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Park S, Lee CY. Extraction and Upconcentration of Adsorbates from Precisely Defined Area for Quantitative MALDI Mass Spectrometry Imaging. Methods Mol Biol 2022; 2437:159-169. [PMID: 34902147 DOI: 10.1007/978-1-0716-2030-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mass spectrometry imaging (MSI) allows label-free detection of a wide range of biomolecules and simultaneously provides their spatial distributions. In particular, MSI by matrix-assisted laser desorption/ionization mass spectrometry (MALDI) has been widely used in biomolecule analysis. However, quantitation in MALDI-MSI is limited by matrix-deposition heterogeneity, analyte extraction area, and analyte-matrix cocrystallization. In this chapter, a microstructured PDMS stamp is utilized to precisely control the matrix deposition area and the analyte extraction area. We describe here simple steps-including stamp fabrication, matrix application, and data-acquisition guideline-for the quantitative analysis of adsorbed peptides on hydrophobic surfaces.
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Affiliation(s)
- Sanghwan Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Chang Young Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea.
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2
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Structured sequences emerge from random pool when replicated by templated ligation. Proc Natl Acad Sci U S A 2021; 118:2018830118. [PMID: 33593911 PMCID: PMC7923349 DOI: 10.1073/pnas.2018830118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The structure of life emerged from randomness. This is attributed to selection by molecular Darwinian evolution. This study found that random templated ligation led to the simultaneous elongation and sequence selection of oligomers. Product strands showed highly structured sequence motifs which inhibited self-folding and built self-templating reaction networks. By the reduction of the sequence space, the kinetics of duplex formation increased and led to a faster replication through the ligation process. These findings imply that elementary binding properties of nucleotides can lead to an early selection of sequences even before the onset of Darwinian evolution. This suggests that such a simplification of sequence space could result in faster downstream selection for sequence-based function for the origin of life. The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error threshold to avoid that replicated specific sequences become random because of the incorporated replication errors [M. Eigen, Naturwissenschaften 58 (10), 465–523 (1971)]. Here, we showed that linking short oligomers from a random sequence pool in a templated ligation reaction reduced the sequence space of product strands. We started from 12-mer oligonucleotides with two bases in all possible combinations and triggered enzymatic ligation under temperature cycles. Surprisingly, we found the robust creation of long, highly structured sequences with low entropy. At the ligation site, complementary and alternating sequence patterns developed. However, between the ligation sites, we found either an A-rich or a T-rich sequence within a single oligonucleotide. Our modeling suggests that avoidance of hairpins was the likely cause for these two complementary sequence pools. What emerged was a network of complementary sequences that acted both as templates and substrates of the reaction. This self-selecting ligation reaction could be restarted by only a few majority sequences. The findings showed that replication by random templated ligation from a random sequence input will lead to a highly structured, long, and nonrandom sequence pool. This is a favorable starting point for a subsequent Darwinian evolution searching for higher catalytic functions in an RNA world scenario.
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3
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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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4
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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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5
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Gao Y, Qiao H, Pan V, Wang Z, Li J, Wei Y, Ke Y, Qi H. Accurate genotyping of fragmented DNA using a toehold assisted padlock probe. Biosens Bioelectron 2021; 179:113079. [PMID: 33636500 DOI: 10.1016/j.bios.2021.113079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/25/2021] [Accepted: 02/03/2021] [Indexed: 11/15/2022]
Abstract
Fragmented DNA from blood plasma, i.e., cell-free DNA, has received great interest as a noninvasive diagnostic biomarker for "point-of-care" testing or liquid biopsy. Here, we present a new approach for accurate genotyping of highly fragmented DNA. Based on toehold-mediated strand displacement, a toehold-assisted padlock probe and toehold blocker were designed and demonstrated with new controllability in significantly suppressing undesired cross-reaction, promoting target recycling and point mutation detection by tuning the thermodynamic properties. Furthermore, toehold-assisted padlock probe systems were elaborately designed for 14 different single-nucleotide variants (SNVs) and were demonstrated to be able to detect low concentration of variant alleles (0.1%). In addition, a target, spanning a narrow sequence window of 29 nucleotides on average is sufficient for the toehold-assisted padlock probe system, which is valuable for the analysis of highly fragmented DNA molecules from clinical samples. We further demonstrated that the toehold-assisted padlock probe, in combination with a unique asymmetric PCR technique, could detect more target SNVs at low allele fractions (1%) in highly fragmented cfDNA. This allows accurate genotyping and provides a new commercial approach for high-resolution analysis of genetic variation.
