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Ngo TTM, Liu B, Wang F, Basu A, Wu C, Ha T. Dependence of nucleosome mechanical stability on DNA mismatches. eLife 2024; 13:RP95514. [PMID: 38656237 DOI: 10.7554/elife.95514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of DNA. To investigate how DNA mismatches affect the mechanical stability and the exposure of nucleosomal DNA, we used an optical trap combined with single-molecule FRET and a single-molecule FRET cyclization assay. We found that a single base-pair C-C mismatch enhances DNA bendability and nucleosome mechanical stability for the 601-nucleosome positioning sequence. An increase in force required for DNA unwrapping from the histone core is observed for single base-pair C-C mismatches placed at three tested positions: at the inner turn, at the outer turn, or at the junction of the inner and outer turn of the nucleosome. The results support a model where nucleosomal DNA accessibility is reduced by mismatches, potentially explaining the preferred accumulation of single-nucleotide substitutions in the nucleosome core and serving as the source of genetic variation during evolution and cancer progression. Mechanical stability of an intact nucleosome, that is mismatch-free, is also dependent on the species as we find that yeast nucleosomes are mechanically less stable and more symmetrical in the outer turn unwrapping compared to Xenopus nucleosomes.
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Affiliation(s)
- Thuy T M Ngo
- Department of Physics, Center for Physics in Living Cells University of Illinois Urbana-Champaign, Urbana, United States
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Oregon Health and Science University, Portland, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States
- Division of Oncological Sciences, Oregon Health and Science University, Portland, United States
| | - Bailey Liu
- Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Feng Wang
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, United States
| | - Aakash Basu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Carl Wu
- Department of Biology, Johns Hopkins University, Baltimore, United States
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, United States
| | - Taekjip Ha
- Department of Physics, Center for Physics in Living Cells University of Illinois Urbana-Champaign, Urbana, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, United States
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, United States
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States
- Department of Pediatrics, Harvard Medical School, Boston, United States
- Howard Hughes Medical Institute, Boston, United States
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Ershova AS, Eliseeva IA, Nikonov OS, Fedorova AD, Vorontsov IE, Papatsenko D, Kulakovskiy IV. Enhanced C/EBP binding to G·T mismatches facilitates fixation of CpG mutations in cancer and adult stem cells. Cell Rep 2021; 35:109221. [PMID: 34107262 DOI: 10.1016/j.celrep.2021.109221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 03/21/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022] Open
Abstract
Somatic mutations in regulatory sites of human stem cells affect cell identity or cause malignant transformation. By mining the human genome for co-occurrence of mutations and transcription factor binding sites, we show that C/EBP binding sites are strongly enriched with [C > T]G mutations in cancer and adult stem cells, which is of special interest because C/EBPs regulate cell fate and differentiation. In vitro protein-DNA binding assay and structural modeling of the CEBPB-DNA complex show that the G·T mismatch in the core CG dinucleotide strongly enhances affinity of the binding site. We conclude that enhanced binding of C/EBPs shields CpG·TpG mismatches from DNA repair, leading to selective accumulation of [C > T]G mutations and consequent deterioration of the binding sites. This mechanism of targeted mutagenesis highlights the effect of a mutational process on certain regulatory sites and reveals the molecular basis of putative regulatory alterations in stem cells.
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Affiliation(s)
- Anna S Ershova
- Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
| | - Irina A Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Oleg S Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Alla D Fedorova
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Ilya E Vorontsov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Dmitry Papatsenko
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.
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3
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Abstract
Electrochemical impedance spectroscopy (EIS) was used to detect non-Watson-Crick base pairs of DNA. Thiol-modified DNA as a probe and mercaptohexanol (MCH) were co-immobilized to form a DNA/MCH mixed self-assembled monolayer on a gold electrode surface and then hybridized with complementary DNAs. The DNA layers were measured by the EIS method and interpreted by equivalent circuits. Every terminal base mismatch of the DNA duplex brought about an increase in the charge-transfer resistance (Rct), unlike the case with a fully matched DNA duplex. The value of Rct was highly sensitive to the number of base mismatches for both unpaired and overhang DNA at the terminal. For internal base mismatches, however, no significant increase in Rct was observed. These experimental results proved that the charge transfer of redox molecules to the electrode surface is largely hindered by an end fraying motion due to base unpairing and dangling overhang. EIS was able to detect these steric properties of DNA strands. Furthermore, an electrode modified with G-quadruplex (G4) DNA demonstrated the influences of bulkiness and loop structure on the accessibility of the redox probe to the electrode.
