1
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Murphy ZR, Shields DA, Evrony GD. Serial enrichment of heteroduplex DNA using a MutS-magnetic bead system. Biotechnol J 2023; 18:e2200323. [PMID: 36317440 PMCID: PMC9839629 DOI: 10.1002/biot.202200323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/13/2022] [Accepted: 10/26/2022] [Indexed: 11/05/2022]
Abstract
Numerous applications in molecular biology and genomics require characterization of mutant DNA molecules present at low levels within a larger sample of non-mutant DNA. This is often achieved either by selectively amplifying mutant DNA, or by sequencing all the DNA followed by computational identification of the mutant DNA. However, selective amplification is challenging for insertions and deletions (indels). Additionally, sequencing all the DNA in a sample may not be cost effective when only the presence of a mutation needs to be ascertained rather than its allelic fraction. The MutS protein evolved to detect DNA heteroduplexes in which the two DNA strands are mismatched. Prior methods have utilized MutS to enrich mutant DNA by hybridizing mutant to non-mutant DNA to create heteroduplexes. However, the purity of heteroduplex DNA these methods achieve is limited because they can only feasibly perform one or two enrichment cycles. We developed a MutS-magnetic bead system that enables rapid serial enrichment cycles. With six cycles, we achieve complete purification of heteroduplex indel DNA originally present at a 5% fraction and over 40-fold enrichment of heteroduplex DNA originally present at a 1% fraction. This system may enable novel approaches for enriching mutant DNA for targeted sequencing.
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Affiliation(s)
- Zachary R. Murphy
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Danielle A. Shields
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Gilad D. Evrony
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
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2
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Bae W, Yoon TY, Jeong C. Direct evaluation of self-quenching behavior of fluorophores at high concentrations using an evanescent field. PLoS One 2021; 16:e0247326. [PMID: 33606817 PMCID: PMC7895399 DOI: 10.1371/journal.pone.0247326] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/04/2021] [Indexed: 01/09/2023] Open
Abstract
The quantum yield of a fluorophore is reduced when two or more identical fluorophores are in close proximity to each other. The study of protein folding or particle aggregation is can be done based on this above-mentioned phenomenon—called self-quenching. However, it is challenging to characterize the self-quenching of a fluorophore at high concentrations because of the inner filter effect, which involves depletion of excitation light and re-absorption of emission light. Herein, a novel method to directly evaluate the self-quenching behavior of fluorophores was developed. The evanescent field from an objective-type total internal reflection fluorescence (TIRF) microscope was used to reduce the path length of the excitation and emission light to ~100 nm, thereby supressing the inner filter effect. Fluorescence intensities of sulforhodamine B, fluorescein isothiocyanate (FITC), and calcein solutions with concentrations ranging from 1 μM to 50 mM were directly measured to evaluate the concentration required for 1000-fold degree of self-quenching and to examine the different mechanisms through which the fluorophores undergo self-quenching.
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Affiliation(s)
- Wooli Bae
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, South Kensington Campus, London, United Kingdom
- * E-mail: (WB); (CJ)
| | - Tae-Young Yoon
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Institute for Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Cherlhyun Jeong
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul, Republic of Korea
- KHU‑KIST Department of Converging Science and Technology, Kyunghee University, Seoul, Republic of Korea
- * E-mail: (WB); (CJ)
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3
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Zhang J, Wang Y, Chai B, Wang J, Li L, Liu M, Zhao G, Yao L, Gao X, Yin Y, Xu J. Efficient and Low-Cost Error Removal in DNA Synthesis by a High-Durability MutS. ACS Synth Biol 2020; 9:940-952. [PMID: 32135061 DOI: 10.1021/acssynbio.0c00079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzyme-based error correction is a key step in de novo DNA synthesis, yet the inherent instability of error-correction enzymes such as MutS has hindered the throughput and efficiency of DNA synthesis workflows. Here we introduce a process called Improved MICC (iMICC), in which all error-correction steps of oligos and fragments within a complete gene-synthesis cycle are completed in a simple, efficient, and low-cost manner via a MutS protein engineered for high durability. By establishing a disulfide bond of L157C-G233C, full-activity shelf life of E. coli MutS (eMutS) was prolonged from 7 to 49 days and was further extended to 63 days via cellulose-bound 4 °C storage. In synthesis of 10 Cas9 homologues in-solution and 10 xylose reductase (XR) homologues on-chip, iMICC reduced error frequency to 0.64/Kb and 0.41/Kb, respectively, with 72.1% and 86.4% of assembled fragments being error-free. By elevating base accuracy by 37.6-fold while avoiding repetitive preparation of fresh enzymes, iMICC is more efficient and robust than the wild-type eMutS, and it is 6.6-fold more accurate and 26.7-fold cheaper than CorrectASE. These advantages promise its broad applications in industrial DNA synthesis.