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Affiliation(s)
- Yanmin Gao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Hongyan Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, United States
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Jiaojiao Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Yanan Wei
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, United States
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China.
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6
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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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7
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Osman EA, Alladin-Mustan BS, Hales SC, Matharu GK, Gibbs JM. Enhanced mismatch selectivity of T4 DNA ligase far above the probe: Target duplex dissociation temperature. Biopolymers 2020; 112:e23393. [PMID: 32896905 DOI: 10.1002/bip.23393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 11/06/2022]
Abstract
T4 DNA ligase is a widely used ligase in many applications; yet in single nucleotide polymorphism analysis, it has been found generally lacking owing to its tendency to ligate mismatches quite efficiently. To address this lack of selectivity, we explored the effect of temperature on the selectivity of the ligase in discriminating single base pair mismatches at the 3'-terminus of the ligating strand using short ligation probes (9-mers). Remarkably, we observe outstanding selectivities when the assay temperature is increased to 7 °C to 13 °C above the dissociation temperature of the matched probe:target duplexes using commercially available enzyme at low concentration. Higher enzyme concentration shifts the temperature range to 13 °C to 19 °C above the probe:target dissociation temperatures. Finally, substituting the 5'-phosphate terminus with an abasic nucleotide decreases the optimal temperature range to 7 °C to 10 °C above the matched probe:target duplex. We compare the temperature dependence of the T4 DNA ligase catalyzed ligation and a nonenzymatic ligation system to contrast the origin of their modes of selectivity. For the latter, temperatures above the probe:target duplex dissociation lead to lower ligation conversions even for the perfect matched system. This difference between the two ligation systems reveals the uniqueness of the T4 DNA ligase's ability to maintain excellent ligation yields for the matched system at elevated temperatures. Although our observations are consistent with previous mechanistic work on T4 DNA ligase, by mapping out the temperature dependence for different ligase concentrations and probe modifications, we identify simple strategies for introducing greater selectivity into SNP discrimination based on ligation yields.
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Affiliation(s)
- Eiman A Osman
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Sarah C Hales
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Gunwant K Matharu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Julianne M Gibbs
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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8
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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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9
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Kightlinger W, Lin L, Rosztoczy M, Li W, DeLisa MP, Mrksich M, Jewett MC. Design of glycosylation sites by rapid synthesis and analysis of glycosyltransferases. Nat Chem Biol 2018; 14:627-635. [PMID: 29736039 DOI: 10.1038/s41589-018-0051-2] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/07/2018] [Indexed: 01/17/2023]
Abstract
Glycosylation is an abundant post-translational modification that is important in disease and biotechnology. Current methods to understand and engineer glycosylation cannot sufficiently explore the vast experimental landscapes required to accurately predict and design glycosylation sites modified by glycosyltransferases. Here we describe a systematic platform for glycosylation sequence characterization and optimization by rapid expression and screening (GlycoSCORES), which combines cell-free protein synthesis and mass spectrometry of self-assembled monolayers. We produced six N- and O-linked polypeptide-modifying glycosyltransferases from bacteria and humans in vitro and rigorously determined their substrate specificities using 3,480 unique peptides and 13,903 unique reaction conditions. We then used GlycoSCORES to optimize and design small glycosylation sequence motifs that directed efficient N-linked glycosylation in vitro and in the Escherichia coli cytoplasm for three heterologous proteins, including the human immunoglobulin Fc domain. We find that GlycoSCORES is a broadly applicable method to facilitate fundamental understanding of glycosyltransferases and engineer synthetic glycoproteins.