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Affiliation(s)
| | - Surachada Chuaychob
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research.,Graduate School of Frontier Sciences, The University of Tokyo
| | - Masahiro Fujita
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research.,Graduate School of Frontier Sciences, The University of Tokyo
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Threatt SD, Synold TW, Wu J, Barton JK. In vivo anticancer activity of a rhodium metalloinsertor in the HCT116 xenograft tumor model. Proc Natl Acad Sci U S A 2020; 117:17535-42. [PMID: 32661159 DOI: 10.1073/pnas.2006569117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mismatch repair (MMR) deficiencies are a hallmark of various cancers causing accumulation of DNA mutations and mismatches, which often results in chemotherapy resistance. Metalloinsertor complexes, including [Rh(chrysi)(phen)(PPO)]Cl2 (Rh-PPO), specifically target DNA mismatches and selectively induce cytotoxicity within MMR-deficient cells. Here, we present an in vivo analysis of Rh-PPO, our most potent metalloinsertor. Studies with HCT116 xenograft tumors revealed a 25% reduction in tumor volume and 12% increase in survival with metalloinsertor treatment (1 mg/kg; nine intraperitoneal doses over 20 d). When compared to oxaliplatin, Rh-PPO displays ninefold higher potency at tumor sites. Pharmacokinetic studies revealed rapid absorption of Rh-PPO in plasma with notable accumulation in the liver compared to tumors. Additionally, intratumoral metalloinsertor administration resulted in enhanced anticancer effects, pointing to a need for more selective delivery methods. Overall, these data show that Rh-PPO inhibits xenograft tumor growth, supporting the strategy of using Rh-PPO as a chemotherapeutic targeted to MMR-deficient cancers.
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Teng Y, Pramanik S, Tateishi-Karimata H, Ohyama T, Sugimoto N. Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition. Biochem Biophys Res Commun 2018; 496:601-607. [PMID: 29339157 DOI: 10.1016/j.bbrc.2018.01.083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 12/28/2017] [Accepted: 01/11/2018] [Indexed: 10/18/2022]
Abstract
The trinucleotide repeat d(CXG) (X = A, C, G or T) is the most common sequence causing repeat expansion disorders. The formation of non-canonical structures, such as hairpin structures with X-X mismatches, has been proposed to affect gene expression and regulation, which are important in pathological studies of these devastating neurological diseases. However, little information is available regarding the thermodynamics of the repeat sequence under crowded cellular conditions where many non-canonical structures such as G-quadruplexes are highly stabilized, while duplexes are destabilised. In this study, we investigated the different stabilities of X-X mismatches in the context of internal d(CXG) self-complementary sequences in an environment with a high concentration of cosolutes to mimic the crowding conditions in cells. The stabilities of full-matched duplexes and duplexes with A-A, G-G, and T-T mismatched base pairs under molecular crowding conditions were notably decreased compared to under dilute conditions. However, the stability of the DNA duplex with a C-C mismatch base pair was only slightly destabilised. Investigating different stabilities of X-X mismatches in d(CXG) sequences is important for improving our understanding of the formation and transition of multiple non-canonical structures in trinucleotide repeat diseases, and may provide insights for pathological studies and drug development.