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Affiliation(s)
- Jia Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yefei Wang
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Baihui Chai
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jichao Wang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Li
- LC-BIO Technologies CO., LTD., Hangzhou 310018, China
| | - Min Liu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lishan Yao
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolian Gao
- LC-BIO Technologies CO., LTD., Hangzhou 310018, China
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004-5001, United States
| | - Yifeng Yin
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Single gold-bridged nanoprobes for identification of single point DNA mutations. Nat Commun 2019; 10:836. [PMID: 30783107 PMCID: PMC6381086 DOI: 10.1038/s41467-019-08769-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 01/23/2019] [Indexed: 01/15/2023] Open
Abstract
Consensus ranking of protein affinity to identify point mutations has not been established. Therefore, analytical techniques that can detect subtle variations without interfering with native biomolecular interactions are required. Here we report a rapid method to identify point mutations by a single nanoparticle sensing system. DNA-directed gold crystallization forms rod-like nanoparticles with bridges based on structural design. The nanoparticles enhance Rayleigh light scattering, achieving high refractive-index sensitivity, and enable the system to monitor even a small number of protein-DNA binding events without interference. Analysis of the binding affinity can compile an atlas to distinguish the potential of various point mutations recognized by MutS protein. We use the atlas to analyze the presence and type of single point mutations in BRCA1 from samples of human breast and ovarian cancer cell lines. The strategy of synthesis-by-design of plasmonic nanoparticles for sensors enables direct identification of subtle biomolecular binding distortions and genetic alterations.
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5
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Lubock NB, Zhang D, Sidore AM, Church GM, Kosuri S. A systematic comparison of error correction enzymes by next-generation sequencing. Nucleic Acids Res 2017; 45:9206-9217. [PMID: 28911123 PMCID: PMC5587813 DOI: 10.1093/nar/gkx691] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 07/14/2017] [Accepted: 07/31/2017] [Indexed: 11/13/2022] Open
Abstract
Gene synthesis, the process of assembling gene-length fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by errors produced during oligo synthesis and subsequent assembly. Enzymatic error correction methods are cost-effective means to ameliorate errors in gene synthesis. Previous analyses of these methods relied on cloning and Sanger sequencing to evaluate their efficiencies, limiting quantitative assessment. Here, we develop a method to quantify errors in synthetic DNA by next-generation sequencing. We analyzed errors in model gene assemblies and systematically compared six different error correction enzymes across 11 conditions. We find that ErrASE and T7 Endonuclease I are the most effective at decreasing average error rates (up to 5.8-fold relative to the input), whereas MutS is the best for increasing the number of perfect assemblies (up to 25.2-fold). We are able to quantify differential specificities such as ErrASE preferentially corrects C/G transversions whereas T7 Endonuclease I preferentially corrects A/T transversions. More generally, this experimental and computational pipeline is a fast, scalable and extensible way to analyze errors in gene assemblies, to profile error correction methods, and to benchmark DNA synthesis methods.
