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Kawai H, Sato K, Kato T, Kamiya H. Correction of substitution, deletion, and insertion mutations by 5'-tailed duplexes. J Biosci Bioeng 2024; 137:157-164. [PMID: 38216338 DOI: 10.1016/j.jbiosc.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
Germline and somatic mutations cause various diseases, including cancer. Clinical applications of genome editing are keenly anticipated, since it can cure genetic diseases. Recently, we reported that a 5'-tailed duplex (TD), consisting of an approximately 80-base editor strand oligodeoxyribonucleotide and a 35-base assistant strand oligodeoxyribonucleotide, could edit a target gene on plasmid DNA and correct a single-base substitution mutation without an artificial nuclease in human cells. In this study, we assessed the ability of the TD to correct base substitution mutations located consecutively or separately, and deletion and insertion mutations. A TD with an 80-base editor strand was co-introduced into human U2OS cells with plasmid DNA bearing either a wild-type or mutated copepod green fluorescent protein (copGFP) gene. Among the mutations, three-base consecutive substitutions were efficiently repaired. The correction efficiencies of deletion mutations were similar to those of substitution mutations, and two to three times higher than those of insertion mutations. Up to three-base substitution, deletion, and insertion mutations were excellent targets for correction by TDs. These results suggested that the TDs are useful for editing disease-causing genes with small mutations.
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Affiliation(s)
- Hidehiko Kawai
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Kento Sato
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Taiki Kato
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan.
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Méndez-Scolari JE, Florentín-Pavía MM, Mujica MP, Rojas N, Sotelo PH. A qPCR Targeted Against the Viral Replication Origin Designed to Quantify Total Amount of Filamentous Phages and Phagemids. Indian J Microbiol 2019; 59:365-369. [PMID: 31388215 DOI: 10.1007/s12088-019-00798-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/19/2019] [Indexed: 10/27/2022] Open
Abstract
Filamentous bacteriophages are widely used in phage display technology. The most common quantification method is lysis plaque formation test (PFT). This technique has several disadvantages, and only quantifies infective phages and is not effective when phagemids are used. We developed a qPCR method directed against the M13 replication origin, which detects between 3.3 × 103 and 3.3 × 108 viral genome copies with a linearity of R 2 = 0.9998. Using this method we were able to observe a difference of approximately ten more phages than with the PFT. This difference was not due to the presence of a free genome, which suggests the presence of non-infective particles. Using a DNaseI treatment, we observed the presence of 30% to 40% of unpackaged genome in recombinant phage modified in PIII or PVIII. The qPCR method with a DNase I treatment is an efficient method to quantify the total amount of filamentous phages.
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Affiliation(s)
- J E Méndez-Scolari
- Dpto. de Biotecnología, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, Campus Universitario, San Lorenzo, Paraguay
| | - M M Florentín-Pavía
- Dpto. de Biotecnología, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, Campus Universitario, San Lorenzo, Paraguay
| | - M P Mujica
- Dpto. de Biotecnología, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, Campus Universitario, San Lorenzo, Paraguay
| | - N Rojas
- Dpto. de Biotecnología, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, Campus Universitario, San Lorenzo, Paraguay
| | - P H Sotelo
- Dpto. de Biotecnología, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, Campus Universitario, San Lorenzo, Paraguay
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Peng X, Nguyen A, Ghosh D. Quantification of M13 and T7 bacteriophages by TaqMan and SYBR green qPCR. J Virol Methods 2017; 252:100-107. [PMID: 29196210 DOI: 10.1016/j.jviromet.2017.11.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/23/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022]
Abstract
TaqMan and SYBR Green quantitative PCR (qPCR) methods were developed as DNA-based approaches to reproducibly enumerate M13 and T7 phages from phage display selection experiments individually and simultaneously. The genome copies of M13 and T7 phages were quantified by TaqMan or SYBR Green qPCR referenced against M13 and T7 DNA standard curves of known concentrations. TaqMan qPCR was capable of quantifying M13 and T7 phage DNA simultaneously with a detection range of 2.75*101-2.75*108genome copies(gc)/μL and 2.66*101-2.66*108 genome copies(gc)/μL respectively. TaqMan qPCR demonstrated an efficient amplification efficiency (Es) of 0.97 and 0.90 for M13 and T7 phage DNA, respectively. SYBR Green qPCR was ten-fold more sensitive than TaqMan qPCR, able to quantify 2.75-2.75*107gc/μL and 2.66*101-2.66*107gc/μL of M13 and T7 phage DNA, with an amplification efficiency Es of 1.06 and 0.78, respectively. Due to its superior sensitivity, SYBR Green qPCR was used to enumerate M13 and T7 phage display clones selected against a cell line, and quantified titers demonstrated accuracy comparable to titers from traditional double-layer plaque assay. Compared to enzyme linked immunosorbent assay, both qPCR methods exhibited increased detection sensitivity and reproducibility. These qPCR methods are reproducible, sensitive, and time-saving to determine their titers and to quantify a large number of phage samples individually or simultaneously, thus avoiding the need for time-intensive double-layer plaque assay. These findings highlight the attractiveness of qPCR for phage enumeration for applications ranging from selection to next-generation sequencing (NGS).
