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Shen K, Flood JJ, Zhang Z, Ha A, Shy B, Dueber J, Douglas S. Engineering an Escherichia coli strain for production of long single-stranded DNA. Nucleic Acids Res 2024; 52:4098-4107. [PMID: 38499480 PMCID: PMC11040142 DOI: 10.1093/nar/gkae189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Long single-stranded DNA (ssDNA) is a versatile molecular reagent with applications including RNA-guided genome engineering and DNA nanotechnology, yet its production is typically resource-intensive. We introduce a novel method utilizing an engineered Escherichia coli 'helper' strain and phagemid system that simplifies long ssDNA generation to a straightforward transformation and purification procedure. Our method obviates the need for helper plasmids and their associated contamination by integrating M13mp18 genes directly into the E. coli chromosome. We achieved ssDNA lengths ranging from 504 to 20 724 nt with titers up to 250 μg/l following alkaline lysis purification. The efficacy of our system was confirmed through its application in primary T-cell genome modifications and DNA origami folding. The reliability, scalability and ease of our approach promise to unlock new experimental applications requiring large quantities of long ssDNA.
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Affiliation(s)
- Konlin Shen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158 USA
| | - Jake J Flood
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720 USA
| | - Zhihuizi Zhang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158 USA
| | - Alvin Ha
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143 USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, 94158 USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, 94143 USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143 USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, 94158 USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, 94143 USA
| | - John E Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720 USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Shawn M Douglas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158 USA
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Shen K, Flood JJ, Zhang Z, Ha A, Shy BR, Dueber JE, Douglas SM. Engineering an Escherichia coli strain for production of long single-stranded DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582394. [PMID: 38464036 PMCID: PMC10925301 DOI: 10.1101/2024.02.27.582394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Long single-stranded DNA (ssDNA) is a versatile molecular reagent with applications including RNA-guided genome engineering and DNA nanotechnology, yet its production is typically resource-intensive. We introduce a novel method utilizing an engineered E. coli "helper" strain and phagemid system that simplifies long ssDNA generation to a straightforward transformation and purification procedure. Our method obviates the need for helper plasmids and their associated contamination by integrating M13mp18 genes directly into the E. coli chromosome. We achieved ssDNA lengths ranging from 504 to 20,724 nucleotides with titers up to 250 μg/L following alkaline-lysis purification. The efficacy of our system was confirmed through its application in primary T cell genome modifications and DNA origami folding. The reliability, scalability, and ease of our approach promises to unlock new experimental applications requiring large quantities of long ssDNA.
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Affiliation(s)
- Konlin Shen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Jake J Flood
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhihuizi Zhang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Alvin Ha
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - John E Dueber
- Department of Bioengineering, University of California, Berkeley, CA, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shawn M Douglas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
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Iyer S, Mir A, Vega-Badillo J, Roscoe BP, Ibraheim R, Zhu LJ, Lee J, Liu P, Luk K, Mintzer E, Guo D, Soares de Brito J, Emerson CP, Zamore PD, Sontheimer EJ, Wolfe SA. Efficient Homology-Directed Repair with Circular Single-Stranded DNA Donors. CRISPR J 2022; 5:685-701. [PMID: 36070530 PMCID: PMC9595650 DOI: 10.1089/crispr.2022.0058] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
While genome editing has been revolutionized by the advent of CRISPR-based nucleases, difficulties in achieving efficient, nuclease-mediated, homology-directed repair (HDR) still limit many applications. Commonly used DNA donors such as plasmids suffer from low HDR efficiencies in many cell types, as well as integration at unintended sites. In contrast, single-stranded DNA (ssDNA) donors can produce efficient HDR with minimal off-target integration. In this study, we describe the use of ssDNA phage to efficiently and inexpensively produce long circular ssDNA (cssDNA) donors. These cssDNA donors serve as efficient HDR templates when used with Cas9 or Cas12a, with integration frequencies superior to linear ssDNA (lssDNA) donors. To evaluate the relative efficiencies of imprecise and precise repair for a suite of different Cas9 or Cas12a nucleases, we have developed a modified traffic light reporter (TLR) system (TLR-multi-Cas variant 1 [MCV1]) that permits side-by-side comparisons of different nuclease systems. We used this system to assess editing and HDR efficiencies of different nuclease platforms with distinct DNA donor types. We then extended the analysis of DNA donor types to evaluate efficiencies of fluorescent tag knockins at endogenous sites in HEK293T and K562 cells. Our results show that cssDNA templates produce efficient and robust insertion of reporter tags. Targeting efficiency is high, allowing production of biallelic integrants using cssDNA donors. cssDNA donors also outcompete lssDNA donors in template-driven repair at the target site. These data demonstrate that circular donors provide an efficient, cost-effective method to achieve knockins in mammalian cell lines.