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Affiliation(s)
- Weston Kightlinger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Liang Lin
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Madisen Rosztoczy
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Wenhao Li
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.,Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Milan Mrksich
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA. .,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA. .,Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA. .,Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA. .,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
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10
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Wood SE, Sinsinbar G, Gudlur S, Nallani M, Huang CF, Liedberg B, Mrksich M. A Bottom-Up Proteomic Approach to Identify Substrate Specificity of Outer-Membrane Protease OmpT. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707535] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sarah E. Wood
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Gaurav Sinsinbar
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Sushanth Gudlur
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Madhavan Nallani
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Che-Fan Huang
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Bo Liedberg
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
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11
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Wood SE, Sinsinbar G, Gudlur S, Nallani M, Huang CF, Liedberg B, Mrksich M. A Bottom-Up Proteomic Approach to Identify Substrate Specificity of Outer-Membrane Protease OmpT. Angew Chem Int Ed Engl 2017; 56:16531-16535. [DOI: 10.1002/anie.201707535] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/06/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Sarah E. Wood
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Gaurav Sinsinbar
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Sushanth Gudlur
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Madhavan Nallani
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Che-Fan Huang
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Bo Liedberg
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
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12
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Park G, Park JK, Shin SH, Jeon HJ, Kim NKD, Kim YJ, Shin HT, Lee E, Lee KH, Son DS, Park WY, Park D. Characterization of background noise in capture-based targeted sequencing data. Genome Biol 2017; 18:136. [PMID: 28732520 PMCID: PMC5521083 DOI: 10.1186/s13059-017-1275-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 07/06/2017] [Indexed: 12/31/2022] Open
Abstract
Background Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred during specific steps of the capture-based targeted sequencing process. Results We removed most sequencing artifacts by filtering out low-quality bases and then analyze the remaining background noise. By recognizing that plasma DNA is naturally fragmented to be of a size comparable to that of mono-nucleosomal DNA, we were able to identify and characterize errors that are specifically associated with acoustic shearing. Two-thirds of C:G > A:T errors and one quarter of C:G > G:C errors were attributed to the oxidation of guanine during acoustic shearing, and this was further validated by comparative experiments conducted under different shearing conditions. The acoustic shearing step also causes A > G and A > T substitutions localized to the end bases of sheared DNA fragments, indicating a probable association of these errors with DNA breakage. Finally, the hybrid selection step contributes to one-third of the remaining C:G > A:T and one-fifth of the C > T errors. Conclusions The results of this study provide a comprehensive summary of various errors incurred during targeted deep sequencing, and their underlying causes. This information will be invaluable to drive technical improvements in this sequencing method, and may increase the future usage of targeted deep sequencing methods for low-allelic fraction variant detection. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1275-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gahee Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Joo Kyung Park
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Korea
| | - Seung-Ho Shin
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, 06351, Korea
| | - Hyo-Jeong Jeon
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea
| | - Nayoung K D Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea
| | - Yeon Jeong Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea
| | - Hyun-Tae Shin
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea
| | - Eunjin Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea
| | - Kwang Hyuck Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, 06351, Korea
| | - Dae-Soon Son
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea. .,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, 06351, Korea. .,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
| | - Donghyun Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea.
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13
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Lei Y, Hili R. Structure-activity relationships of the ATP cofactor in ligase-catalysed oligonucleotide polymerisations. Org Biomol Chem 2017; 15:2349-2352. [PMID: 28244520 DOI: 10.1039/c6ob02792j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A T4 DNA ligase-catalysed oligonucleotide polymerisation process has been recently developed to enable the incorporation of multiple functional groups throughout a nucleic acid polymer. T4 DNA ligase requires ATP as a cofactor to catalyse phosphodiester bond formation during the polymerisation process. Herein, we describe the structure-activity relationship of ATP within the context of T4 DNA ligase-catalyzed oligonucleotide polymerisation. Using high-throughput sequencing, we study not only the influence of ATP modification on polymerisation efficiency, but also on the fidelity and sequence bias of the polymerisation process.