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Affiliation(s)
- Ye Teng
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Smritimoy Pramanik
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan; Department of Chemistry, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata, 700009, India
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan; Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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Su KY, Lai HM, Goodman SD, Hu WY, Cheng WC, Lin LI, Yang YC, Fang WH. Application of single nucleotide extension and MALDI-TOF mass spectrometry in proofreading and DNA repair assay. DNA Repair (Amst) 2018; 61:63-75. [PMID: 29223016 DOI: 10.1016/j.dnarep.2017.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/07/2017] [Accepted: 11/30/2017] [Indexed: 01/20/2023]
Abstract
Proofreading and DNA repair are important factors in maintaining the high fidelity of genetic information during DNA replication. Herein, we designed a non-labeled and non-radio-isotopic simple method to measure proofreading. An oligonucleotide primer is annealed to a template DNA forming a mismatched site and is proofread by Klenow fragment of Escherichia coli DNA polymerase I (pol I) in the presence of all four dideoxyribonucleotide triphosphates. The proofreading excision products and re-synthesis products of single nucleotide extension are subjected to MALDI-TOF mass spectrometry (MS). The proofreading at the mismatched site is identified by the mass change of the primer. We examined proofreading of Klenow fragment with DNAs containing various base mismatches. Single mismatches at the primer terminus can be proofread efficiently. Internal single mismatches can also be proofread at different efficiencies, with the best correction for mismatches located 2-4-nucleotides from the primer terminus. For mismatches located 5-nucleotides from the primer terminus there was partial correction and extension. No significant proofreading was observed for mismatches located 6-9-nucleotides from the primer terminus. We also subjected primers containing 3' penultimate deoxyinosine (dI) lesions, which mimic endonuclease V nicked repair intermediates, to pol I repair assay. The results showed that T-I was a better substrate than G-I and A-I, however C-I was refractory to repair. The high resolution of MS results clearly demonstrated that all the penultimate T-I, G-I and A-I substrates had been excised last 2 dI-containing nucleotides by pol I before adding a correct ddNMP, however, pol I proofreading exonuclease tolerated the penultimate C-I mismatch allowing the primer to be extended by polymerase activity.
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Hasegawa Y, Takada T, Nakamura M, Yamana K. Ferrocene conjugated oligonucleotide for electrochemical detection of DNA base mismatch. Bioorg Med Chem Lett 2017; 27:3555-7. [PMID: 28583799 DOI: 10.1016/j.bmcl.2017.05.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 05/01/2017] [Accepted: 05/16/2017] [Indexed: 01/25/2023]
Abstract
We describe the synthesis, binding, and electrochemical properties of ferrocene-conjugated oligonucleotides (Fc-oligos). The key step for the preparation of Fc-oligos contains the coupling of vinylferrocene to 5-iododeoxyuridine via Heck reaction. The Fc-conjugated deoxyuridine phosphoramidite was used in the Fc-oligonucleotide synthesis. We show that thiol-modified Fc-oligos deposited onto gold electrodes possess potential ability in electrochemical detection of DNA base mismatch.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Miao P, Tang Y, Wang L. DNA Modified Fe 3O 4@Au Magnetic Nanoparticles as Selective Probes for Simultaneous Detection of Heavy Metal Ions. ACS Appl Mater Interfaces 2017; 9:3940-3947. [PMID: 28079364 DOI: 10.1021/acsami.6b14247] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Driven by the urgent need to detect trace heavy metal ions in various real water samples, this article demonstrates for the first time an electrochemical biosensor based on DNA modified Fe3O4@Au magnetic nanoparticles (NPs). Three DNA probes are designed to contain certain mismatched base pairs. One is thiolated and modified on the surface of Fe3O4@Au NPs (DNA 1). The other two probes (DNA 2 and 3) are labeled with two independent electrochemical species. Stable structures of cytosine-Ag+-cytosine and thymine-Hg2+-thymine formed in the presence of Ag+ and Hg2+ can assist the hybridization of DNA 1/DNA 2 and DNA 1/DNA 3, which locate corresponding electrochemical species onto the surface of the magnetic NPs. The achieved nanocomposites are then used as selective electrochemical probes for the detection of heavy metal ions by recording the square wave voltammetry signals. Simultaneous detection of Ag+ and Hg2+ is demonstrated without significant interference, and their individual high sensitivities are fundamentally preserved, which meet the requirements of U.S. Environmental Protection Agency (USEPA). Furthermore, the proposed method has been challenged by various real water samples. The results confirm the DNA modified magnetic NPs based sensing method may have potential applications for the monitoring of heavy metal ions in real sample analysis.