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Affiliation(s)
- Sukanya Iyer
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA
| | - Aamir Mir
- RNA Therapeutics Institute; Worcester, Massachusetts, USA
| | | | - Benjamin P. Roscoe
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA
| | - Raed Ibraheim
- RNA Therapeutics Institute; Worcester, Massachusetts, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA.,Program in Bioinformatics and Integrative Biology; Worcester, Massachusetts, USA
| | - Jooyoung Lee
- RNA Therapeutics Institute; Worcester, Massachusetts, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA
| | - Esther Mintzer
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA
| | - Dongsheng Guo
- Wellstone Program, Department of Neurology; Worcester, Massachusetts, USA
| | | | - Charles P. Emerson
- Wellstone Program, Department of Neurology; Worcester, Massachusetts, USA
| | - Phillip D. Zamore
- RNA Therapeutics Institute; Worcester, Massachusetts, USA.,Howard Hughes Medical Institute; Worcester, Massachusetts, USA
| | - Erik J. Sontheimer
- RNA Therapeutics Institute; Worcester, Massachusetts, USA.,Program in Molecular Medicine; and Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Disease Research; University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.,Address correspondence to: Erik J. Sontheimer, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 364 Plantation Street, Worcester, MA 01605-2324, USA,
| | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology; Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Disease Research; University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.,Address correspondence to: Scot A. Wolfe, Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, L.R.B. 619, 364 Plantation Street, Worcester, MA 01605, USA,
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McSweeney MA, Styczynski MP. Effective Use of Linear DNA in Cell-Free Expression Systems. Front Bioeng Biotechnol 2021; 9:715328. [PMID: 34354989 PMCID: PMC8329657 DOI: 10.3389/fbioe.2021.715328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/06/2021] [Indexed: 12/27/2022] Open
Abstract
Cell-free expression systems (CFEs) are cutting-edge research tools used in the investigation of biological phenomena and the engineering of novel biotechnologies. While CFEs have many benefits over in vivo protein synthesis, one particularly significant advantage is that CFEs allow for gene expression from both plasmid DNA and linear expression templates (LETs). This is an important and impactful advantage because functional LETs can be efficiently synthesized in vitro in a few hours without transformation and cloning, thus expediting genetic circuit prototyping and allowing expression of toxic genes that would be difficult to clone through standard approaches. However, native nucleases present in the crude bacterial lysate (the basis for the most affordable form of CFEs) quickly degrade LETs and limit expression yield. Motivated by the significant benefits of using LETs in lieu of plasmid templates, numerous methods to enhance their stability in lysate-based CFEs have been developed. This review describes approaches to LET stabilization used in CFEs, summarizes the advancements that have come from using LETs with these methods, and identifies future applications and development goals that are likely to be impactful to the field. Collectively, continued improvement of LET-based expression and other linear DNA tools in CFEs will help drive scientific discovery and enable a wide range of applications, from diagnostics to synthetic biology research tools.
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Affiliation(s)
- Megan A McSweeney
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| | - Mark P Styczynski
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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Hao M, Wang Z, Qiao H, Yin P, Qiao J, Qi H. Dynamic Genome Editing Using In Vivo Synthesized Donor ssDNA in Escherichia coli. Cells 2020; 9:E467. [PMID: 32085579 PMCID: PMC7072734 DOI: 10.3390/cells9020467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/07/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
As a key element of genome editing, donor DNA introduces the desired exogenous sequence while working with other crucial machinery such as CRISPR-Cas or recombinases. However, current methods for the delivery of donor DNA into cells are both inefficient and complicated. Here, we developed a new methodology that utilizes rolling circle replication and Cas9 mediated (RC-Cas-mediated) in vivo single strand DNA (ssDNA) synthesis. A single-gene rolling circle DNA replication system from Gram-negative bacteria was engineered to produce circular ssDNA from a Gram-positive parent plasmid at a designed sequence in Escherichia coli. Furthermore, it was demonstrated that the desired linear ssDNA fragment could be cut out using CRISPR-associated protein 9 (CRISPR-Cas9) nuclease and combined with lambda Red recombinase as donor for precise genome engineering. Various donor ssDNA fragments from hundreds to thousands of nucleotides in length were synthesized in E. coli cells, allowing successive genome editing in growing cells. We hope that this RC-Cas-mediated in vivo ssDNA on-site synthesis system will be widely adopted as a useful new tool for dynamic genome editing.