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Affiliation(s)
- Nathan B. Lubock
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Di Zhang
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Angus M. Sidore
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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6
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Banasik M, Stanisławska-Sachadyn A, Hildebrandt E, Sachadyn P. In vitro affinity of Deinococcus radiodurans MutS towards mismatched DNA exceeds that of its orthologues from Escherichia coli and Thermus thermophilus. J Biotechnol 2017; 252:55-64. [PMID: 28506931 DOI: 10.1016/j.jbiotec.2017.05.010] [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: 01/31/2017] [Revised: 04/29/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
Abstract
The mismatch binding protein MutS is responsible for the recognition of mispaired and unpaired bases, which is the initial step in DNA repair. Among the MutS proteins most extensively studied in vitro are those derived from Thermus thermophilus, Thermus aquaticus and Escherichia coli. Here, we present the first report on the in vitro examination of DNA mismatch binding activity of MutS protein from Deinococcus radiodurans and confront this with the properties of those from E. coli and T. thermophilus. The analyses which included mobility gel-shift assay, colorimetric and qPCR estimation of MutS-bound DNA clearly showed that D. radiodurans MutS exhibited much higher affinity towards mismatched DNA in vitro than its counterparts from E. coli and T. thermophilus. In addition, D. radiodurans MutS displayed a significantly higher specificity of DNA mismatch binding than the two other orthologues. The specificity expressed as the ratio of mismatched to fully complementary DNA bound reached over 4 and 20-fold higher values for D. radiodurans than for T. thermophilus and E. coli MutS, respectively. The results demonstrate mainly the biotechnological potential of D. radiodurans MutS but the in vitro characteristics of the MutS orthologues could reflect substantial differences in DNA mismatch binding activities existing in vivo.
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Affiliation(s)
- Michał Banasik
- Department of Molecular Biotechnology and Microbiology, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Anna Stanisławska-Sachadyn
- Department of Molecular Biotechnology and Microbiology, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Ewa Hildebrandt
- Department of Molecular Biotechnology and Microbiology, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Paweł Sachadyn
- Department of Molecular Biotechnology and Microbiology, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland.
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7
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Wan W, Wang D, Gao X, Hong J. Immobilized MutS-Mediated Error Removal of Microchip-Synthesized DNA. Methods Mol Biol 2017; 1472:217-235. [PMID: 27671944 DOI: 10.1007/978-1-4939-6343-0_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Applications of microchip-synthesized oligonucleotides for de novo gene synthesis are limited primarily by their high error rates. The mismatch binding protein MutS, which can specifically recognize and bind to mismatches, is one of the cheapest tools for error correction of synthetic DNA. Here, we describe a protocol for removing errors in microchip-synthesized oligonucleotides and for the assembly of DNA segments using these oligonucleotides. This protocol can also be used in traditional de novo gene DNA synthesis.
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Affiliation(s)
- Wen Wan
- School of Life Science, University of Science and Technology of China, No 443 Huangshan Road, Hefei, Anhui, 230026, People's Republic of China
| | - Dongmei Wang
- School of Life Science, University of Science and Technology of China, No 443 Huangshan Road, Hefei, Anhui, 230026, People's Republic of China
| | - Xiaolian Gao
- School of Life Science, University of Science and Technology of China, No 443 Huangshan Road, Hefei, Anhui, 230026, People's Republic of China
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, 230026, Anhui, People's Republic of China
| | - Jiong Hong
- School of Life Science, University of Science and Technology of China, No 443 Huangshan Road, Hefei, Anhui, 230026, People's Republic of China.
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, 230026, Anhui, People's Republic of China.