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Affiliation(s)
- Yi Lei
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA.
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14
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Chauleau M, Shuman S. Kinetic mechanism and fidelity of nick sealing by Escherichia coli NAD+-dependent DNA ligase (LigA). Nucleic Acids Res 2016; 44:2298-309. [PMID: 26857547 PMCID: PMC4797296 DOI: 10.1093/nar/gkw049] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 01/18/2016] [Indexed: 11/15/2022] Open
Abstract
Escherichia coli DNA ligase (EcoLigA) repairs 3′-OH/5′-PO4 nicks in duplex DNA via reaction of LigA with NAD+ to form a covalent LigA-(lysyl-Nζ)–AMP intermediate (step 1); transfer of AMP to the nick 5′-PO4 to form an AppDNA intermediate (step 2); and attack of the nick 3′-OH on AppDNA to form a 3′-5′ phosphodiester (step 3). A distinctive feature of EcoLigA is its stimulation by ammonium ion. Here we used rapid mix-quench methods to analyze the kinetic mechanism of single-turnover nick sealing by EcoLigA–AMP. For substrates with correctly base-paired 3′-OH/5′-PO4 nicks, kstep2 was fast (6.8–27 s−1) and similar to kstep3 (8.3–42 s−1). Absent ammonium, kstep2 and kstep3 were 48-fold and 16-fold slower, respectively. EcoLigA was exquisitely sensitive to 3′-OH base mispairs and 3′ N:abasic lesions, which elicited 1000- to >20000-fold decrements in kstep2. The exception was the non-canonical 3′ A:oxoG configuration, which EcoLigA accepted as correctly paired for rapid sealing. These results underscore: (i) how EcoLigA requires proper positioning of the nick 3′ nucleoside for catalysis of 5′ adenylylation; and (ii) EcoLigA's potential to embed mutations during the repair of oxidative damage. EcoLigA was relatively tolerant of 5′-phosphate base mispairs and 5′ N:abasic lesions.
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Affiliation(s)
- Mathieu Chauleau
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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15
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Xu Q, Huang SQ, Ma F, Tang B, Zhang CY. Controllable Mismatched Ligation for Bioluminescence Screening of Known and Unknown Mutations. Anal Chem 2016; 88:2431-9. [DOI: 10.1021/acs.analchem.5b04540] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Qinfeng Xu
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced
Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Si-qiang Huang
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced
Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Fei Ma
- College
of Chemistry, Chemical Engineering and Materials Science, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Key Laboratory of Molecular and Nano Probes,
Ministry of Education, Shandong Provincial Key Laboratory of Clean
Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Bo Tang
- College
of Chemistry, Chemical Engineering and Materials Science, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Key Laboratory of Molecular and Nano Probes,
Ministry of Education, Shandong Provincial Key Laboratory of Clean
Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Chun-yang Zhang
- College
of Chemistry, Chemical Engineering and Materials Science, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Key Laboratory of Molecular and Nano Probes,
Ministry of Education, Shandong Provincial Key Laboratory of Clean
Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced
Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
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16
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Ma L, Lei Z, Liu X, Liu D, Wang Z. Surface ligation-based resonance light scattering analysis of methylated genomic DNA on a microarray platform. Analyst 2016; 141:3084-9. [DOI: 10.1039/c6an00488a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A surface ligation-based RLS method is developed on a microarray platform for a sensitive and specific assay of methylated genomic DNA.
