1
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Gurard-Levin ZA, McMillan B, Whittington DA, Doyon B, Scholle MD, Ermolieff J, Bandi M, Liu MS, Amor A, Mallender WD. A duplexed high-throughput mass spectrometry assay for bifunctional POLB polymerase and lyase activity. SLAS Technol 2024; 29:100173. [PMID: 39094983 DOI: 10.1016/j.slast.2024.100173] [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: 06/15/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Polymerase β (POLB), with dual functionality as a lyase and polymerase, plays a critical role in the base excision repair (BER) pathway to maintain genomic stability. POLB knockout and rescue studies in BRCA1/2-mutant cancer cell lines revealed that inhibition of lyase and polymerase activity is required for the synthetic lethal interaction observed with PARP inhibitors, highlighting POLB as a valuable therapeutic target. Traditional biochemical assays to screen for enzyme inhibitors focus on a single substrate to product relationship and limit the comprehensive analysis of enzymes such as POLB that utilize multiple substrates or catalyze a multi-step reaction. This report describes the first high-throughput mass spectrometry-based screen to measure the two distinct biochemical activities of POLB in a single assay using a duplexed self-assembled monolayer desorption ionization (SAMDI) mass spectrometry methodology. A multiplexed assay for POLB dual enzymatic activities was developed optimizing for kinetically balanced conditions and a collection of 200,000 diverse small molecules was screened in the duplexed format. Small molecule modulators identified in the screen were confirmed in a traditional fluorescence-based polymerase strand-displacement assay and an orthogonal label-free binding assay using SAMDI affinity selection mass spectrometry (ASMS). This work demonstrates the flexibility of high-throughput mass spectrometry approaches in drug discovery and highlights a novel application of SAMDI technology that opens new avenues for multiplexed high-throughput screening.
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Affiliation(s)
| | - Brian McMillan
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA; Jnana Therapeutics. One Design Center Place, Suite 19-400, Boston, MA, 02210, USA
| | | | - Brian Doyon
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA
| | | | - Jacques Ermolieff
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA; DICE Therapeutics/Lilly, 400 E Jamie CT, Third Floor, South San Francisco, CA, 94080, USA
| | - Madhavi Bandi
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA
| | - Mu-Sen Liu
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA
| | - Alvaro Amor
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA
| | - William D Mallender
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA
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2
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Label-free duplex SAMDI-MS screen reveals novel SARS-CoV-2 3CLpro inhibitors. Antiviral Res 2022; 200:105279. [PMID: 35278580 PMCID: PMC8906060 DOI: 10.1016/j.antiviral.2022.105279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/01/2022] [Accepted: 03/06/2022] [Indexed: 11/20/2022]
Abstract
The 3-chymotrypsin-like cysteine protease (3CLpro) of severe acute respiratory syndrome conoravirus 2 (SARS-CoV-2) remains a promising therapeutic target to combat COVID-19. Our group recently described a novel duplexed biochemical assay that combines self-assembled monolayers of alkanethiolates on gold with matrix assisted laser desorption ionization (MALDI) time of flight (TOF) mass spectrometry (MS) to simultaneously measure 3CLpro and human rhinovirus 3C protease activities. This study describes applying the assay for the completion of a high-throughput duplexed screen of 300,000 diverse, drug-like small molecules in 3 days. The hits were confirmed and evaluated in dose response analyses against recombinant 3CLpro, HRV3C, and the human Cathepsin L proteases. The 3CLpro specific inhibitors were further assessed for activity in cellular cytotoxicity and anti-viral assays. Structure activity relationship studies informed on structural features required for activity and selectivity to 3CLpro over HRV3C. These results will guide the optimization of 3CLpro selective inhibitors to combat COVID-19 along with antiviral compounds against coronaviruses and rhinoviruses.
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3
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Mahajan AS, Stegh AH. Spherical Nucleic Acids as Precision Therapeutics for the Treatment of Cancer-From Bench to Bedside. Cancers (Basel) 2022; 14:cancers14071615. [PMID: 35406387 PMCID: PMC8996871 DOI: 10.3390/cancers14071615] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Spherical Nucleic Acids (SNAs) emerged as a new class of nanotherapeutics consisting of a nanoparticle core densely functionalized with a shell of radially oriented synthetic oligonucleotides. The unique three-dimensional architecture of SNAs protects the oligonucleotides from nuclease-mediated degradation, increases oligonucleotide bioavailability, and in the absence of auxiliary transfection agents, enables robust uptake into tumor and immune cells through polyvalent association with cell surface pattern recognition receptors. When composed of gene-regulatory small interfering (si)RNA or immunostimulatory DNA or RNA oligonucleotides, SNAs silence gene expression and induce immune responses superior to those raised by the oligonucleotides in their "free" form. Early phase clinical trials of gene-regulatory siRNA-based SNAs in glioblastoma (NCT03020017) and immunostimulatory Toll-like receptor 9 (TLR9)-agonistic SNAs carrying unmethylated CpG-rich oligonucleotides in solid tumors (NCT03086278) have shown that SNAs represent a safe, brain-penetrant therapy for inhibiting oncogene expression and stimulating immune responses against tumors. This review focuses on the application of SNAs as precision cancer therapeutics, summarizes the findings from first-in-human clinical trials of SNAs in solid tumors, describes the most recent preclinical efforts to rationally design next-generation multimodal SNA architectures, and provides an outlook on future efforts to maximize the anti-neoplastic activity of the SNA platform.
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Affiliation(s)
- Akanksha S. Mahajan
- Ken and Ruth Davee Department of Neurology, The International Institute for Nanotechnology, The Malnati Brain Tumor Institute, Feinberg School of Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA;
| | - Alexander H. Stegh
- Ken and Ruth Davee Department of Neurology, The International Institute for Nanotechnology, The Malnati Brain Tumor Institute, Feinberg School of Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA;
- Department of Neurological Surgery, The Brain Tumor Center, Washington University School of Medicine, Alvin J. Siteman Comprehensive Cancer Center, St. Louis, MO 63110, USA
- Correspondence:
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4
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Kim J, Kim N, Kim S, Kim Y, Yeo W. Immobilization of phenol‐containing compounds via electrochemical activation of a urazole derivative. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jisu Kim
- Department of Bioscience and Biotechnology Bio/Molecular Informatics Center Konkuk University Seoul South Korea
| | - Noo‐ri Kim
- Department of Bioscience and Biotechnology Bio/Molecular Informatics Center Konkuk University Seoul South Korea
| | - Seung‐Woo Kim
- Department of Chemistry Dongguk University‐Seoul Campus Seoul South Korea
| | - Young‐Kwan Kim
- Department of Chemistry Dongguk University‐Seoul Campus Seoul South Korea
| | - Woon‐Seok Yeo
- Department of Bioscience and Biotechnology Bio/Molecular Informatics Center Konkuk University Seoul South Korea
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5
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Scholle MD, Liu C, Deval J, Gurard-Levin ZA. Label-Free Screening of SARS-CoV-2 NSP14 Exonuclease Activity Using SAMDI Mass Spectrometry. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:766-774. [PMID: 33870746 PMCID: PMC8053483 DOI: 10.1177/24725552211008854] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the global COVID-19 pandemic. Nonstructural protein 14 (NSP14), which features exonuclease (ExoN) and guanine N7 methyltransferase activity, is a critical player in SARS-CoV-2 replication and fidelity and represents an attractive antiviral target. Initiating drug discovery efforts for nucleases such as NSP14 remains a challenge due to a lack of suitable high-throughput assay methodologies. This report describes the combination of self-assembled monolayers and matrix-assisted laser desorption ionization mass spectrometry to enable the first label-free and high-throughput assay for NSP14 ExoN activity. The assay was used to measure NSP14 activity and gain insight into substrate specificity and the reaction mechanism. Next, the assay was optimized for kinetically balanced conditions and miniaturized, while achieving a robust assay (Z factor > 0.8) and a significant assay window (signal-to-background ratio > 200). Screening 10,240 small molecules from a diverse library revealed candidate inhibitors, which were counterscreened for NSP14 selectivity and RNA intercalation. The assay methodology described here will enable, for the first time, a label-free and high-throughput assay for NSP14 ExoN activity to accelerate drug discovery efforts and, due to the assay flexibility, can be more broadly applicable for measuring other enzyme activities from other viruses or implicated in various pathologies.