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8
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Hingorani MM. Mismatch binding, ADP-ATP exchange and intramolecular signaling during mismatch repair. DNA Repair (Amst) 2016; 38:24-31. [PMID: 26704427 PMCID: PMC4740199 DOI: 10.1016/j.dnarep.2015.11.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 09/08/2015] [Accepted: 11/30/2015] [Indexed: 12/16/2022]
Abstract
The focus of this article is on the DNA binding and ATPase activities of the mismatch repair (MMR) protein, MutS-our current understanding of how this protein uses ATP to fuel its actions on DNA and initiate repair via interactions with MutL, the next protein in the pathway. Structure-function and kinetic studies have yielded detailed views of the MutS mechanism of action in MMR. How MutS and MutL work together after mismatch recognition to enable strand-specific nicking, which leads to strand excision and synthesis, is less clear and remains an active area of investigation.
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9
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Chang K, Deng S, Chen M. Novel biosensing methodologies for improving the detection of single nucleotide polymorphism. Biosens Bioelectron 2015; 66:297-307. [DOI: 10.1016/j.bios.2014.11.041] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/28/2014] [Accepted: 11/20/2014] [Indexed: 12/11/2022]
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10
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Khoshfetrat SM, Mehrgardi MA. Amplified electrochemical genotyping of single-nucleotide polymorphisms using a graphene–gold nanoparticles modified glassy carbon platform. RSC Adv 2015. [DOI: 10.1039/c5ra03794h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A triple signal amplification strategy for the single nucleotide polymorphisms (SNPs) genotyping is reported using the graphene–gold nanoparticles (GR–AuNPs) as a sensitive platform and monobase-modified silver and gold nanoparticles (M-NPs).
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11
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Wan W, Li L, Xu Q, Wang Z, Yao Y, Wang R, Zhang J, Liu H, Gao X, Hong J. Error removal in microchip-synthesized DNA using immobilized MutS. Nucleic Acids Res 2014; 42:e102. [PMID: 24829454 PMCID: PMC4081059 DOI: 10.1093/nar/gku405] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The development of economical de novo gene synthesis methods using microchip-synthesized oligonucleotides has been limited by their high error rates. In this study, a low-cost, effective and improved-throughput (up to 32 oligos per run) error-removal method using an immobilized cellulose column containing the mismatch binding protein MutS was produced to generate high-quality DNA from oligos, particularly microchip-synthesized oligonucleotides. Error-containing DNA in the initial material was specifically retained on the MutS-immobilized cellulose column (MICC), and error-depleted DNA in the eluate was collected for downstream gene assembly. Significantly, this method improved a population of synthetic enhanced green fluorescent protein (720 bp) clones from 0.93% to 83.22%, corresponding to a decrease in the error frequency of synthetic gene from 11.44/kb to 0.46/kb. In addition, a parallel multiplex MICC error-removal strategy was also evaluated in assembling 11 genes encoding ∼21 kb of DNA from 893 oligos. The error frequency was reduced by 21.59-fold (from 14.25/kb to 0.66/kb), resulting in a 24.48-fold increase in the percentage of error-free assembled fragments (from 3.23% to 79.07%). Furthermore, the standard MICC error-removal process could be completed within 1.5 h at a cost as low as $0.374 per MICC.
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Affiliation(s)
- Wen Wan
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, People's Republic of China
| | - Lulu Li
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, People's Republic of China
| | - Qianqian Xu
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, People's Republic of China
| | - Zhefan Wang
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, People's Republic of China
| | - Yuan Yao
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, People's Republic of China
| | - Rongliang Wang
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, People's Republic of China
| | - Jia Zhang
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, People's Republic of China
| | - Haiyan Liu
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, People's Republic of China
| | - Xiaolian Gao
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, People's Republic of China Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Jiong Hong
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People's Republic of China Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, People's Republic of China
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12
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DeRocco VC, Sass LE, Qiu R, Weninger KR, Erie DA. Dynamics of MutS-mismatched DNA complexes are predictive of their repair phenotypes. Biochemistry 2014; 53:2043-52. [PMID: 24588663 PMCID: PMC3985873 DOI: 10.1021/bi401429b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
MutS
recognizes base–base mismatches and base insertions/deletions
(IDLs) in newly replicated DNA. Specific interactions between MutS
and these errors trigger a cascade of protein–protein interactions
that ultimately lead to their repair. The inability to explain why
different DNA errors are repaired with widely varying efficiencies in vivo remains an outstanding example of our limited knowledge
of this process. Here, we present single-molecule Förster resonance
energy transfer measurements of the DNA bending dynamics induced by Thermus aquaticus MutS and the E41A mutant of MutS, which
is known to have error specific deficiencies in signaling repair.