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Affiliation(s)
- Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences , Suzhou 215163, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences , Suzhou 215163, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Lei Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences , Suzhou 215163, People's Republic of China
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Abstract
Colorectal cancer (CRC) is a heterogeneous disease for which the treatment backbone has primarily been cytotoxic chemotherapy. With better understanding of the involved molecular mechanisms, it is now known that there are a number of epigenetic and genetic events, which are involved in CRC pathogenesis. Specific biomarkers have been identified which can be used to determine the clinical outcome of patients beyond tumor staging and predict for treatment efficacy. Molecular testing is now routinely performed to select for patients that will benefit the most from targeted agents and immunotherapy. In addition to KRAS, NRAS, and BRAF mutation (MT), analysis of DNA mismatch repair (MMR) status, tumor infiltrating lymphocytes, and checkpoint protein expression may be helpful to determine whether patients are eligible for certain therapies. The focus of this article is to discuss present and upcoming biomarkers for immunotherapy in CRC.
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Affiliation(s)
- Manojkumar Bupathi
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, Richard Solove Research Institute and James Cancer Hospital, Columbus, Ohio, USA
| | - Christina Wu
- Division of Medical Oncology, The Ohio State University Wexner Medical Center, Richard Solove Research Institute and James Cancer Hospital, Columbus, Ohio, USA
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Abstract
A simple microplate method was designed for rapid testing DNA-binding activity of proteins. The principle of the assay involves binding of tested DNA by his-tagged protein immobilized on a nickel-coated ELISA plate, following colorimetric detection of biotinylated DNA with avidin conjugated to horseradish peroxidase. The method was used to compare DNA mismatch binding activities of MutS proteins from three bacterial species. The assay required relatively low amounts of tested protein (approximately 0.5-10 pmol) and DNA (0.1-10 pmol) and a relatively short time of analysis (up to 60 min). The method is very simple to apply and convenient to test different buffer conditions of DNA-protein binding. Sensitive colorimetric detection enables naked eye observations and quantitation with an ELISA reader. The performance of the assay, which we believe is a distinguishing trait of the method, is based on two strong and specific molecular interactions: binding of a his-tagged protein to a nickel-coated microplate and binding of biotinylated DNA to avidin. In the reported experiments, the solution was used to optimize the conditions for DNA mismatch binding by MutS protein; however, the approach could be implemented to test nucleic acids interactions with any protein of interest.
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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
| | - Paweł Sachadyn
- Department of Molecular Biotechnology and Microbiology, Gdańsk University of Technology, ul. Narutowicza 11/12, 80-233, Gdańsk, Poland.
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Lee CC, Yang YC, Goodman SD, Lin CJ, Chen YA, Wang YT, Cheng WC, Lin LI, Fang WH. The excision of 3' penultimate errors by DNA polymerase I and its role in endonuclease V-mediated DNA repair. DNA Repair (Amst) 2013; 12:899-911. [PMID: 24012058 DOI: 10.1016/j.dnarep.2013.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 11/28/2022]
Abstract
Deamination of adenine can occur spontaneously under physiological conditions, and is enhanced by exposure of DNA to ionizing radiation, UV light, nitrous acid, or heat, generating the highly mutagenic lesion of deoxyinosine in DNA. Such DNA lesions tends to generate A:T to G:C transition mutations if unrepaired. In Escherichia coli, deoxyinosine is primarily removed through a repair pathway initiated by endonuclease V (endo V). In this study, we compared the repair of three mutagenic deoxyinosine lesions of A-I, G-I, and T-I using E. coli cell-free extracts as well as reconstituted protein system. We found that 3'-5' exonuclease activity of DNA polymerase I (pol I) was very important for processing all deoxyinosine lesions. To understand the nature of pol I in removing damaged nucleotides, we systemically analyzed its proofreading to 12 possible mismatches 3'-penultimate of a nick, a configuration that represents a repair intermediate generated by endo V. The results showed all mismatches as well as deoxyinosine at the 3' penultimate site were corrected with similar efficiency. This study strongly supports for the idea that the 3'-5' exonuclease activity of E. coli pol I is the primary exonuclease activity for removing 3'-penultimate deoxyinosines derived from endo V nicking reaction.
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Affiliation(s)
- Chia-Chia Lee
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 100-02, Taiwan, ROC
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