kwan Soo Hong
- Biopharmaceutical Research Center, Ochang Institute of Biological and Environmental Science, Korea Basic Science Institute (KBSI), Cheongju, 28119, Republic of Korea.
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon, 34134, Republic of Korea.
- Department of Chemistry, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Hye Sun Park
- Biopharmaceutical Research Center, Ochang Institute of Biological and Environmental Science, Korea Basic Science Institute (KBSI), Cheongju, 28119, Republic of Korea.
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2
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Lu H, Zhang H, Li L. Chemical tagging mass spectrometry: an approach for single-cell omics. Anal Bioanal Chem 2023; 415:6901-6913. [PMID: 37466681 PMCID: PMC10729908 DOI: 10.1007/s00216-023-04850-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Single-cell (SC) analysis offers new insights into the study of fundamental biological phenomena and cellular heterogeneity. The superior sensitivity, high throughput, and rich chemical information provided by mass spectrometry (MS) allow MS to emerge as a leading technology for molecular profiling of SC omics, including the SC metabolome, lipidome, and proteome. However, issues such as ionization suppression, low concentration, and huge span of dynamic concentrations of SC components lead to poor MS response for certain types of molecules. It is noted that chemical tagging/derivatization has been adopted in SCMS analysis, and this strategy has been proven an effective solution to circumvent these issues in SCMS analysis. Herein, we review the basic principle and general strategies of chemical tagging/derivatization in SCMS analysis, along with recent applications of chemical derivatization to single-cell metabolomics and multiplexed proteomics, as well as SCMS imaging. Furthermore, the challenges and opportunities for the improvement of chemical derivatization strategies in SCMS analysis are discussed.
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Affiliation(s)
- Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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3
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A Protein Aerogel with Distinctive Filtration Capabilities for Formaldehyde and Particulate Pollutants. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2023.123179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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4
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Ayinla ZA, Ademakinwa AN, Gross RA, Agboola FK. Biochemical and biophysical characterisation of a small purified lipase from Rhizopus oryzae ZAC3. BIOCATAL BIOTRANSFOR 2021. [DOI: 10.1080/10242422.2021.1883006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Zainab A. Ayinla
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Adedeji N. Ademakinwa
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Richard A. Gross
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Femi K. Agboola
- Department of Biochemistry and Molecular Biology, Obafemi Awolowo University, Ile-Ife, Nigeria
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5
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Giri A, Pant D. Carbonic anhydrase modification for carbon management. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:1294-1318. [PMID: 31797268 DOI: 10.1007/s11356-019-06667-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Carbonic anhydrase modification (chemical and biological) is an attractive strategy for its diverse application to accelerate the absorption of CO2 from a flue gas with improved activity and stability. This article reports various possibilities of CA modification using metal-ligand homologous chemistry, cross-linking agents, and residue- and group-specific and genetic modifications, and assesses their role in carbon management. Chemically modified carbonic anhydrase is able to improve the absorption of carbon dioxide from a gas stream into mediation compounds with enhanced sequestration and mineral formation. Genetically modified CA polypeptide can also increase carbon dioxide conversion. Chemical modification of CA can be categorized in terms of (i) residue-specific modification (involves protein-ligand interaction in terms of substitution/addition) and group-specific modifications (based on the functional groups of the target CA). For every sustainable change, there should be no/limited toxic or immunological response. In this review, several CA modification pathways and biocompatibility rules are proposed as a theoretical support for emerging research in this area.
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Affiliation(s)
- Anand Giri
- Department of Environmental Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Deepak Pant
- School of Chemical Sciences, Central University of Haryana, Mahendragarh, Haryana, 123029, India.
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Golghalyani V, Neupärtl M, Wittig I, Bahr U, Karas M. ArgC-Like Digestion: Complementary or Alternative to Tryptic Digestion? J Proteome Res 2017; 16:978-987. [DOI: 10.1021/acs.jproteome.6b00921] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Vahid Golghalyani
- Institute
of Pharmaceutical Chemistry, Goethe-University, Frankfurt am Main 60438, Germany
| | - Moritz Neupärtl
- Institute
of Pharmaceutical Chemistry, Goethe-University, Frankfurt am Main 60438, Germany
| | - Ilka Wittig
- Functional
Proteomics, Centre for Biochemistry, Medical School, Goethe-University, Frankfurt 60590, Germany
- Cluster
of Excellence “Macromolecular Complexes”, Goethe University, Frankfurt am Main 60438, Germany
- German
Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt 60590, Germany
| | - Ute Bahr
- Institute
of Pharmaceutical Chemistry, Goethe-University, Frankfurt am Main 60438, Germany
| | - Michael Karas
- Institute
of Pharmaceutical Chemistry, Goethe-University, Frankfurt am Main 60438, Germany
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Chen S, Zhang J, Jiang S, Lin G, Luo B, Yao H, Lin Y, He C, Liu G, Lin Z. Self-Assembled Superparamagnetic Iron Oxide Nanoclusters for Universal Cell Labeling and MRI. NANOSCALE RESEARCH LETTERS 2016; 11:263. [PMID: 27216601 PMCID: PMC4877342 DOI: 10.1186/s11671-016-1479-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/12/2016] [Indexed: 05/14/2023]
Abstract
Superparamagnetic iron oxide (SPIO) nanoparticles have been widely used in a variety of biomedical applications, especially as contrast agents for magnetic resonance imaging (MRI) and cell labeling. In this study, SPIO nanoparticles were stabilized with amphiphilic low molecular weight polyethylenimine (PEI) in an aqueous phase to form monodispersed nanocomposites with a controlled clustering structure. The iron-based nanoclusters with a size of 115.3 ± 40.23 nm showed excellent performance on cellular uptake and cell labeling in different types of cells, moreover, which could be tracked by MRI with high sensitivity. The SPIO nanoclusters presented negligible cytotoxicity in various types of cells as detected using MTS, LDH, and flow cytometry assays. Significantly, we found that ferritin protein played an essential role in protecting stress from SPIO nanoclusters. Taken together, the self-assembly of SPIO nanoclusters with good magnetic properties provides a safe and efficient method for universal cell labeling with noninvasive MRI monitoring capability.