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Affiliation(s)
| | - Cheng Liu
- Aligos Therapeutics, Inc., South San Francisco, CA, USA
| | - Jerome Deval
- Aligos Therapeutics, Inc., South San Francisco, CA, USA
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6
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Scholle MD, Gurard-Levin ZA. Development of a Novel Label-Free and High-Throughput Arginase-1 Assay Using Self-Assembled Monolayer Desorption Ionization Mass Spectrometry. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:775-782. [PMID: 33754845 DOI: 10.1177/24725552211000677] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Arginase-1, an enzyme that catalyzes the reaction of L-arginine to L-ornithine, is implicated in the tumor immune response and represents an interesting therapeutic target in immuno-oncology. Initiating arginase drug discovery efforts remains a challenge due to a lack of suitable high-throughput assay methodologies. This report describes the combination of self-assembled monolayers and matrix-assisted laser desorption ionization mass spectrometry to enable the first label-free and high-throughput assay for arginase activity. The assay was optimized for kinetically balanced conditions and miniaturized, while achieving a robust assay (Z-factor > 0.8) and a significant assay window [signal-to-background ratio > 20] relative to fluorescent approaches. To validate the assay, the inhibition of the reference compound nor-NOHA (Nω-hydroxy-nor-L-arginine) was evaluated, and the IC50 measured to be in line with reported results (IC50 = 180 nM). The assay was then used to complete a screen of 175,000 compounds, demonstrating the high-throughput capacity of the approach. The label-free format also eliminates opportunities for false-positive results due to interference from library compounds and optical readouts. The assay methodology described here enables new opportunities for drug discovery for arginase and, due to the assay flexibility, can be more broadly applicable for measuring other amino acid-metabolizing enzymes.
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7
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Anderson SE, Longbotham JE, O'Kane PT, Ugur FS, Fujimori DG, Mrksich M. Exploring the Ligand Preferences of the PHD1 Domain of Histone Demethylase KDM5A Reveals Tolerance for Modifications of the Q5 Residue of Histone 3. ACS Chem Biol 2021; 16:205-213. [PMID: 33314922 PMCID: PMC8168426 DOI: 10.1021/acschembio.0c00891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding the ligand preferences of epigenetic reader domains enables identification of modification states of chromatin with which these domains associate and can yield insight into recruitment and catalysis of chromatin-acting complexes. However, thorough exploration of the ligand preferences of reader domains is hindered by the limitations of traditional protein-ligand binding assays. Here, we evaluate the binding preferences of the PHD1 domain of histone demethylase KDM5A using the protein interaction by SAMDI (PI-SAMDI) assay, which measures protein-ligand binding in a high-throughput and sensitive manner via binding-induced enhancement in the activity of a reporter enzyme, in combination with fluorescence polarization. The PI-SAMDI assay was validated by confirming its ability to accurately profile the relative binding affinity of a set of well-characterized histone 3 (H3) ligands of PHD1. The assay was then used to assess the affinity of PHD1 for 361 H3 mutant ligands, a select number of which were further characterized by fluorescence polarization. Together, these experiments revealed PHD1's tolerance for H3Q5 mutations, including an unexpected tolerance for aromatic residues in this position. Motivated by this finding, we further demonstrate a high-affinity interaction between PHD1 and recently identified Q5-serotonylated H3. This work yields interesting insights into permissible PHD1-H3 interactions and demonstrates the value of interfacing PI-SAMDI and fluorescence polarization in investigations of protein-ligand binding.
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Affiliation(s)
- Sarah E Anderson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Patrick T O'Kane
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, California 94158, United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Cell and Developmental Biology, Northwestern University, Evanston, Illinois 60208, United States
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8
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Yoo J, Kang H, Kim MK, Chong Y, Bae SW, Yeo W. Tetrahydrofuran Highly Enhances
SAMDI
Efficiency. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jin Yoo
- Department of Bioscience and Biotechnology Konkuk University Seoul 143‐701 South Korea
| | - Hyunook Kang
- Department of Bioscience and Biotechnology Konkuk University Seoul 143‐701 South Korea
| | - Mi Kyoung Kim
- Department of Bioscience and Biotechnology Konkuk University Seoul 143‐701 South Korea
| | - Youhoon Chong
- Department of Bioscience and Biotechnology Konkuk University Seoul 143‐701 South Korea
| | - Se Won Bae
- Department of Chemistry and Cosmetics Jeju National University Jeju 63243 South Korea
| | - Woon‐Seok Yeo
- Department of Bioscience and Biotechnology Konkuk University Seoul 143‐701 South Korea
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9
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Pluchinsky AJ, Wackelin DJ, Huang X, Arnold FH, Mrksich M. High Throughput Screening with SAMDI Mass Spectrometry for Directed Evolution. J Am Chem Soc 2020; 142:19804-19808. [PMID: 33174742 DOI: 10.1021/jacs.0c07828] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Advances in directed evolution have led to an exploration of new and important chemical transformations; however, many of these efforts still rely on the use of low-throughput chromatography-based screening methods. We present a high-throughput strategy for screening libraries of enzyme variants for improved activity. Unpurified reaction products are immobilized to a self-assembled monolayer and analyzed by mass spectrometry, allowing for direct evaluation of thousands of variants in under an hour. The method was demonstrated with libraries of randomly mutated cytochrome P411 variants to identify improved catalysts for C-H alkylation. The technique may be tailored to evolve enzymatic activity for a variety of transformations where higher throughput is needed.
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Affiliation(s)
| | - Daniel J Wackelin
- Division of Chemistry and Chemical Engineering MC 210-41, California Institute of Technology, Pasadena, California 91125, United States
| | - Xiongyi Huang
- Division of Chemistry and Chemical Engineering MC 210-41, California Institute of Technology, Pasadena, California 91125, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering MC 210-41, California Institute of Technology, Pasadena, California 91125, United States
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10
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Anderson SE, Fahey NS, Park J, O'Kane PT, Mirkin CA, Mrksich M. A high-throughput SAMDI-mass spectrometry assay for isocitrate dehydrogenase 1. Analyst 2020; 145:3899-3908. [PMID: 32297889 PMCID: PMC7440924 DOI: 10.1039/d0an00174k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The enzyme isocitrate dehydrogenase 1 (IDH1) catalyzes the conversion of isocitrate to alpha-ketoglutarate (αKG) and has emerged as an important therapeutic target for glioblastoma multiforme (GBM). Current methods for assaying IDH1 remain poorly suited for high-throughput screening of IDH1 antagonists. This paper describes a high-throughput and quantitative assay for IDH1 that is based on the self-assembled monolayers for matrix-assisted laser desorption/ionization-mass spectrometry (SAMDI-MS) method. The assay uses a self-assembled monolayer presenting a hydrazide group that covalently captures the αKG product of IDH1, where it can then be detected by MALDI-TOF mass spectrometry. Co-capture of an isotopically-labeled αKG internal standard allows the αKG concentration to be quantitated. The assay was used to analyze a series of standard αKG solutions and produced minimal error in measured αKG concentration values. The suitability of the assay for high-throughput analysis was evaluated in a 384-sample biochemical IDH1 screen. Cells expressing IDH1 were lysed and the lysate was applied to the monolayer to capture αKG, which was then quantitated using the SAMDI-MS assay. Cells in which IDH1 expression was reduced by small-interfering RNA exhibited a corresponding decrease in αKG concentration as measured by the assay. Application of the assay toward the high-throughput screening of IDH1 inhibitors or knockdown agents may facilitate the discovery of treatments for GBM.
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Affiliation(s)
- Sarah E Anderson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA.