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Affiliation(s)
- Xiujuan Peng
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy
| | - Alex Nguyen
- College of Natural Science, University of Texas, Austin, United States
| | - Debadyuti Ghosh
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy.
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Kamiya H, Nishigaki N, Ikeda A, Yukawa S, Morita Y, Nakatsu Y, Tsuzuki T, Harashima H. Insertion and Deletion Mismatches Distant from the Target Position Improve Gene Correction with a Tailed Duplex. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:379-88. [PMID: 27253876 DOI: 10.1080/15257770.2016.1163384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A 5'-tailed duplex (TD) DNA corrects a base-substitution mutation. In this study, the effects of insertion and deletion (indel) mismatches distant from the target position on the gene correction were examined. Three target plasmid DNAs with and without indel mismatches ∼330 bases distant from the correction target position were prepared, and introduced into HeLa cells together with the TD. The indel mismatches improved the gene correction efficiency and specificity without sequence conversions at the indel mismatch site. These results suggested that the gene correction efficiency and specificity are increased when an appropriate second mismatch is introduced into the TD fragment.
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Affiliation(s)
- Hiroyuki Kamiya
- a Graduate School of Science and Engineering, Ehime University , Matsuyama , Japan.,b Graduate School of Biomedical and Health Sciences, Hiroshima University , Minami-ku, Hiroshima , Japan.,c Faculty of Pharmaceutical Sciences, Hokkaido University , Sapporo , Japan
| | - Natsuki Nishigaki
- a Graduate School of Science and Engineering, Ehime University , Matsuyama , Japan.,b Graduate School of Biomedical and Health Sciences, Hiroshima University , Minami-ku, Hiroshima , Japan
| | - Akihiro Ikeda
- a Graduate School of Science and Engineering, Ehime University , Matsuyama , Japan
| | - Seiya Yukawa
- a Graduate School of Science and Engineering, Ehime University , Matsuyama , Japan
| | - Yukiko Morita
- c Faculty of Pharmaceutical Sciences, Hokkaido University , Sapporo , Japan
| | - Yoshimichi Nakatsu
- d Graduate School of Medical Sciences, Kyushu University , Higashi-ku, Fukuoka , Japan
| | - Teruhisa Tsuzuki
- d Graduate School of Medical Sciences, Kyushu University , Higashi-ku, Fukuoka , Japan
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Morita Y, Tsuchiya H, Harashima H, Kamiya H. Correction of frameshift mutations with tailed duplex DNAs. Biol Pharm Bull 2011; 34:1465-8. [PMID: 21881234 DOI: 10.1248/bpb.34.1465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tailed duplex (TD) DNAs, prepared by annealing an oligonucleotide to a several-hundred-base single-stranded (ss) DNA fragment, correct a base-substitution mutation with high efficiency. In the present study, the abilities of TD fragments to correct single-base insertion and deletion mutations were examined, using hygromycin-resistance and enhanced green fluorescent protein fusion (Hyg-EGFP) genes inactivated by +G and -C frameshift mutations. The 5'-TD and 3'-TD DNA fragments were co-transfected with plasmid DNA containing the inactivated Hyg-EGFP gene into CHO-K1 cells, and the gene correction efficiencies were determined by introducing the plasmid DNA recovered from the transfected cells into Escherichia coli cells. In contrast to their efficiencies for the substitution mutation, the gene correction abilities of the TD fragments were relatively low. The correction efficiencies by the TD fragments were apparently higher than that by a ss DNA fragment, one of the DNA fragments employed for gene correction. These results suggest that the TD fragments have the potential to correct frameshift mutations, although further improvement is required.