We compared three DNA mismatches/IDLs (T-bulge, GT, and CC) with repair
efficiencies ranging from high to low. We identify three dominant
DNA bending states [slightly bent/unbent (U), intermediately
bent (I), and significantly bent (B)] and
find that the kinetics of interconverting among states varies widely
for different complexes. The increased stability of MutS–mismatch/IDL
complexes is associated with stabilization of U and lowering
of the B to U transition barrier. Destabilization
of U is always accompanied by a destabilization of B, supporting the suggestion that B is a “required”
precursor to U. Comparison of MutS and MutS-E41A dynamics
on GT and the T-bulge suggests that hydrogen bonding to MutS facilitates
the changes in base–base hydrogen bonding that are required
to achieve the U state, which has been implicated in
repair signaling. Taken together with repair propensities, our data
suggest that the bending kinetics of MutS–mismatched DNA complexes
may control the entry into functional pathways for downstream signaling
of repair.
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Affiliation(s)
- Vanessa C DeRocco
- Department of Chemistry and ‡Curriculum in Applied Sciences and Engineering, The University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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13
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Slow conformational changes in MutS and DNA direct ordered transitions between mismatch search, recognition and signaling of DNA repair. J Mol Biol 2013; 425:4192-205. [PMID: 23973435 DOI: 10.1016/j.jmb.2013.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 01/04/2023]
Abstract
MutS functions in mismatch repair (MMR) to scan DNA for errors, identify a target site and trigger subsequent events in the pathway leading to error removal and DNA re-synthesis. These actions, enabled by the ATPase activity of MutS, are now beginning to be analyzed from the perspective of the protein itself. This study provides the first ensemble transient kinetic data on MutS conformational dynamics as it works with DNA and ATP in MMR. Using a combination of fluorescence probes (on Thermus aquaticus MutS and DNA) and signals (intensity, anisotropy and resonance energy transfer), we have monitored the timing of key conformational changes in MutS that are coupled to mismatch binding and recognition, ATP binding and hydrolysis, as well as sliding clamp formation and signaling of repair. Significant findings include (a) a slow step that follows weak initial interaction between MutS and DNA, in which concerted conformational changes in both macromolecules control mismatch recognition, and (b) rapid, binary switching of MutS conformations that is concerted with ATP binding and hydrolysis and (c) is stalled after mismatch recognition to control formation of the ATP-bound MutS sliding clamp. These rate-limiting pre- and post-mismatch recognition events outline the mechanism of action of MutS on DNA during initiation of MMR.
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14
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Highly sensitive and selective colorimetric genotyping of single-nucleotide polymorphisms based on enzyme-amplified ligation on magnetic beads. Biosens Bioelectron 2012; 36:89-94. [DOI: 10.1016/j.bios.2012.03.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 03/26/2012] [Accepted: 03/29/2012] [Indexed: 11/22/2022]
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15
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Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling. EMBO J 2012; 31:2528-40. [PMID: 22505031 DOI: 10.1038/emboj.2012.95] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 03/21/2012] [Indexed: 12/18/2022] Open
Abstract
MutS protein recognizes mispaired bases in DNA and targets them for mismatch repair. Little is known about the transient conformations of MutS as it signals initiation of repair. We have used single-molecule fluorescence resonance energy transfer (FRET) measurements to report the conformational dynamics of MutS during this process. We find that the DNA-binding domains of MutS dynamically interconvert among multiple conformations when the protein is free and while it scans homoduplex DNA. Mismatch recognition restricts MutS conformation to a single state. Steady-state measurements in the presence of nucleotides suggest that both ATP and ADP must be bound to MutS during its conversion to a sliding clamp form that signals repair. The transition from mismatch recognition to the sliding clamp occurs via two sequential conformational changes. These intermediate conformations of the MutS:DNA complex persist for seconds, providing ample opportunity for interaction with downstream proteins required for repair.