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11
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Szymczak LC, Sykora DJ, Mrksich M. Using Peptide Arrays to Profile Phosphatase Activity in Cell Lysates. Chemistry 2020; 26:165-170. [PMID: 31691395 DOI: 10.1002/chem.201904364] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/31/2019] [Indexed: 12/30/2022]
Abstract
Phosphorylation is an important post-translational modification on proteins involved in many cellular processes; however, understanding of the regulation and mechanisms of global phosphorylation remains limited. Herein, we utilize self-assembled monolayers on gold for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) with three phosphorylated peptide arrays to profile global phosphatase activity in cell lysates derived from five mammalian cell lines. Our results reveal significant differences in the activities of protein phosphatases on phospho- serine, threonine, and tyrosine substrates and suggest that phosphatases play a much larger role in the regulation of global phosphorylation on proteins than previously understood.
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Affiliation(s)
- Lindsey C Szymczak
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Daniel J Sykora
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
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12
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Yu G, Yeo WS. Mass spectrometric analysis of acid-assisted photochemical release of the trimethyl lock system on the monolayers on gold. RSC Adv 2020; 10:17914-17917. [PMID: 35515585 PMCID: PMC9053594 DOI: 10.1039/d0ra02110e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/03/2020] [Indexed: 11/24/2022] Open
Abstract
We report the acid-assisted photolysis of the trimethyl lock system which has long been harnessed for a variety of applications such as drug delivery, cellular imaging, enzyme activity assays, and surface patterning. By mass spectrometric analysis, we found that photoinduced intramolecular cyclization and the ensuing release of the pendant groups of the trimethyl lock on the self-assembled monolayers proceeded cleanly in the presence of HCl, to give a high yield. The acid-assisted photolysis of the trimethyl lock on the surface was characterized by mass spectrometry.![]()
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Affiliation(s)
- Geunhyeok Yu
- Department of Bioscience and Biotechnology
- Bio/Molecular Informatics Center
- Konkuk University
- Seoul 05029
- Korea
| | - Woon-Seok Yeo
- Department of Bioscience and Biotechnology
- Bio/Molecular Informatics Center
- Konkuk University
- Seoul 05029
- Korea
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13
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Buker SM, Gurard-Levin ZA, Wheeler BD, Scholle MD, Case AW, Hirsch JL, Ribich S, Copeland RA, Boriack-Sjodin PA. A Mass Spectrometric Assay of METTL3/METTL14 Methyltransferase Activity. SLAS DISCOVERY 2019; 25:361-371. [PMID: 31585521 DOI: 10.1177/2472555219878408] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A variety of covalent modifications of RNA have been identified and demonstrated to affect RNA processing, stability, and translation. Methylation of adenosine at the N6 position (m6A) in messenger RNA (mRNA) is currently the most well-studied RNA modification and is catalyzed by the RNA methyltransferase complex METTL3/METTL14. Once generated, m6A can modulate mRNA splicing, export, localization, degradation, and translation. Although potent and selective inhibitors exist for several members of the Type I S-adenosylmethionine (SAM)-dependent methyltransferase family, no inhibitors have been reported for METTL3/METTL14 to date. To facilitate drug discovery efforts, a sensitive and robust mass spectrometry-based assay for METTL3/METTL14 using self-assembled monolayer desorption/ionization (SAMDI) technology has been developed. The assay uses an 11-nucleotide single-stranded RNA compared to a previously reported 27-nucleotide substrate. IC50 values of mechanism-based inhibitors S-adenosylhomocysteine (SAH) and sinefungin (SFG) are comparable between the SAMDI and radiometric assays that use the same substrate. This work demonstrates that SAMDI technology is amenable to RNA substrates and can be used for high-throughput screening and compound characterization for RNA-modifying enzymes.
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Affiliation(s)
| | | | - Benjamin D Wheeler
- Confluence Discovery Technologies, St. Louis, MO, USA.,Biomedical Science Program, University of California, San Francisco, CA, USA
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14
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Hanley L, Wickramasinghe R, Yung YP. Laser Desorption Combined with Laser Postionization for Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:225-245. [PMID: 30786215 DOI: 10.1146/annurev-anchem-061318-115447] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Lasers with pulse lengths from nanoseconds to femtoseconds and wavelengths from the mid-infrared to extreme ultraviolet (UV) have been used for desorption or ablation in mass spectrometry. Such laser sampling can often benefit from the addition of a second laser for postionization of neutrals. The advantages offered by laser postionization include the ability to forego matrix application, high lateral resolution, decoupling of ionization from desorption, improved analysis of electrically insulating samples, and potential for high sensitivity and depth profiling while minimizing differential detection. A description of postionization by vacuum UV radiation is followed by a consideration of multiphoton, short pulse, and other postionization strategies. The impacts of laser pulse length and wavelength are considered for laser desorption or laser ablation at low pressures. Atomic and molecular analysis via direct laser desorption/ionization using near-infrared ultrashort pulses is described. Finally, the postionization of clusters, the role of gaseous collisions, sampling at ambient pressure, atmospheric pressure photoionization, and the addition of UV postionization to MALDI are considered.
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Affiliation(s)
- Luke Hanley
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA;
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15
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O’Kane PT, Dudley QM, McMillan AK, Jewett MC, Mrksich M. High-throughput mapping of CoA metabolites by SAMDI-MS to optimize the cell-free biosynthesis of HMG-CoA. SCIENCE ADVANCES 2019; 5:eaaw9180. [PMID: 31183410 PMCID: PMC6551189 DOI: 10.1126/sciadv.aaw9180] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/02/2019] [Indexed: 05/30/2023]
Abstract
Metabolic engineering uses enzymes to produce small molecules with industrial, pharmaceutical, and energy applications. However, efforts to optimize enzymatic pathways for commercial production are limited by the throughput of assays for quantifying metabolic intermediates and end products. We developed a multiplexed method for profiling CoA-dependent pathways that uses a cysteine-terminated peptide to covalently capture CoA-bound metabolites. Captured metabolites are then rapidly separated from the complex mixture by immobilization onto arrays of self-assembled monolayers and directly quantified by SAMDI mass spectrometry. We demonstrate the throughput of the assay by characterizing the cell-free synthesis of HMG-CoA, a key intermediate in the biosynthesis of isoprenoids, collecting over 10,000 individual spectra to map more than 800 unique reaction conditions. We anticipate that our rapid and robust analytical method will accelerate efforts to engineer metabolic pathways.
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Affiliation(s)
- Patrick T. O’Kane
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Quentin M. Dudley
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Aislinn K. McMillan
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Michael C. Jewett
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Milan Mrksich
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
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16
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Szymczak LC, Mrksich M. Using Peptide Arrays To Discover the Sequence-Specific Acetylation of the Histidine-Tyrosine Dyad. Biochemistry 2019; 58:1810-1817. [PMID: 30817132 DOI: 10.1021/acs.biochem.9b00022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reactions that can selectively modify amino acid sequences within peptides and proteins are important for preparing protein reagents, immobilizing proteins, and making antibody-drug conjugates. The development of new reactions often begins with known chemistries and optimizes yields using a small set of peptide reactants. This article describes the use of peptide arrays and self-assembled monolayers for matrix-assisted laser desorption/ionization mass spectrometry (SAMDI-MS) to discover and characterize unanticipated sequence-selective reactions of peptides. This work reports the selective acetylation of HY (histidine-tyrosine) and YH (tyrosine-histidine) dyads when treated with acetic anhydride in aqueous conditions. More broadly, this example illustrates the benefits of using peptide arrays and a label-free analysis method to discover peptide-modifying reactions and gain mechanistic insight into their sequence specificity.