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Affiliation(s)
- Yukiko Morita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Japan
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Bedayat B, Abdolmohamadi A, Ye L, Maurisse R, Parsi H, Schwarz J, Emamekhoo H, Nicklas JA, O'Neill JP, Gruenert DC. Sequence-specific correction of genomic hypoxanthine-guanine phosphoribosyl transferase mutations in lymphoblasts by small fragment homologous replacement. Oligonucleotides 2010; 20:7-16. [PMID: 19995283 DOI: 10.1089/oli.2009.0205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Oligo/polynucleotide-based gene targeting strategies provide new options for achieving sequence-specific modification of genomic DNA and have implications for the development of new therapies and transgenic animal models. One such gene modification strategy, small fragment homologous replacement (SFHR), was evaluated qualitatively and quantitatively in human lymphoblasts that contain a single base substitution in the hypoxanthine-guanine phosphoribosyl transferase (HPRT1) gene. Because HPRT1 mutant cells are readily discernable from those expressing the wild type (wt) gene through growth in selective media, it was possible to identify and isolate cells that have been corrected by SFHR. Transfection of HPRT1 mutant cells with polynucleotide small DNA fragments (SDFs) comprising wild type HPRT1 (wtHPRT1) sequences resulted in clones of cells that grew in hypoxanthine-aminopterin-thymidine (HAT) medium. Initial studies quantifying the efficiency of correction in 3 separate experiments indicate frequencies ranging from 0.1% to 2%. Sequence analysis of DNA and RNA showed correction of the HPRT1 mutation. Random integration was not indicated after transfection of the mutant cells with an SDF comprised of green fluorescent protein (GFP) sequences that are not found in human genomic DNA. Random integration was also not detected following Southern blot hybridization analysis of an individual corrected cell clone.
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Affiliation(s)
- Babak Bedayat
- California Pacific Medical Center Research Institute, San Francisco, California 94107, USA
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McLachlan J, Fernandez S, Helleday T, Bryant HE. Specific targeted gene repair using single-stranded DNA oligonucleotides at an endogenous locus in mammalian cells uses homologous recombination. DNA Repair (Amst) 2009; 8:1424-33. [PMID: 19854687 DOI: 10.1016/j.dnarep.2009.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Revised: 09/23/2009] [Accepted: 09/29/2009] [Indexed: 01/29/2023]
Abstract
The feasibility of introducing point mutations in vivo using single-stranded DNA oligonucleotides (ssON) has been demonstrated but the efficiency and mechanism remain elusive and potential side effects have not been fully evaluated. Understanding the mechanism behind this potential therapy may help its development. Here, we demonstrate the specific repair of an endogenous non-functional hprt gene by a ssON in mammalian cells, and show that the frequency of such an event is enhanced when cells are in S-phase of the cell cycle. A potential barrier in using ssONs as gene therapy could be non-targeted mutations or gene rearrangements triggered by the ssON. Both the non-specific mutation frequencies and the frequency of gene rearrangements were largely unaffected by ssONs. Furthermore, we find that the introduction of a mutation causing the loss of a functional endogenous hprt gene by a ssON occurred at a similarly low but statistically significant frequency in wild type cells and in cells deficient in single strand break repair, nucleotide excision repair and mismatch repair. However, this mutation was not induced in XRCC3 mutant cells deficient in homologous recombination. Thus, our data suggest ssON-mediated targeted gene repair is more efficient in S-phase and involves homologous recombination.
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Affiliation(s)
- Jennifer McLachlan
- The Institute for Cancer Studies, University of Sheffield, Sheffield S10 2RX, UK
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Zhou B, Dong Q, Ma R, Chen Y, Yang J, Sun LZ, Huang C. Rapid isolation of highly pure single-stranded DNA from phagemids. Anal Biochem 2009; 389:177-9. [PMID: 19348781 DOI: 10.1016/j.ab.2009.03.044] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 03/30/2009] [Accepted: 03/30/2009] [Indexed: 10/20/2022]
Abstract
Single-stranded DNA (ssDNA) has many applications in molecular biology and biotechnology. The conventional method for the preparation of ssDNA from phagemids is laborious, costly, and inefficient. Here we describe an integrated protocol for consistent production of phagemid ssDNA from a bacteria/phagemid/help phage complex and rapid isolation and purification of the ssDNA with a silica column followed by duplex-specific nuclease digestion. The major advantages of our method are the expediency, low cost, and consistent yield of highly pure ssDNA that is suitable for direct sequencing and other applications. This method is especially useful for large-scale preparation of high-quality ssDNA.
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Affiliation(s)
- Bisheng Zhou
- Institute of Watershed Science and Environmental Ecology, Wenzhou Medical College, Wenzhou 325035, People's Republic of China
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Harashima H, Kogure K, Yamada Y, Akita H, Kamiya H. [Development of multifunctional envelope type artificial viral-like gene delivery system]. YAKUGAKU ZASSHI 2007; 127:1655-72. [PMID: 17917423 DOI: 10.1248/yakushi.127.1655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This review introduces a new concept "Programmed Packaging" to develop a non-viral gene delivery system. Based on this concept, multifunctional envelope type nano devices (MEND) were developed for in vitro, in situ and in vivo conditions. A quantitative study to identify a rate limiting step in intracellular trafficking was also shown between viral and non-viral vectors, which indicated an important role of controlled intranuclear disposition for development a safe and efficient non-viral gene delivery system. This review will provide a future direction of non-viral gene delivery system.
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Affiliation(s)
- Hideyoshi Harashima
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Kita 12 Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
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