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Kawai H, Yazama K, Yanai Y, Kamitsubo R, Kamiya H. Gene correction by 5'-tailed duplexes with short editor oligodeoxyribonucleotides. J Biosci Bioeng 2021; 132:552-559. [PMID: 34518106 DOI: 10.1016/j.jbiosc.2021.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 01/02/2023]
Abstract
Various diseases, including cancer, are caused by genetic mutations. A 5'-tailed duplex (TD) DNA, consisting of a long single-stranded (ss) editor DNA and a short (∼35-base) ss assistant oligodeoxyribonucleotide, can introduce a base-substitution in living cells and thus correct mutated genes. Previously, several hundred-base DNAs were employed as the editor DNAs. In this study, 5'-TDs were prepared from various editor DNAs with different lengths and examined for their gene correction abilities, using plasmid DNA bearing a mutated copepod green fluorescent protein (copGFP) gene, in human cells. High-throughput analysis was performed by the reactivated fluorescence of the wild-type protein encoded by the corrected gene as the indicator. The analysis revealed that 5'-TDs with ∼100-base ss editor DNAs enabled gene editing at least as efficiently as those with longer editor DNAs. Moreover, the antisense strand was more effective as the editor than the sense strand, in contrast to the 5'-TDs with longer editor strands. These results indicated that the 5'-TD fragments with shorter editor strands than those used in previous studies are useful nucleic acids for gene correction.
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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
| | - Kentaro Yazama
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Yuri Yanai
- Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Ryotaro Kamitsubo
- 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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Suzuki T, Yanai Y, Nishigaki N, Nakatsu Y, Tsuzuki T, Kamiya H. Effects of mismatches distant from the target position on gene correction with a 5′-tailed duplex. J Biosci Bioeng 2018; 125:619-623. [DOI: 10.1016/j.jbiosc.2017.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/14/2017] [Accepted: 12/17/2017] [Indexed: 11/16/2022]
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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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Suzuki T, Imada T, Nishigaki N, Kobayashi M, Matsuoka I, Kamiya H. Cleavage of Target DNA Promotes Sequence Conversion with a Tailed Duplex. Biol Pharm Bull 2016; 39:1392-5. [DOI: 10.1248/bpb.b16-00325] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Tetsuya Suzuki
- Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Takashi Imada
- Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Natsuki Nishigaki
- Graduate School of Biomedical and Health Sciences, Hiroshima University
- Graduate School of Science and Engineering, Ehime University
| | | | | | - Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University
- Graduate School of Science and Engineering, Ehime University
- College of Pharmaceutical Sciences, Matsuyama University
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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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Sargent RG, Kim S, Gruenert DC. Oligo/polynucleotide-based gene modification: strategies and therapeutic potential. Oligonucleotides 2011; 21:55-75. [PMID: 21417933 DOI: 10.1089/oli.2010.0273] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oligonucleotide- and polynucleotide-based gene modification strategies were developed as an alternative to transgene-based and classical gene targeting-based gene therapy approaches for treatment of genetic disorders. Unlike the transgene-based strategies, oligo/polynucleotide gene targeting approaches maintain gene integrity and the relationship between the protein coding and gene-specific regulatory sequences. Oligo/polynucleotide-based gene modification also has several advantages over classical vector-based homologous recombination approaches. These include essentially complete homology to the target sequence and the potential to rapidly engineer patient-specific oligo/polynucleotide gene modification reagents. Several oligo/polynucleotide-based approaches have been shown to successfully mediate sequence-specific modification of genomic DNA in mammalian cells. The strategies involve the use of polynucleotide small DNA fragments, triplex-forming oligonucleotides, and single-stranded oligodeoxynucleotides to mediate homologous exchange. The primary focus of this review will be on the mechanistic aspects of the small fragment homologous replacement, triplex-forming oligonucleotide-mediated, and single-stranded oligodeoxynucleotide-mediated gene modification strategies as it relates to their therapeutic potential.
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Affiliation(s)
- R Geoffrey Sargent
- Department of Otolaryngology-Head and Neck Surgery, University of California , San Francisco, California 94115, USA
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Kamiya H, Uchiyama M, Piao J, Nakatsu Y, Tsuzuki T, Harashima H. Targeted sequence alteration of a chromosomal locus in mouse liver. Int J Pharm 2010; 387:180-3. [DOI: 10.1016/j.ijpharm.2009.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 12/04/2009] [Accepted: 12/10/2009] [Indexed: 10/20/2022]
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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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