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Affiliation(s)
- Lindsey C Szymczak
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Milan Mrksich
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States.,Department of Biomedical Engineering , Northwestern University , Evanston , Illinois 60208 , United States
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17
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Kang H, Jung W, Yeo WS. Facile Preparation of Functional Group Gradient Surfaces by Desorption and Re
-Adsorption of Alkanethiols on Gold. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hyunook Kang
- Department of Bioscience and Biotechnology; Bio/Molecular Informatics Center, Konkuk University; Seoul 05029 South Korea
| | - Woong Jung
- Department of Emergency Medicine; Kyung Hee University Hospital at Kangdong; Seoul 05278 South Korea
| | - Woon-Seok Yeo
- Department of Bioscience and Biotechnology; Bio/Molecular Informatics Center, Konkuk University; Seoul 05029 South Korea
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18
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Hwang HJ, Choi I, Kim YJ, Kim YK, Yeo WS. Immobilization of phenol-containing molecules on self-assembled monolayers on gold via surface chemistry. Colloids Surf B Biointerfaces 2018; 173:164-170. [PMID: 30292024 DOI: 10.1016/j.colsurfb.2018.09.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 11/28/2022]
Abstract
Various phenol-containing molecules such as flavonoids have a wide range of biological effects including anticancer, antimicrobial, and anti-inflammatory properties, and, therefore, they have become subjects of active research for various medicinal and biological applications. To construct applicable materials incorporated with phenol-containing molecules, strategies for immobilization of phenol-containing molecules on solid substrates are required. Although several immobilization methods have been devised and reported, mostly harnessing phenol functionality, however, development of a general immobilization method has been hampered due to its complicated chemical reactions and low reaction yields on surfaces. Furthermore, the use of phenol as a reaction center may compromise the biological activity of phenol-containing molecules. Here, we describe a simple, fast, and reliable method for the surface immobilization of phenol-containing molecules by introducing chemical functional groups, carboxylic acid, thiol, and azide, while maintaining phenol functionality by way of the Mannich-type condensation reaction. We examined the chemical functionalization of naphthol, tyrosine, and flavanone and their immobilization to the self-assembled monolayers on gold via various surface chemistries: the carbodiimide coupling reaction, Michael addition, and the 'click' reaction. We strongly believe our method can be a general and practical platform for immobilization of various phenol-containing molecules on surfaces of various materials.
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Affiliation(s)
- Hye-Jeong Hwang
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Inseong Choi
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, 143-701, Republic of Korea
| | - Young-Jin Kim
- Carbon Composite Materials Research Center, Institute of Advanced Composite Materials, Korea Institute of Science and Technology, Wanju-gun, Jeollabuk-do, 565-905, Republic of Korea
| | - Young-Kwan Kim
- Carbon Composite Materials Research Center, Institute of Advanced Composite Materials, Korea Institute of Science and Technology, Wanju-gun, Jeollabuk-do, 565-905, Republic of Korea.
| | - Woon-Seok Yeo
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, 143-701, Republic of Korea.
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19
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Choi I, Lee J, Kim W, Kang H, Bae SW, Chang R, Kim S, Yeo WS. On-Demand Modulation of Bacterial Cell Fates on Multifunctional Dynamic Substrates. ACS APPLIED MATERIALS & INTERFACES 2018; 10:4324-4332. [PMID: 29318876 DOI: 10.1021/acsami.7b18132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This paper reports unprecedented dynamic surfaces based on zwitterionic low-density self-assembled monolayers (LDSAMs) of alkanethiolates on gold, which integrate three interconvertible states-bacteria-adherable, bactericidal, and nonfouling states-through electrical modulations. The conformations of alkanethiolates were electrically modulated to generate zwitterionic, anionic, and cationic surfaces, which responded differently to bacteria and determined the fate of bacteria. Furthermore, the reversible switching of multifunctions of the surface was realized for killing bacteria and subsequently releasing dead bacteria from the surface. For practical application of our strategy, we examined the selective antibacterial effect of our surface for eradication of mycoplasma contaminants in contaminated mammalian cell cultures.
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Affiliation(s)
| | | | - Wontae Kim
- Department of Chemistry, Kwangwoon University , Seoul 139-741, Republic of Korea
| | | | - Se Won Bae
- Green Materials and Process Group, Research Institute of Sustainable Manufacturing System, Korea Institute of Industrial Technology , Cheonan 31056, Korea
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University , Seoul 139-741, Republic of Korea
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20
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Yoo M, Yeo WS. Determining the Ratio of Two Types of Prostate Specific Antigens with Biochips and Gold Nanoparticles for Accurate Prostate Cancer Diagnosis. ANAL SCI 2018; 32:1117-1121. [PMID: 27725614 DOI: 10.2116/analsci.32.1117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Prostate-specific antigen (PSA) is a well-known biomarker for prostate-cancer diagnosis. However, the serum PSA measurement alone is insufficient for accurate diagnoses because the correlation with cancer is weak within the gray zone-the biomarker level range wherein a clear-cut diagnosis is impossible. As such, accurate prostate cancer diagnosis has been supplemented by measurements of the ratio of two types of PSA: free PSA (fPSA) and complexed PSA (cPSA; α-1-antichymotrypsin-bound PSA). Herein, we describe a new method for measuring the ratio of these two types of PSA by using gold nanoparticles (AuNPs) and biochips. Both types of PSA in a sample are captured by the antibody immobilized on a biochip based on self-assembled monolayers on gold. fPSA and cPSA on the biochip are then distinguished by AuNPs that present antibodies against fPSA and cPSA, respectively. The presence of PSAs in a sample is detected with laser desorption/ionization time-of-flight mass spectrometry by observing reporter molecules, called amplification tags (Am-tags), on the AuNPs. One of the reporter molecules is an Am-tag without isotope labeling, and the other is a deuterium-labeled Am-tag (dAm-tag). These tags amplify mass signals so as to enhance the sensitivity of the method. A comparison of the mass intensities between the Am-tag and dAm-tag signals allows the determination of the ratio between fPSA and cPSA. We validated the selective measurement of fPSA and cPSA at different ratios in 50, 75, and 100 pM of total PSA (fPSA + cPSA) solutions corresponding to the gray zone in prostate-cancer diagnosis (4 - 10 ng/mL). Finally, the two types of PSA were spiked in fetal bovine serum at various ratios, and our strategy greatly afforded their accurate ratios as spiked based on a constructed calibration curve. These results clearly indicate that the strategy is applicable to human serum as a diagnostic and prognostic assay for prostate cancer.
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Affiliation(s)
- Minyoung Yoo
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University
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21
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Affiliation(s)
- Lindsey C. Szymczak
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Hsin-Yu Kuo
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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22
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Soares J, Iwaki LEO, Soares AC, Rodrigues VC, Melendez ME, Fregnani JHG, Reis RM, Carvalho AL, Corrêa DS, Oliveira ON. Immunosensor for Pancreatic Cancer Based on Electrospun Nanofibers Coated with Carbon Nanotubes or Gold Nanoparticles. ACS OMEGA 2017; 2:6975-6983. [PMID: 30023536 PMCID: PMC6044935 DOI: 10.1021/acsomega.7b01029] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/05/2017] [Indexed: 05/15/2023]
Abstract
We report the fabrication of immunosensors based on nanostructured mats of electrospun nanofibers of polyamide 6 and poly(allylamine hydrochloride) coated either with multiwalled carbon nanotubes (MWCNTs) or gold nanoparticles (AuNPs), whose three-dimensional structure was suitable for the immobilization of anti-CA19-9 antibodies to detect the pancreatic cancer biomarker CA19-9. Using impedance spectroscopy, the sensing platform was able to detect CA19-9 with a detection limit of 1.84 and 1.57 U mL-1 for the nanostructured architectures containing MWCNTs and AuNPs, respectively. The high sensitivity achieved can be attributed to the irreversible adsorption between antibodies and antigens, as confirmed with polarization-modulated infrared reflection absorption spectroscopy. The adsorption mechanism was typical Langmuir-Freundlich processes. The high sensitivity and selectivity of the immunosensors were also explored in tests with blood serum from patients with distinct concentrations of CA19-9, for which the impedance spectra data were processed with a multidimensional projection technique. The robustness of the immunosensors in dealing with patient samples without suffering interference from analytes present in biological fluids is promising for a simple, effective diagnosis of pancreatic cancer at early stages.