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Detection of the strand exchange reaction using DNAzyme and Thermotoga maritima recombinase A. Anal Biochem 2012; 421:313-20. [DOI: 10.1016/j.ab.2011.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 10/22/2011] [Accepted: 11/09/2011] [Indexed: 11/23/2022]
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Jeong C, Cho WK, Song KM, Cook C, Yoon TY, Ban C, Fishel R, Lee JB. MutS switches between two fundamentally distinct clamps during mismatch repair. Nat Struct Mol Biol 2011; 18:379-85. [PMID: 21278758 PMCID: PMC3060787 DOI: 10.1038/nsmb.2009] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 11/19/2010] [Indexed: 12/19/2022]
Abstract
Single molecule trajectory analysis has suggested DNA repair proteins may perform a 1–dimensional (1D) search on naked DNA encompassing >10,000 nucleotides. Organized cellular DNA (chromatin) presents substantial barriers to such lengthy searches. Using dynamic single molecule fluorescence resonance energy transfer (smFRET) we determined that the mismatch repair (MMR) initiation protein MutS forms a transient clamp that scans duplex DNA for mismatched nucleotides by 1D diffusion for 1 sec (~700 bp) while in continuous rotational contact with the DNA. Mismatch identification provokes ATP binding (3 s) that induces distinctly different MutS sliding clamps with unusual stability on DNA (~600 s), which may be released by adjacent single–stranded DNA (ssDNA). These observations suggest that ATP transforms short–lived MutS lesion scanning clamps into highly stable MMR signaling clamps capable of competing with chromatin and recruiting MMR machinery, yet are recycled by ssDNA excision tracts.
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Affiliation(s)
- Cherlhyun Jeong
- Department of Physics, Pohang University of Science and Technology, Pohang, Korea
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Kim S, Kim TG, Byon HR, Shin HJ, Ban C, Choi HC. Recognition of single mismatched DNA using MutS-immobilized carbon nanotube field effect transistor devices. J Phys Chem B 2009; 113:12164-8. [PMID: 19685907 DOI: 10.1021/jp9063559] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Label-free and real-time detections of mismatched dsDNAs are demonstrated using MutS-protein-immobilized, single-walled carbon nanotube field effect transistor (SWNT-FET) devices. The E. coli MutS proteins specifically recognizing mismatched dsDNAs are immobilized on SWNT-FET devices that have been fabricated for high sensitivity using a shadow mask lithographic technique to obtain a thin and wide Schottky contact region. The MutS-immobilized SWNT-FETs have successfully detected 40 base pair dsDNAs having single G-T mismatches at the 20th base pair positions by displaying significant electrical conductance drops at as low as 100 pM concentration. Systematic control experiments have revealed that the signal changes indeed originated from specific recognitions of mismatched DNAs by the immobilized MutS proteins.
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Wang K, Gao Y, Peng X, Yang G, Gao F, Li S, Zhu Y. Using FAM labeled DNA oligos to do RNA electrophoretic mobility shift assay. Mol Biol Rep 2009; 37:2871-5. [PMID: 19784797 DOI: 10.1007/s11033-009-9841-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Accepted: 09/15/2009] [Indexed: 11/30/2022]
Abstract
The electrophoretic mobility shift assay is a useful tool to identify proteins and nucleic acids interactions. Traditionally, the nucleic acids fragments are end-labeled with (32)P. We present here the use of fluorescent methodologies for studies of RNA in place of radioactivity. The method is highly sensitive and quantitative with the use of an infrared fluorescence imaging system. Fluorescently labeled primers can be used to monitor protein-RNA interactions by fluorescent mobility shift assays. The simplicity and validity of this approach may have more advantages than that of previous methods that traditionally used hazardous radioisotopes. This method was successfully tested in the study of the interactions between MS2 Coat Protein and its RNA target.