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Affiliation(s)
- Lan Ma
- Analysis and Testing Center
- Ningxia University
- Yinchuan
- P. R. China
- State Key Laboratory of Electroanalytical Chemistry
| | - Zhen Lei
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Xia Liu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Dianjun Liu
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
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17
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Abstract
With the advent of nanotechnology, a variety of nanoarchitectures with varied physicochemical properties have been designed. Owing to the unique characteristics, DNAs have been used as a functional building block for novel nanoarchitecture. In particular, a self-assembly of long DNA molecules via a piece DNA staple has been utilized to attain such constructs. However, it needs many talented prerequisites (e.g., complicated computer program) with fewer yields of products. In addition, it has many limitations to overcome: for instance, (i) thermal instability under moderate environments and (ii) restraint in size caused by the restricted length of scaffold strands. Alternatively, the enzymatic sewing linkage of short DNA blocks is simply designed into long DNA assemblies but it is more error-prone due to the undeveloped sequence data. Here, we present, for the first time, a comprehensive study for directly combining DNA structures into higher DNA sewing constructs through the 5′-end cohesive ligation of T4 enzyme. Inspired by these achievements, the synthesized DNA nanomaterials were also utilized for effective detection and real-time diagnosis of cancer-specific and cytosolic RNA markers. This generalized protocol for generic DNA sewing is expected to be useful in several DNA nanotechnology as well as any nucleic acid-related fields.
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18
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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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19
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Lohman GJS, Bauer RJ, Nichols NM, Mazzola L, Bybee J, Rivizzigno D, Cantin E, Evans TC. A high-throughput assay for the comprehensive profiling of DNA ligase fidelity. Nucleic Acids Res 2015; 44:e14. [PMID: 26365241 PMCID: PMC4737175 DOI: 10.1093/nar/gkv898] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/28/2015] [Indexed: 11/24/2022] Open
Abstract
DNA ligases have broad application in molecular biology, from traditional cloning methods to modern synthetic biology and molecular diagnostics protocols. Ligation-based detection of polynucleotide sequences can be achieved by the ligation of probe oligonucleotides when annealed to a complementary target sequence. In order to achieve a high sensitivity and low background, the ligase must efficiently join correctly base-paired substrates, while discriminating against the ligation of substrates containing even one mismatched base pair. In the current study, we report the use of capillary electrophoresis to rapidly generate mismatch fidelity profiles that interrogate all 256 possible base-pair combinations at a ligation junction in a single experiment. Rapid screening of ligase fidelity in a 96-well plate format has allowed the study of ligase fidelity in unprecedented depth. As an example of this new method, herein we report the ligation fidelity of Thermus thermophilus DNA ligase at a range of temperatures, buffer pH and monovalent cation strength. This screen allows the selection of reaction conditions that maximize fidelity without sacrificing activity, while generating a profile of specific mismatches that ligate detectably under each set of conditions.
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Affiliation(s)
| | | | | | | | - Joanna Bybee
- New England BioLabs, Inc., Ipswich, MA 01938-2723, USA
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20
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Zhang L, Wang J, Coetzer M, Angione S, Kantor R, Tripathi A. One-Step Ligation on RNA Amplification for the Detection of Point Mutations. J Mol Diagn 2015; 17:679-88. [PMID: 26322949 DOI: 10.1016/j.jmoldx.2015.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 06/16/2015] [Accepted: 07/01/2015] [Indexed: 12/16/2022] Open
Abstract
The detection of point mutations is required in the diagnosis of many human diseases. The conformal specificity of DNA ligases was elegantly used to distinguish single-nucleotide mismatches. However, to detect point mutations in RNA retroviruses, conventional ligase-mediated approaches require the reverse transcription of viral genomes before separate ligation and amplification steps. We developed one-step ligation on RNA amplification (LRA) for the direct detection of RNA point mutations. The process combines the ligase-mediated joining of two oligonucleotides and subsequent hot start amplification into a single-tube reaction. We report that modifications to the structure of the oligonucleotide ligation probes improve the rate of ligation and the specificity of mutation detection on RNA. We applied LRA to the detection of a common, clinically relevant HIV-1 reverse transcriptase drug-resistant point mutation, K103N, and compared it with allele-specific PCR and pyrosequencing. LRA achieved a limit of specific quantitation of 1:100 (1%), and a limit of specific detection for mutant K103N RNA transcripts among excess wild-type strands of 1:10,000 (0.01%). LRA also exhibited good detection threshold of 5 × 10(2) copies/μL K103N RNA transcripts. LRA is a novel point mutation detection method, with potential utilization in HIV drug resistance detection and early diagnostics of genetic disorders associated with other infectious diseases and cancer.