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Affiliation(s)
- Min Hao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hongyan Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Peng Yin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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Hao M, Qiao J, Qi H. Current and Emerging Methods for the Synthesis of Single-Stranded DNA. Genes (Basel) 2020; 11:E116. [PMID: 31973021 PMCID: PMC7073533 DOI: 10.3390/genes11020116] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/21/2022] Open
Abstract
Methods for synthesizing arbitrary single-strand DNA (ssDNA) fragments are rapidly becoming fundamental tools for gene editing, DNA origami, DNA storage, and other applications. To meet the rising application requirements, numerous methods have been developed to produce ssDNA. Some approaches allow the synthesis of freely chosen user-defined ssDNA sequences to overcome the restrictions and limitations of different length, purity, and yield. In this perspective, we provide an overview of the representative ssDNA production strategies and their most significant challenges to enable the readers to make informed choices of synthesis methods and enhance the availability of increasingly inexpensive synthetic ssDNA. We also aim to stimulate a broader interest in the continued development of efficient ssDNA synthesis techniques and improve their applications in future research.
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Affiliation(s)
- Min Hao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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Shimpi GG, Vargas S, Wörheide G. Modified parallel strategies for preparation of heteroduplex plasmids for in vitro mismatch repair assays. Anal Biochem 2018; 556:35-39. [PMID: 29940140 DOI: 10.1016/j.ab.2018.06.020] [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] [Received: 05/09/2018] [Revised: 06/17/2018] [Accepted: 06/20/2018] [Indexed: 11/19/2022]
Abstract
We present efficient and reproducible parallel strategies for preparing large quantities of pure heteroduplex plasmids containing defined mismatches. The strategies described involve the use of synthetic oligonucleotides, the commercially available pGEM-T plasmid, and nicking enzymes to prepare prerequisite ssDNA. Alternatively, bacterial packaging cell lines containing an engineered phagemid construct to produce ssDNA without the need of a helper phage were utilized, hence providing added flexibility and choice. These integrated approaches help to construct different mismatch substrates of choice in large quantities, thus enhancing the usability of mismatch repair assays and extending their range and accessibility to wider research groups.
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Affiliation(s)
- Gaurav G Shimpi
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany.
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany.
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany; GeoBio-Center(LMU), Richard-Wagner-Str. 10, 80333, Munich, Germany; SNSB -Bavarian State Collections of Palaeontology and Geology, Richard-Wagner-Str. 10, 80333, Munich, Germany.
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8
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Petrova L, Gran C, Bjoras M, Doetsch PW. Efficient and Reliable Production of Vectors for the Study of the Repair, Mutagenesis, and Phenotypic Consequences of Defined DNA Damage Lesions in Mammalian Cells. PLoS One 2016; 11:e0158581. [PMID: 27362559 PMCID: PMC4928824 DOI: 10.1371/journal.pone.0158581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/17/2016] [Indexed: 11/28/2022] Open
Abstract
Mammalian cells are constantly and unavoidably exposed to DNA damage from endogenous and exogenous sources, frequently to the detriment of genomic integrity and biological function. Cells acquire a large number of chemically diverse lesions per day, and each can have a different genetic fate and biological consequences. However, our knowledge of how and when specific lesions are repaired or how they may compromise the fidelity of DNA replication or transcription and lead to deleterious biological endpoints in mammalian cells is limited. Studying individual lesions requires technically challenging approaches for the targeted introduction of defined lesions into relevant DNA sequences of interest. Here, we present a systematic analysis of factors influencing yield and an improved, efficient and reliable protocol for the production of mammalian expression phagemid vectors containing defined DNA base modifications in any sequence position of either complementary DNA strand. We applied our improved protocol to study the transcriptional mutagenesis-mediated phenotypic consequences of the common oxidative lesion 5-hydroxyuracil, placed in the G12 mutational hotspot of the KRAS oncogene. 5-OHU induced sustained oncogenic signaling in Neil1-/-Neil2-/- mouse cells. The resulting advance in technology will have broad applicability for investigation of single lesion DNA repair, mutagenesis, and DNA damage responses in mammalian cells.