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Affiliation(s)
- Kun Wang
- Key Laboratory of MOE for Plant Developmental Biology, College of Life Sciences, Wuhan University, 430072 Wuhan, People's Republic of China
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Lopez-Crapez E, Malinge JM, Gatchitch F, Casano L, Langlois T, Pugnière M, Roquet F, Mathis G, Bazin H. A homogeneous resonance energy transfer-based assay to monitor MutS/DNA interactions. Anal Biochem 2008; 383:301-6. [PMID: 18824153 DOI: 10.1016/j.ab.2008.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2008] [Revised: 08/29/2008] [Accepted: 09/03/2008] [Indexed: 10/21/2022]
Abstract
Probing the interactions of the DNA mismatch repair protein MutS with altered and damaged DNA is of great interest both for the understanding of the mismatch repair system function and for the development of tools to detect mutations. Here we describe a homogeneous time-resolved fluorescence (HTRF) assay to study the interactions of Escherichia coli MutS protein with various DNA substrates. First, we designed an indirect HTRF assay on a microtiter plate format and demonstrated its general applicability through the analysis of the interactions between MutS and mismatched DNA or DNA containing the most common lesion of the anticancer drug cisplatin. Then we directly labeled MutS with the long-lived fluorescent donor molecule europium tris-bipyridine cryptate ([TBP(Eu(3+))]) and demonstrated by electrophoretic mobility shift assay that this chemically labeled protein retained DNA mismatch binding property. Consequently, we used [TBP(Eu(3+))]-MutS to develop a faster and simpler semidirect HTRF assay.
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Affiliation(s)
- Evelyne Lopez-Crapez
- Department of Oncobiology, Cancer Research Center, CRLC Val d'Aurelle-Paul Lamarque, 34298 Montpellier Cedex 5, France.
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Cho M, Han MS, Ban C. Detection of mismatched DNAs via the binding affinity of MutS using a gold nanoparticle-based competitive colorimetric method. Chem Commun (Camb) 2008:4573-5. [DOI: 10.1039/b811346g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nag N, Rao BJ, Krishnamoorthy G. Altered dynamics of DNA bases adjacent to a mismatch: a cue for mismatch recognition by MutS. J Mol Biol 2007; 374:39-53. [PMID: 17919654 DOI: 10.1016/j.jmb.2007.08.065] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 08/27/2007] [Accepted: 08/27/2007] [Indexed: 10/22/2022]
Abstract
The structural deviations as well as the alteration in the dynamics of DNA at mismatch sites are considered to have a crucial role in mismatch recognition followed by its repair utilizing mismatch repair family proteins. To compare the dynamics at a mismatch and a non-mismatch site, we incorporated 2-aminopurine, a fluorescent analogue of adenine next to a G.T mismatch, a C.C mismatch, or an unpaired T, and at several other non-mismatch positions. Rotational diffusion of 2-aminopurine at these locations, monitored by time-resolved fluorescence anisotropy, showed distinct differences in the dynamics. This alteration in the motional dynamics is largely confined to the normally matched base-pairs that are immediately adjacent to a mismatch/ unpaired base and could be used by MutS as a cue for mismatch-specific recognition. Interestingly, the enhanced dynamics associated with base-pairs adjacent to a mismatch are significantly restricted upon MutS binding, perhaps "resetting" the cues for downstream events that follow MutS binding. Recognition of such details of motional dynamics of DNA for the first time in the current study enabled us to propose a model that integrates the details of mismatch recognition by MutS as revealed by the high-resolution crystal structure with that of observed base dynamics, and unveils a minimal composite read-out involving the base mismatch and its adjacent normal base-pairs.
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Affiliation(s)
- Nabanita Nag
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
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