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Affiliation(s)
- Juliana
C. Soares
- São
Carlos Institute of Physics, University
of São Paulo, 13560-60 São Carlos, Brazil
| | - Leonardo E. O. Iwaki
- São
Carlos Institute of Physics, University
of São Paulo, 13560-60 São Carlos, Brazil
- Department
of Materials Engineering, São Carlos School of Engineering, University of São Paulo, 13563-120 São Carlos, Brazil
| | - Andrey C. Soares
- São
Carlos Institute of Physics, University
of São Paulo, 13560-60 São Carlos, Brazil
- Department
of Materials Engineering, São Carlos School of Engineering, University of São Paulo, 13563-120 São Carlos, Brazil
| | | | - Matias E. Melendez
- Molecular
Oncology Research Center, Barretos Cancer
Hospital, 14784-400 Barretos, Brazil
| | | | - Rui M. Reis
- Molecular
Oncology Research Center, Barretos Cancer
Hospital, 14784-400 Barretos, Brazil
- ICVS/3B’s-PT
Government Associate Laboratory, Life and Health Sciences Research
Institute (ICVS), University of Minho, 4710-057 Braga, Portugal
| | - Andre L. Carvalho
- Molecular
Oncology Research Center, Barretos Cancer
Hospital, 14784-400 Barretos, Brazil
| | - Daniel S. Corrêa
- Nanotechnology
National Laboratory for Agriculture (LNNA), Embrapa Instrumentação, 13560-970 São Carlos, Brazil
| | - Osvaldo N. Oliveira
- São
Carlos Institute of Physics, University
of São Paulo, 13560-60 São Carlos, Brazil
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23
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Cabezas M, Mirkin CA, Mrksich M. Nanopatterned Extracellular Matrices Enable Cell-Based Assays with a Mass Spectrometric Readout. NANO LETTERS 2017; 17:1373-1377. [PMID: 28120616 PMCID: PMC5501326 DOI: 10.1021/acs.nanolett.6b04176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 01/24/2017] [Indexed: 05/27/2023]
Abstract
Cell-based assays are finding wider use in evaluating compounds in primary screens for drug development, yet it is still challenging to measure enzymatic activities as an end point in a cell-based assay. This paper reports a strategy that combines state-of-the-art cantilever free polymer pen lithography (PPL) with self-assembled monolayer laser desorption-ionization (SAMDI) mass spectrometry to guide cell localization and measure cellular enzymatic activities. Experiments are conducted with a 384 spot array, in which each spot is composed of ∼400 nanoarrays and each array has a 10 × 10 arrangement of 750 nm features that present extracellular matrix (ECM) proteins surrounded by an immobilized phosphopeptide. Cells attach to the individual nanoarrays, where they can be cultured and treated with small molecules, after which the media is removed and the cells are lysed. Phosphatase enzymes in the proximal lysate can then act on the immobilized phosphopeptide substrate to convert it to the dephosphorylated form. After the lysate is removed, the array is analyzed by SAMDI mass spectrometry to identify the extent of dephosphorylation and, therefore, the amount of enzyme activity in the cell. This novel approach of using nanopatterning to mediate cell adhesion and SAMDI to record enzyme activities in the proximal lysate will enable a broad range of cellular assays for applications in drug discovery and research not possible with conventional strategies.
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Affiliation(s)
- Maria
D. Cabezas
- Department of Chemistry and International Institute for Nanotechnology and Department of Biomedical
Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Chad A. Mirkin
- Department of Chemistry and International Institute for Nanotechnology and Department of Biomedical
Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department of Chemistry and International Institute for Nanotechnology and Department of Biomedical
Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department
of Cell and Molecular Biology, Feinberg
School of Medicine, 303
East Chicago Avenue, Chicago, Illinois 60611, United
States
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24
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Choi I, Kim DE, Ahn JH, Yeo WS. On-chip enzymatic assay for chloramphenicol acetyltransferase using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Colloids Surf B Biointerfaces 2015; 136:465-9. [PMID: 26448379 DOI: 10.1016/j.colsurfb.2015.09.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/13/2015] [Accepted: 09/26/2015] [Indexed: 10/23/2022]
Abstract
Herein, we report a chloramphenicol (CAP) acetyltransferase (CAT) activity assay based on self-assembled monolayers on gold as an alternative to conventional CAT reporter gene assay systems, which sometimes require toxic materials and complicated steps that limit their use. A CAP derivative presented on a monolayer was converted to the acetylated CAP by CAT in the presence of acetyl-CoA. The conversion was directly monitored by observing the molecular weight changes in CAP using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. CAT activity was determined under various reaction conditions by changing reaction times, CAT and acetyl-CoA concentrations. As a practical application, we identified gene expression in bacteria that were transformed with pCAT plasmid DNA. Our strategy can provide a simple and rapid assay that eliminates some commonly used but potentially detrimental steps in enzymatic assays, such as radioactive labeling and complicated separation and purification of analytes prior to detection.
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Affiliation(s)
- Inseong Choi
- Department of Bioscience and Biotechnology, Konkuk University, Republic of Korea; Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Republic of Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Republic of Korea
| | - Joong-Hoon Ahn
- Department of Bioscience and Biotechnology, Konkuk University, Republic of Korea; Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Republic of Korea
| | - Woon-Seok Yeo
- Department of Bioscience and Biotechnology, Konkuk University, Republic of Korea; Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Republic of Korea.
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25
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Kim S, Nam J, Yeo WS. A Method for Generation and Characterization of Orthogonal Three-Component Gradient Surfaces. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Sehee Kim
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center; Konkuk University; Seoul 143-701 Korea
| | - Jungchan Nam
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center; Konkuk University; Seoul 143-701 Korea
| | - Woon-Seok Yeo
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center; Konkuk University; Seoul 143-701 Korea
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26
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Soares JC, Shimizu FM, Soares AC, Caseli L, Ferreira J, Oliveira ON. Supramolecular Control in Nanostructured Film Architectures for Detecting Breast Cancer. ACS APPLIED MATERIALS & INTERFACES 2015; 7:11833-41. [PMID: 25989820 DOI: 10.1021/acsami.5b03761] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The need for early detection of various diseases, including breast cancer, has motivated research into nanomaterials that can be assembled in organized films which serve as biosensors. Owing to the variety of possible materials and film architectures, procedures are required to design optimized biosensors. In this study, we combine surface-specific methods to monitor the assembly of antibodies on nanostructured films with two distinct architectures. In the first, a layer of the antibody type mouse anti-HER2 (clone tab250) was immobilized on a self-assembled monolayer (SAM) of 11-mercaptoundecanoic acid modified with N-hydroxysuccinimide (NHS) and 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide (EDC). In the second approach, a SAM of cysteamine was coated with a biotin/spreptavidin bilayer on which a layer of biotinylated antibody type MSx2HUp185/her biotin was adsorbed. The rougher, less passivating coating with cysteamine determined from cyclic voltammetry and scanning electron microscopy led to biosensors that are more sensitive to detect the breast cancer ERBB2 (HER2) biomarker in impedance spectroscopy measurements. This higher distinguishing ability of the cysteamine-containing film architecture was proven with information visualization methods to treat the impedance data. Polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS) confirmed that biosensing resulted from the antibody-ERBB2 antigen affinity.
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Affiliation(s)
- Juliana Coatrini Soares
- †São Carlos Institute of Physics, University of São Paulo, 369, 13560-970 São Carlos, São Paulo, Brazil
| | - Flavio Makoto Shimizu
- †São Carlos Institute of Physics, University of São Paulo, 369, 13560-970 São Carlos, São Paulo, Brazil
| | - Andrey Coatrini Soares
- †São Carlos Institute of Physics, University of São Paulo, 369, 13560-970 São Carlos, São Paulo, Brazil
| | - Luciano Caseli
- ‡Institute of Environmental, Chemical and Pharmaceutical Sciences, Federal University of Sao Paulo, 09972-970 Diadema, São Paulo, Brazil
| | - Jacqueline Ferreira
- §Institute of Chemistry, Federal University of Rio Grande do Sul, 15003, 91501-970 Porto Alegre, Rio Grande do Sul, Brazil
| | - Osvaldo N Oliveira
- †São Carlos Institute of Physics, University of São Paulo, 369, 13560-970 São Carlos, São Paulo, Brazil
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27
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Kim S, Oh H, Yeo WS. Analysis of alkanethiolates on gold with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/s13765-015-0018-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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28
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Zoueshtiagh F, Baudoin M, Guerrin D. Capillary tube wetting induced by particles: towards armoured bubbles tailoring. SOFT MATTER 2014; 10:9403-9412. [PMID: 25271805 DOI: 10.1039/c4sm01648c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this paper, we report on the strongly modified dynamics of a liquid finger pushed inside a capillary tube, when partially wettable particles are lying on the walls. Particles promote the appearance of new regimes and enable the tailored synthesis of bubbles encapsulated in a monolayer of particles (so-called "armoured bubbles"). This remarkable behavior arises due to the collection of particles at the air-liquid interface, which modify the global energy balance and stabilize the interface. Armoured-bubbles are of primary interest in industrial processes since they display increased stability, interfacial rigidity and can even sustain non-spherical shapes. This work opens perspective for a low cost bubbles-on-demand technology enabling the synthesis of armoured bubbles with specific sizes, shapes and composition.