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Affiliation(s)
- Lucy Petrova
- Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, United States of America
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Christine Gran
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Magnar Bjoras
- Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Paul W. Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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Urayama SI, Yoshida-Takashima Y, Yoshida M, Tomaru Y, Moriyama H, Takai K, Nunoura T. A New Fractionation and Recovery Method of Viral Genomes Based on Nucleic Acid Composition and Structure Using Tandem Column Chromatography. Microbes Environ 2015; 30:199-203. [PMID: 26004793 PMCID: PMC4462933 DOI: 10.1264/jsme2.me14174] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/14/2015] [Indexed: 11/12/2022] Open
Abstract
Metagenomic studies have revealed the unexplored diversity of the environmental virosphere. However, most studies are biased towards specific types of viral genomes due to the absence of universal methods to access all viral genome types. In the present study, we established a novel system to efficiently separate single- and double-stranded DNA/RNA viral genomes using hydroxyapatite and cellulose chromatography. This method will allow us to quantitatively and simultaneously access four types of viral genomes and will provide important clues to further understand previously unexplored environmental viral populations and obtain potentially unbiased libraries from environmental viral communities.
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Affiliation(s)
- Syun-ichi Urayama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061Japan
| | - Yukari Yoshida-Takashima
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061Japan
| | - Mitsuhiro Yoshida
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061Japan
| | - Yuji Tomaru
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency2–17–5 Maruishi, Hatsukaichi, Hiroshima 739–0452Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology3–5–8 Saiwaicho, Fuchu, Tokyo 183–8509Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, JAMSTEC2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061Japan
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Chen Y, Huang C, Bai C, Gao H, Ma R, Liu X, Dong Q. Benzo[α]pyrene repressed DNA mismatch repair in human breast cancer cells. Toxicology 2013; 304:167-72. [DOI: 10.1016/j.tox.2013.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/12/2012] [Accepted: 01/04/2013] [Indexed: 10/27/2022]
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Iwaizumi M, Tseng-Rogenski S, Carethers JM. DNA mismatch repair proficiency executing 5-fluorouracil cytotoxicity in colorectal cancer cells. Cancer Biol Ther 2011; 12:756-64. [PMID: 21814034 DOI: 10.4161/cbt.12.8.17169] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND 5-fluorouracil (5FU)-based chemotherapy is the standard treatment for advanced stage colorectal cancer (CRC) patients. Several groups including ours have reported that stage II-III colorectal cancer patients whose tumors retain DNA Mismatch repair (MMR) function derive a benefit from 5FU, but patients with tumors that lost MMR function do not. Although MMR recognition of 5FU incorporated in DNA has been demonstrated biochemically, it has not been demonstrated within cells to execute 5FU cytotoxicity. AIM To establish an efficient construction model for 5FU within DNA and demonstrate that 5FU incorporated into DNA can trigger cellular cytotoxicity executed by the DNA MMR system. METHODS We constructed a 5FdU-containing heteroduplex plasmid (5FdU plasmid) and 5FdU-containing linear dsDNA (5FdU linear DNA), and transfected these into MMR-proficient, hMLH1-/- and hMSH6-/- cells. We observed cell growth characteristics of both transfectants for 5FU-induced cytotoxicity. RESULTS MMR- proficient cells transfected with the 5FdU plasmid but not the 5FdU linear DNA showed reduced cell proliferation by MTS and clonogenic assays, and demonstrated cell morphological change consistent with apoptosis. In MMR-deficient cells, neither the 5FdU plasmid nor 5FdU linear DNA induced cell growth or morphological changes different from controls. CONCLUSION 5FdU as heteroduplex DNA in plasmid but not linear form triggered cytotoxicity in a MMR-dependent manner. Thus 5FU incorporated into DNA, separated from its effects on RNA, can be recognized by DNA MMR to trigger cell death.
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Affiliation(s)
- Moriya Iwaizumi
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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