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Affiliation(s)
- Lei Zhang
- Center for Biomedical Engineering and the School of Engineering and Medical Sciences, Brown University, Providence, Rhode Island
| | - Jingjing Wang
- Center for Biomedical Engineering and the School of Engineering and Medical Sciences, Brown University, Providence, Rhode Island
| | - Mia Coetzer
- Division of Infectious Diseases, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Stephanie Angione
- Center for Biomedical Engineering and the School of Engineering and Medical Sciences, Brown University, Providence, Rhode Island
| | - Rami Kantor
- Division of Infectious Diseases, Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | - Anubhav Tripathi
- Center for Biomedical Engineering and the School of Engineering and Medical Sciences, Brown University, Providence, Rhode Island.
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21
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Patel K, Sherrill J, Mrksich M, Scholle MD. Discovery of SIRT3 Inhibitors Using SAMDI Mass Spectrometry. ACTA ACUST UNITED AC 2015; 20:842-8. [PMID: 26024947 DOI: 10.1177/1087057115588512] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/01/2015] [Indexed: 12/11/2022]
Abstract
Lysine acetylation plays a critical role in cellular regulation and is implicated in human disease. Sirtuin deacetylases remove acetyl groups from modified lysine residues, and sirtuin 3 (SIRT3) has been identified as a target for cancer therapeutics. Robust and high-throughput screening methods for these targets will be important to the development of therapeutics. This article describes the use of self-assembled monolayer desorption/ionization mass spectrometry, or SAMDI-MS-a label-free drug discovery tool--to characterize SIRT3 activity and discover inhibitors. SAMDI-MS was used to analyze a peptide array having 361 distinct acetylated peptides to identify an active SIRT3 substrate (GYK(Ac)RGC). This peptide was used in a screen of 100,000 small molecules to identify inhibitors of SIRT3. A total of 306 SIRT3 inhibitors were identified, with one compound, SDX-437, having an IC(50) of 700 nM with >100-fold selectivity for SIRT3 over SIRT1.
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Affiliation(s)
| | | | - Milan Mrksich
- Department of Biomedical Engineering, Department of Chemistry, and Department of Cell & Molecular Biology, Northwestern University, Evanston, IL, USA
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22
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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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23
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Gobet N, Ketterer S, Meier M. Design and validation of DNA libraries for multiplexing proximity ligation assays. PLoS One 2014; 9:e112629. [PMID: 25386748 PMCID: PMC4227721 DOI: 10.1371/journal.pone.0112629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/20/2014] [Indexed: 11/18/2022] Open
Abstract
Here, we present an in silico, analytical procedure for designing and testing orthogonal DNA templates for multiplexing of the proximity ligation assay (PLA). PLA is a technology for the detection of protein interactions, post-translational modifications, and protein concentrations. To enable multiplexing of the PLA, the target information of antibodies was encoded within the DNA template of a PLA, where each template comprised four single-stranded DNA molecules. Our DNA design procedure followed the principles of minimizing the free energy of DNA cross-hybridization. To validate the functionality, orthogonality, and efficiency of the constructed template libraries, we developed a high-throughput solid-phase rolling-circle amplification assay and solid-phase PLA on a microfluidic platform. Upon integration on a microfluidic chip, 640 miniaturized pull-down assays for oligonucleotides or antibodies could be performed in parallel together with steps of DNA ligation, isothermal amplification, and detection under controlled microenvironments. From a large computed PLA template library, we randomly selected 10 template sets and tested all DNA combinations for cross-reactivity in the presence and absence of antibodies. By using the microfluidic chip application, we determined rapidly the false-positive rate of the design procedure, which was less than 1%. The combined theoretical and experimental procedure is applicable for high-throughput PLA studies on a microfluidic chip.