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Affiliation(s)
- Farzam Zoueshtiagh
- International Laboratory LEMAC/LICS, IEMN, UMR CNRS 8520, Université Lille 1, Avenue Poincaré, 59652 Villeneuve d'Ascq, France.
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29
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AbouElfetouh A, Kuhn ML, Hu LI, Scholle MD, Sorensen DJ, Sahu AK, Becher D, Antelmann H, Mrksich M, Anderson WF, Gibson BW, Schilling B, Wolfe AJ. The E. coli sirtuin CobB shows no preference for enzymatic and nonenzymatic lysine acetylation substrate sites. Microbiologyopen 2014; 4:66-83. [PMID: 25417765 PMCID: PMC4335977 DOI: 10.1002/mbo3.223] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/21/2014] [Accepted: 10/24/2014] [Indexed: 01/22/2023] Open
Abstract
Nε-lysine acetylation is an abundant posttranslational modification of thousands of proteins involved in diverse cellular processes. In the model bacterium Escherichia coli, the ε-amino group of a lysine residue can be acetylated either catalytically by acetyl-coenzyme A (acCoA) and lysine acetyltransferases, or nonenzymatically by acetyl phosphate (acP). It is well known that catalytic acCoA-dependent Nε-lysine acetylation can be reversed by deacetylases. Here, we provide genetic, mass spectrometric, structural and immunological evidence that CobB, a deacetylase of the sirtuin family of NAD+-dependent deacetylases, can reverse acetylation regardless of acetyl donor or acetylation mechanism. We analyzed 69 lysines on 51 proteins that we had previously detected as robustly, reproducibly, and significantly more acetylated in a cobB mutant than in its wild-type parent. Functional and pathway enrichment analyses supported the hypothesis that CobB regulates protein function in diverse and often essential cellular processes, most notably translation. Combined mass spectrometry, bioinformatics, and protein structural data provided evidence that the accessibility and three-dimensional microenvironment of the target acetyllysine help determine CobB specificity. Finally, we provide evidence that CobB is the predominate deacetylase in E. coli.
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Affiliation(s)
- Alaa AbouElfetouh
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, 60153; Department of Microbiology, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
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30
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Kang H, Kim Y, Choi I, Chang R, Yeo WS. Determination of self-exchange rate of alkanethiolates in self-assembled monolayers on gold using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Chim Acta 2014; 843:38-45. [PMID: 25150695 DOI: 10.1016/j.aca.2014.07.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/18/2014] [Accepted: 07/20/2014] [Indexed: 10/25/2022]
Abstract
In this paper, we describe a new method for determining the exchange rates of alkanethiolates in self-assembled monolayers (SAMs) on gold using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the compositions of the alkanethiolate in SAMs rapidly and directly. In particular, to investigate the self-exchange of alkanethiols, we prepared a deuterated alkanethiol that has the same molecular properties as the non-deuterated alkanethiol but a different molecular weight. SAMs consisting of deuterated alkanethiolates were immersed in a solution of the non-deuterated alkanethiol, and the influences of the immersion time, temperature, concentration, and solvent on the self-exchange rates were investigated. Furthermore, we assessed the exchange rates among alkanethiols with different carbon chain lengths and different size of ethylene glycol units. In addition, we performed molecular dynamics simulations using a model SAM system in order to understand the molecular mechanism of the exchange process.
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Affiliation(s)
- Hyunook Kang
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Republic of Korea
| | - Yongbin Kim
- Department of Chemistry, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Inseong Choi
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Republic of Korea
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Woon-Seok Yeo
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Republic of Korea.
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31
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Kuhn ML, Zemaitaitis B, Hu LI, Sahu A, Sorensen D, Minasov G, Lima BP, Scholle M, Mrksich M, Anderson WF, Gibson BW, Schilling B, Wolfe AJ. Structural, kinetic and proteomic characterization of acetyl phosphate-dependent bacterial protein acetylation. PLoS One 2014; 9:e94816. [PMID: 24756028 PMCID: PMC3995681 DOI: 10.1371/journal.pone.0094816] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 03/19/2014] [Indexed: 01/27/2023] Open
Abstract
The emerging view of Nε-lysine acetylation in eukaryotes is of a relatively abundant post-translational modification (PTM) that has a major impact on the function, structure, stability and/or location of thousands of proteins involved in diverse cellular processes. This PTM is typically considered to arise by the donation of the acetyl group from acetyl-coenzyme A (acCoA) to the ε-amino group of a lysine residue that is reversibly catalyzed by lysine acetyltransferases and deacetylases. Here, we provide genetic, mass spectrometric, biochemical and structural evidence that Nε-lysine acetylation is an equally abundant and important PTM in bacteria. Applying a recently developed, label-free and global mass spectrometric approach to an isogenic set of mutants, we detected acetylation of thousands of lysine residues on hundreds of Escherichia coli proteins that participate in diverse and often essential cellular processes, including translation, transcription and central metabolism. Many of these acetylations were regulated in an acetyl phosphate (acP)-dependent manner, providing compelling evidence for a recently reported mechanism of bacterial Nε-lysine acetylation. These mass spectrometric data, coupled with observations made by crystallography, biochemistry, and additional mass spectrometry showed that this acP-dependent acetylation is both non-enzymatic and specific, with specificity determined by the accessibility, reactivity and three-dimensional microenvironment of the target lysine. Crystallographic evidence shows acP can bind to proteins in active sites and cofactor binding sites, but also potentially anywhere molecules with a phosphate moiety could bind. Finally, we provide evidence that acP-dependent acetylation can impact the function of critical enzymes, including glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, and RNA polymerase.
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Affiliation(s)
- Misty L. Kuhn
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bozena Zemaitaitis
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Linda I. Hu
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Alexandria Sahu
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Dylan Sorensen
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bruno P. Lima
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Michael Scholle
- Departments of Biomedical Engineering, Chemistry, and Cell & Molecular Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Milan Mrksich
- Departments of Biomedical Engineering, Chemistry, and Cell & Molecular Biology, Northwestern University, Evanston, Illinois, United States of America
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Bradford W. Gibson
- Buck Institute for Research on Aging, Novato, California, United States of America
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, United States of America
- * E-mail:
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32
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Manova RK, Joshi S, Debrassi A, Bhairamadgi NS, Roeven E, Gagnon J, Tahir MN, Claassen FW, Scheres LMW, Wennekes T, Schroën K, van Beek TA, Zuilhof H, Nielen MWF. Ambient surface analysis of organic monolayers using direct analysis in real time Orbitrap mass spectrometry. Anal Chem 2014; 86:2403-11. [PMID: 24484216 DOI: 10.1021/ac4031626] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A better characterization of nanometer-thick organic layers (monolayers) as used for engineering surface properties, biosensing, nanomedicine, and smart materials will widen their application. The aim of this study was to develop direct analysis in real time high-resolution mass spectrometry (DART-HRMS) into a new and complementary analytical tool for characterizing organic monolayers. To assess the scope and formulate general interpretation rules, DART-HRMS was used to analyze a diverse set of monolayers having different chemistries (amides, esters, amines, acids, alcohols, alkanes, ethers, thioethers, polymers, sugars) on five different substrates (Si, Si3N4, glass, Al2O3, Au). The substrate did not play a major role except in the case of gold, for which breaking of the weak Au-S bond that tethers the monolayer to the surface, was observed. For monolayers with stronger covalent interfacial bonds, fragmentation around terminal groups was found. For ester and amide-terminated monolayers, in situ hydrolysis during DART resulted in the detection of ions characteristic of the terminal groups (alcohol, amine, carboxylic acid). For ether and thioether-terminated layers, scission of C-O or C-S bonds also led to the release of the terminal part of the monolayer in a predictable manner. Only the spectra of alkane monolayers could not be interpreted. DART-HRMS allowed for the analysis of and distinction between monolayers containing biologically relevant mono or disaccharides. Overall, DART-HRMS is a promising surface analysis technique that combines detailed structural information on nanomaterials and ultrathin films with fast analyses under ambient conditions.