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Affiliation(s)
- Shuzhen Chen
- Department of Microbiology and Immunology, Xiamen Medical College, Xiamen, 361008, China
| | - Jun Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
- Sichuan Key Laboratory of Medical Imaging, Affiliated Hospital of North Sichuan Medical College, North Sichuan Medical College, Nanchong, 637007, China
| | - Shengwei Jiang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Gan Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Bing Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Huan Yao
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Yuchun Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Chengyong He
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
| | - Gang Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China.
| | - Zhongning Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China.
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Deane CD, Burkhart BJ, Blair PM, Tietz JI, Lin A, Mitchell DA. In Vitro Biosynthesis and Substrate Tolerance of the Plantazolicin Family of Natural Products. ACS Chem Biol 2016; 11:2232-43. [PMID: 27248686 PMCID: PMC4992447 DOI: 10.1021/acschembio.6b00369] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Plantazolicin (PZN) is a ribosomally synthesized and post-translationally modified peptide (RiPP) natural product that exhibits extraordinarily narrow-spectrum antibacterial activity toward the causative agent of anthrax, Bacillus anthracis. During PZN biosynthesis, a cyclodehydratase catalyzes cyclization of cysteine, serine, and threonine residues in the PZN precursor peptide (BamA) to azolines. Subsequently, a dehydrogenase oxidizes most of these azolines to thiazoles and (methyl)oxazoles. The final biosynthetic steps consist of leader peptide removal and dimethylation of the nascent N-terminus. Using a heterologously expressed and purified heterocycle synthetase, the BamA peptide was processed in vitro concordant with the pattern of post-translational modification found in the naturally occurring compound. Using a suite of BamA-derived peptides, including amino acid substitutions as well as contracted and expanded substrate variants, the substrate tolerance of the heterocycle synthetase was elucidated in vitro, and the residues crucial for leader peptide binding were identified. Despite increased promiscuity compared to what was previously observed during heterologous production in E. coli, the synthetase retained exquisite selectivity in cyclization of unnatural peptides only at positions which correspond to those cyclized in the natural product. A cleavage site was subsequently introduced to facilitate leader peptide removal, yielding mature PZN variants after enzymatic or chemical dimethylation. In addition, we report the isolation and characterization of two novel PZN-like natural products that were predicted from genome sequences but whose production had not yet been observed.
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Affiliation(s)
- Caitlin D. Deane
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Brandon J. Burkhart
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Patricia M. Blair
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan I. Tietz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alice Lin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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9
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Frey BL, Ladror DT, Sondalle SB, Krusemark CJ, Jue AL, Coon JJ, Smith LM. Chemical derivatization of peptide carboxyl groups for highly efficient electron transfer dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1710-21. [PMID: 23918461 PMCID: PMC3827969 DOI: 10.1007/s13361-013-0701-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/01/2013] [Accepted: 07/06/2013] [Indexed: 05/11/2023]
Abstract
The carboxyl groups of tryptic peptides were derivatized with a tertiary or quaternary amine labeling reagent to generate more highly charged peptide ions that fragment efficiently by electron transfer dissociation (ETD). All peptide carboxyl groups-aspartic and glutamic acid side-chains as well as C-termini-were derivatized with an average reaction efficiency of 99 %. This nearly complete labeling avoids making complex peptide mixtures even more complex because of partially-labeled products, and it allows the use of static modifications during database searching. Alkyl tertiary amines were found to be the optimal labeling reagent among the four types tested. Charge states are substantially higher for derivatized peptides: a modified tryptic digest of bovine serum albumin (BSA) generates ~90% of its precursor ions with z > 2, compared with less than 40 % for the unmodified sample. The increased charge density of modified peptide ions yields highly efficient ETD fragmentation, leading to many additional peptide identifications and higher sequence coverage (e.g., 70 % for modified versus only 43 % for unmodified BSA). The utility of this labeling strategy was demonstrated on a tryptic digest of ribosomal proteins isolated from yeast cells. Peptide derivatization of this sample produced an increase in the number of identified proteins, a >50 % increase in the sequence coverage of these proteins, and a doubling of the number of peptide spectral matches. This carboxyl derivatization strategy greatly improves proteome coverage obtained from ETD-MS/MS of tryptic digests, and we anticipate that it will also enhance identification and localization of post-translational modifications.
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Affiliation(s)
- Brian L. Frey
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
| | - Daniel T. Ladror
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
| | - Samuel B. Sondalle
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
| | - Casey J. Krusemark
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
| | - April L. Jue
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin—Madison, 420 Henry Mall, Madison, WI 53706
- Genome Center of Wisconsin, University of Wisconsin—Madison, 425G Henry Mall, Madison, WI 53706
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, WI 53706
- Genome Center of Wisconsin, University of Wisconsin—Madison, 425G Henry Mall, Madison, WI 53706
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