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Affiliation(s)
- Nicolas Gobet
- IMTEK, Department of Microsystems Engineering, Microfluidic and Biological Engineering, University of Freiburg, Freiburg, Germany
- BIOSS-Centre for Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Simon Ketterer
- IMTEK, Department of Microsystems Engineering, Microfluidic and Biological Engineering, University of Freiburg, Freiburg, Germany
- BIOSS-Centre for Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Matthias Meier
- IMTEK, Department of Microsystems Engineering, Microfluidic and Biological Engineering, University of Freiburg, Freiburg, Germany
- BIOSS-Centre for Signalling Studies, University of Freiburg, Freiburg, Germany
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24
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Gray CJ, Weissenborn MJ, Eyers CE, Flitsch SL. Enzymatic reactions on immobilised substrates. Chem Soc Rev 2014; 42:6378-405. [PMID: 23579870 DOI: 10.1039/c3cs60018a] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review gives an overview of enzymatic reactions that have been conducted on substrates attached to solid surfaces. Such biochemical reactions have become more important with the drive to miniaturisation and automation in chemistry, biology and medicine. Technical aspects such as choice of solid surface and analytical methods are discussed and examples of enzyme reactions that have been successful on these surfaces are provided.
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Affiliation(s)
- Christopher J Gray
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Road, Manchester, M1 7DN, UK
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25
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Zhang Y, Guo Y, Quirke P, Zhou D. Ultrasensitive single-nucleotide polymorphism detection using target-recycled ligation, strand displacement and enzymatic amplification. NANOSCALE 2013; 5:5027-5035. [PMID: 23636707 PMCID: PMC4576341 DOI: 10.1039/c3nr01010d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/04/2013] [Indexed: 05/29/2023]
Abstract
We report herein the development of a highly sensitive and selective approach for label-free DNA detection by combining target-recycled ligation (TRL), magnetic nanoparticle assisted target capture/separation, and efficient enzymatic amplification. We show that our approach can detect as little as 30 amol (600 fM in 50 μL) of unlabelled single-stranded DNA targets and offer an exquisitely high discrimination ratio (up to >380 fold with background correction) between a perfect-match cancer mutant and its single-base mismatch (wild-type) DNA target. Furthermore, it can quantitate the rare cancer mutant (KRAS codon 12) in a large excess of coexisting wild-type DNAs down to 0.75%. This sensor appears to be well-suited for sensitive SNP detection and a wide range of DNA mutation based diagnostic applications.
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Affiliation(s)
- Yue Zhang
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ; ; Fax: +44 (0)113 3436565
| | - Yuan Guo
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ; ; Fax: +44 (0)113 3436565
| | - Philip Quirke
- Section of Pathology and Tumour Biology , Leeds Institute of Molecular Medicine , University of Leeds , Wellcome Trust Brenner Building, St James's University Hospital , Leeds LS9 7TF , UK
| | - Dejian Zhou
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ; ; Fax: +44 (0)113 3436565
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26
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Lohman GJS, Tabor S, Nichols NM. DNA ligases. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2011; Chapter 3:Unit3.14. [PMID: 21472697 DOI: 10.1002/0471142727.mb0314s94] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The DNA ligase enzyme family catalyzes the formation of a phosphodiester bond between juxtaposed 5'-phosphate and 3'-hydroxyl termini in duplex DNA. This activity can seal nicks in duplex DNA or join double-stranded DNA fragments having either blunt or cohesive ends. DNA ligases are central enzymes in molecular biology, nucleic acid research, and in next-generation sequencing applications. Reaction conditions and applications for T4 DNA ligase, E. coli DNA ligase, and thermostable DNA ligases are described in this unit. These enzymes differ in their cofactor requirements, substrate specificity, and thermal stability.
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27
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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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28
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Kim JM, Koo CM, Kim J. Voltammetric Discrimination of DNA Single Base-Pair Mismatches via Taq DNA Ligase-Based Mismatch Recognition. ELECTROANAL 2011. [DOI: 10.1002/elan.201100120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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