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Affiliation(s)
- Radostina K Manova
- Laboratory of Organic Chemistry, Wageningen University , Dreijenplein 8, 6703 HB Wageningen, The Netherlands
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HA MS, SEO H, BAE DH, YEO WS. Detection of Enrofloxacin and Its Metabolite Ciprofloxacin Using Gold Nanoparticles and Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. ANAL SCI 2014; 30:451-5. [DOI: 10.2116/analsci.30.451] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Mi-Sun HA
- Department of Bioscience and Biotechnology, Konkuk University
| | - Hyunjung SEO
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University
| | - Dong-Ho BAE
- Department of Bioscience and Biotechnology, Konkuk University
| | - Woon-Seok YEO
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University
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34
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Patrie SM, Roth MJ, Plymire DA, Maresh E, Zhang J. Measurement of Blood Protease Kinetic Parameters with Self-Assembled Monolayer Ligand Binding Assays and Label-Free MALDI-TOF MS. Anal Chem 2013; 85:10597-604. [DOI: 10.1021/ac402739z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Steven M. Patrie
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072
| | - Michael J. Roth
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072
| | - Daniel A. Plymire
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072
| | - Erica Maresh
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072
| | - Junmei Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9072
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35
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Voelker AE, Viswanathan R. Synthesis of a Suite of Bioorthogonal Glutathione S-Transferase Substrates and Their Enzymatic Incorporation for Protein Immobilization. J Org Chem 2013; 78:9647-58. [DOI: 10.1021/jo401278x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alden E. Voelker
- Department of Chemistry, Case Western Reserve University, Millis Science Center: Rm
216, 2074 Adelbert Road, Cleveland, Ohio 44106-7078, United States
| | - Rajesh Viswanathan
- Department of Chemistry, Case Western Reserve University, Millis Science Center: Rm
216, 2074 Adelbert Road, Cleveland, Ohio 44106-7078, United States
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36
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Ren X, Liu J, Zhang C, Luo H. Direct analysis of samples under ambient condition by high-voltage-assisted laser desorption ionization mass spectrometry in both positive and negative ion mode. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:613-620. [PMID: 23413220 DOI: 10.1002/rcm.6499] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/20/2012] [Accepted: 12/22/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE With the rapid development of ambient mass spectrometry, the hybrid laser-based ambient ionization methods which can generate multiply charged ions of large biomolecules and also characterize small molecules with good signal-to-noise in both positive and negative ion modes are of particular interest. METHODS An ambient ionization method termed high-voltage-assisted laser desorption ionization (HALDI) is developed, in which a 1064 nm laser is used to desorb various liquid samples from the sample target biased at a high potential without the need for an organic matrix. The pre-charged liquid samples are desorbed by the laser to form small charged droplets which may undergo an electrospray-like ionization process to produce multiply charged ions of large biomolecules. RESULTS Various samples including proteins, oligonucleotides (ODNs), drugs, whole milk and chicken eggs have been analyzed by HALDI-MS in both positive and negative ion mode with little or no sample preparation. In addition, HALDI can generate intense signals with better signal-to-noise in negative ion mode than laser desorption spay post-ionization (LDSPI) from the same samples, such as ODNs and some carboxylic-group-containing small drug molecules. CONCLUSIONS HALDI-MS can directly analyze a variety of liquid samples including proteins, ODNs, pharmaceuticals and biological fluids in both positive and negative ion mode without the use of an organic matrix. This technique may be further developed into a useful tool for rapid analysis in many different fields such as pharmaceutical, food, and biological sciences.
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Affiliation(s)
- Xinxin Ren
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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37
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Lee J, Choi I, Yeo WS. Preparation of gradient surfaces by using a simple chemical reaction and investigation of cell adhesion on a two-component gradient. Chemistry 2013; 19:5609-16. [PMID: 23463672 DOI: 10.1002/chem.201203215] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 01/25/2013] [Indexed: 01/23/2023]
Abstract
This article describes a simple method for the generation of multicomponent gradient surfaces on self-assembled monolayers (SAMs) on gold in a precise and predictable manner, by harnessing a chemical reaction on the monolayer, and their applications. A quinone derivative on a monolayer was converted to an amine through spontaneous intramolecular cyclization following first-order reaction kinetics. An amine gradient on the surface on a scale of centimeters was realized by modulating the exposure time of the quinone-presenting monolayer to the chemical reagent. The resulting amine was used as a chemical handle to attach various molecules to the monolayer with formation of multicomponent gradient surfaces. The effectiveness of this strategy was verified by cyclic voltammetry (CV), matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS), MS imaging, and contact-angle measurements. As a practical application, cell adhesion was investigated on RGD/PHSRN peptide/peptide gradient surfaces. Peptide PHSRN was found to synergistically enhance cell adhesion at the position where these two ligands are presented in equal amounts, while these peptide ligands were competitively involved in cell adhesion at other positions. This strategy of generating a gradient may be further expandable to the development of functional gradient surfaces of various molecules and materials, such as DNA, proteins, growth factors, and nanoparticles, and could therefore be useful in many fields of research and practical applications.
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Affiliation(s)
- Jeongwook Lee
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, Korea
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38
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Roth MJ, Maresh EM, Plymire DA, Zhang J, Corbett JR, Robbins R, Patrie SM. Surface preparation strategies for improved parallelization and reproducible MALDI-TOF MS ligand binding assays. ACS APPLIED MATERIALS & INTERFACES 2013; 5:6-10. [PMID: 23249094 DOI: 10.1021/am3024756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Immunoassays are employed in academia and the healthcare and biotech industries for high-throughput, quantitative screens of biomolecules. We have developed monolayer-based immunoassays for MALDI-TOF MS. To improve parallelization, we adapted the workflow to photolithography-generated arrays. Our work shows Parylene-C coatings provide excellent "solvent pinning" for reagents and biofluids, enabling sensitive MS detection of immobilized components. With a unique MALDI-matrix crystallization technique we show routine interassay RSD <10% at picomolar concentrations and highlight platform compatibility for relative and label-free quantitation applications. Parylene-arrays provide high sample densities and promise screening throughputs exceeding 1000 samples/h with modern liquid-handlers and MALDI-TOF systems.
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39
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Grabosch C, Kind M, Gies Y, Schweighöfer F, Terfort A, Lindhorst TK. A ‘dual click’ strategy for the fabrication of bioselective, glycosylated self-assembled monolayers as glycocalyx models. Org Biomol Chem 2013; 11:4006-15. [DOI: 10.1039/c3ob40386f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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40
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Stolowitz ML. On-target and nanoparticle-facilitated selective enrichment of peptides and proteins for analysis by MALDI-MS. Proteomics 2012; 12:3438-50. [DOI: 10.1002/pmic.201200252] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/27/2012] [Accepted: 09/20/2012] [Indexed: 01/09/2023]
Affiliation(s)
- Mark L. Stolowitz
- Canary Center at Stanford for Cancer Early Detection; Department of Radiology; Stanford University School of Medicine; Palo Alto CA USA
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41
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Roth MJ, Kim J, Maresh EM, Plymire DA, Corbett JR, Zhang J, Patrie SM. Thin-layer matrix sublimation with vapor-sorption induced co-crystallization for sensitive and reproducible SAMDI-TOF MS analysis of protein biosensors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1661-1669. [PMID: 22847391 DOI: 10.1007/s13361-012-0442-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 06/19/2012] [Accepted: 06/22/2012] [Indexed: 06/01/2023]
Abstract
Coupling immunoassays on self-assembled monolayers (SAMs) to matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) provides improved assay selectivity compared with traditional photometric detection techniques. We show that thin-layer-transfer (TLT) of α-cyano-4-hydroxycinnaminic acid (CHCA) MALDI matrix via vacuum sublimation followed by organic solvent-based vapor-sorption induced co-crystallization (VIC) results in unique matrix/analyte co-crystallization tendencies that optimizes assay reproducibility and sensitivity. Unique matrix crystal morphologies resulted from VIC solvent vapors, indicating nucleation and crystal growth characteristics depend upon VIC parameters. We observed that CHCA microcrystals generated by methanol VIC resulted in >10× better sensitivity, increased analyte charging, and improved precision compared with dried droplet measurements. The uniformity of matrix/analyte co-crystallization across planar immunoassays directed at intact proteins yielded low spectral variation for single shot replicates (18.5 % relative standard deviation, RSD) and signal averaged spectra (<10 % RSD). We envision that TLT and VIC for MALDI-TOF will enable high-throughput, reproducible array-based immunoassays for protein molecular diagnostic assays in diverse biochemical and clinical applications.
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Affiliation(s)
- Michael J Roth
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, 75390, USA
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42
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Weissenborn MJ, Castangia R, Wehner JW, Šardzík R, Lindhorst TK, Flitsch SL. Oxo-ester mediated native chemical ligation on microarrays: an efficient and chemoselective coupling methodology. Chem Commun (Camb) 2012; 48:4444-6. [PMID: 22456682 DOI: 10.1039/c2cc30844d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report a highly efficient and selective method for the coupling of peptides and glycoconjugates bearing N-terminal cysteines to activated surfaces. This chemoselective method generates stable amide linkages without using any thiol additives.
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Affiliation(s)
- Martin J Weissenborn
- School of Chemistry & Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M17DN, UK
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43
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Hsu CH, Hung SC, Wu CY, Wong CH. Toward automated oligosaccharide synthesis. Angew Chem Int Ed Engl 2011; 50:11872-923. [PMID: 22127846 DOI: 10.1002/anie.201100125] [Citation(s) in RCA: 205] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Indexed: 12/16/2022]
Abstract
Carbohydrates have been shown to play important roles in biological processes. The pace of development in carbohydrate research is, however, relatively slow due to the problems associated with the complexity of carbohydrate structures and the lack of general synthetic methods and tools available for the study of this class of biomolecules. Recent advances in synthesis have demonstrated that many of these problems can be circumvented. In this Review, we describe the methods developed to tackle the problems of carbohydrate-mediated biological processes, with particular focus on the issue related to the development of the automated synthesis of oligosaccharides. Further applications of carbohydrate microarrays and vaccines to human diseases are also highlighted.
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Affiliation(s)
- Che-Hsiung Hsu
- The Genomics Research Center, Academia Sinica, Taipei, Taiwan
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44
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Hsu CH, Hung SC, Wu CY, Wong CH. Auf dem Weg zur automatisierten Oligosaccharid- Synthese. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100125] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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45
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Hassan HMA, Maltman BA. Mixed SAMs and MALDI-ToF MS: preparation of N-glycosylamine derivative and thioctic acid methyl ester bearing 1,2-dithiolane groups and detection of enzymatic reaction on Au. Bioorg Chem 2011; 40:6-9. [PMID: 22130071 DOI: 10.1016/j.bioorg.2011.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 10/28/2011] [Indexed: 10/15/2022]
Abstract
Herein, we report an enzymatic galactosylation reaction of β-glucopyranosylamide 4 and thioctic acid methyl ester 5 bearing 1,2-dithiolane groups to form a new system of mixed self-assembled monolayers (SAMs) on gold. Characterization of the enzymatic activity was conveniently achieved by mass spectrometry.
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Affiliation(s)
- Hani Mutlak A Hassan
- Manchester Interdisciplinary Biocentre (MIB), University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Beatrice A Maltman
- Manchester Interdisciplinary Biocentre (MIB), University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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46
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Glass NR, Tjeung R, Chan P, Yeo LY, Friend JR. Organosilane deposition for microfluidic applications. BIOMICROFLUIDICS 2011; 5:36501-365017. [PMID: 22662048 PMCID: PMC3364836 DOI: 10.1063/1.3625605] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 07/26/2011] [Indexed: 05/05/2023]
Abstract
Treatment of surfaces to change the interaction of fluids with them is a critical step in constructing useful microfluidics devices, especially those used in biological applications. Silanization, the generic term applied to the formation of organosilane monolayers on substrates, is both widely reported in the literature and troublesome in actual application for the uninitiated. These monolayers can be subsequently modified to produce a surface of a specific functionality. Here various organosilane deposition protocols and some application notes are provided as a basis for the novice reader to construct their own silanization procedures, and as a practical resource to a broader range of techniques even for the experienced user.
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Affiliation(s)
- Nick R Glass
- Micro/Nanophysics Research Laboratory, Department of Mechanical Engineering, Monash University, Clayton, Victoria 3800, Australia
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47
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Ha NY, Kim SH, Lee TG, Han SY. Rapid characterization of protein chips using microwave-assisted protein tryptic digestion and MALDI mass spectrometry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:10098-105. [PMID: 21774472 DOI: 10.1021/la201812a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We demonstrate that the microwave-assisted protein enzymatic digestion (MAPED) method can be successfully applied to the mass spectrometric characterization of proteins captured on the affinity surfaces of protein chips. The microwave-assisted on-chip tryptic digestion method was developed using a domestic microwave, completing the on-chip proteolysis reaction in minutes, whereas the previous on-chip digestion methods by incubation took hours of incubation time. For the model protein chips, antibody-presenting surfaces were prepared, where anti-α-tubulin1 and antibovine serum albumin (BSA) were immobilized on self-assembled monolayers. The resulting digestion efficiency, displaying sequence coverages of 30 and 14% for α-tubulin1 and BSA, respectively, was comparable to the previous time-consuming incubation studies. It allowed the characterization of immunosensed proteins by MASCOT search using peptide mass fingerprinting. In an example of this method for protein chip applications, BSA naturally involved in fetal bovine serum was unambiguously identified on a model protein chip by imaging mass spectrometry. This work shows that biomass spectrometry techniques can be implemented for surface mass spectrometry and biochip applications. Along with recent advances in imaging mass spectrometry, this technique will provide a new opportunity for high-speed, and thus high-throughput in the future, label-free mass spectrometric assays using protein arrays.
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Affiliation(s)
- Na Young Ha
- Center for Nano-Bio Convergence, Korea Research Institute of Standards and Science, Daejeon 305-340, Republic of Korea
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48
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Gurard-Levin ZA, Scholle MD, Eisenberg AH, Mrksich M. High-throughput screening of small molecule libraries using SAMDI mass spectrometry. ACS COMBINATORIAL SCIENCE 2011; 13:347-50. [PMID: 21639106 PMCID: PMC3132997 DOI: 10.1021/co2000373] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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High-throughput screening is a common strategy used to identify compounds that modulate biochemical activities, but many approaches depend on cumbersome fluorescent reporters or antibodies and often produce false-positive hits. The development of “label-free” assays addresses many of these limitations, but current approaches still lack the throughput needed for applications in drug discovery. This paper describes a high-throughput, label-free assay that combines self-assembled monolayers with mass spectrometry, in a technique called SAMDI, as a tool for screening libraries of 100 000 compounds in one day. This method is fast, has high discrimination, and is amenable to a broad range of chemical and biological applications.
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Affiliation(s)
- Zachary A. Gurard-Levin
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street. Chicago, Illinois 60637, United States
| | - Michael D. Scholle
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street. Chicago, Illinois 60637, United States
| | - Adam H. Eisenberg
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street. Chicago, Illinois 60637, United States
| | - Milan Mrksich
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street. Chicago, Illinois 60637, United States
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49
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Affiliation(s)
- Xiaoli Liao
- Department of Chemistry, University of Chicago929 East 57th Street, Chicago, IL 60637 (USA)
| | - Rafe T Petty
- Department of Chemistry, University of Chicago929 East 57th Street, Chicago, IL 60637 (USA)
| | - Milan Mrksich
- Department of Chemistry, University of Chicago929 East 57th Street, Chicago, IL 60637 (USA)
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50
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Singh V, Zharnikov M, Gulino A, Gupta T. DNA immobilization, delivery and cleavage on solid supports. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c0jm04359a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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