• BMB Reports
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• v.43 no.11
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• pp.732-737
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• 2010

RNA interference is a post-transcriptional silencing mechanism triggered by the bioavailability and/or exogenous introduction of double-stranded RNA (dsRNA) into cells. Here we describe a novel method for the synthesis of siRNA in a single vessel. The method employs in vitro transcription and a single-stranded DNA (ssDNA) template and design, which incorporates upon self-annealing, two promoters, two templates, and three loop regions. Using this method of synthesis we generated efficacious siRNAs designed to silence both exogenous and endogenous genes in mammalian cells. Due to its unique design the single-stranded template is easily amenable to adaptation for attachment to surface platforms for synthesis of siRNAs. A siRNA synthesis platform was generated using a 3' end-biotinylated ssDNA template tethered to a streptavidin coated surface that generates stable siRNAs under multiple cycles of production. Together these data demonstrate a unique and robust method for scalable siRNA synthesis with potential application in RNAi-based array systems.

• BMB Reports
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• v.51 no.9
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• pp.437-443
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• 2018

Non-homologous end joining (NHEJ), and to a lesser extent, the error-free pathway known as homology-directed repair (HDR) are cellular mechanisms for recovery from double-strand DNA breaks (DSB) induced by RNA-guided programmable nuclease CRISPR/Cas. Since NHEJ is equivalent to using a duck tape to stick two pieces of metals together, the outcome of this repair mechanism is prone to error. Any out-of-frame mutations or premature stop codons resulting from NHEJ repair mechanism are extremely handy for loss-of-function studies. Substitution of a mutation on the genome with the correct exogenous repair DNA requires coordination via an error-free HDR, for targeted transgenesis. However, several practical limitations exist in harnessing the potential of HDR to replace a faulty mutation for therapeutic purposes in all cell types and more so in somatic cells. In germ cells after the DSB, copying occurs from the homologous chromosome, which increases the chances of incorporation of exogenous DNA with some degree of homology into the genome compared with somatic cells where copying from the identical sister chromatid is always preferred. This review summarizes several strategies that have been implemented to increase the frequency of HDR with a focus on somatic cells. It also highlights the limitations of this technology in gene therapy and suggests specific solutions to circumvent those barriers.

• Journal of Plant Biology
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• v.36 no.1
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• pp.19-27
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• 1993

Effects of polyamines on DNA synthesis were studied in synchronized culture of Nicotiana tabacum L. When DFMO and DFMA, inhibitors of ornithine decarboxylase and arginine decarboxylase, respectively were initially applied to the cells, the polyamine contents were rapidly dropped and [methyl-3H] thymidine incorporation into DNA was markedly reduced during the early stage of culture period. Inhibition of DNA synthesis, however, was partially reversed when these inhibitors were applied simultaneously with putrescine. In addition, exogenous administration of putrescine also increased the DNA synthesis during the all over the culture period. In vitro activity of DNA polymerase from Nicotiana tabacum L. was promoted by increasing concentrations of polyamines in the reaction mixture. Maximal activity was shown at 5 mM putrscine, 0.5 mM spermidine and spermine, respectively. Lack of Mg2+ ion in the reaction buffer resulted in an inhibition of the enzyme activity by about 30%. The inhibition could not be completely reversed by application of polyamines at optimal concentrations. These results suggest that polyamines promote the DNA synthesis in vivo and in vitro by stabilizing the DNA-helix upon binding to negatively charged groups on DNA or increasing the activity of DNA polymerase in Nicotiana tabacum L.

• Korean Journal of Heritage: History & Science
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• v.40
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• pp.387-411
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• 2007

The analysis of ancient DNA (aDNA) has become increasingly considerable anthropological, archaeological, biological and public interest. Although this approach is complicated by the natural damage and exogenous contamination of a DNA, archaeologists and biologists have attempted to understand issues such as human evolutionary history, migration and social organization, funeral custom and disease, and even evolutionary phylogeny of extinct animals. Polymerase chain reaction(PCR) is powerful technique that analyzes DNA sequences from a little extract of an ancient specimen. However, deamination and fragmentation are common molecular damages of aDNA and cause enzymatic inhibition in PCR for DNA amplification. Besides, the deamination of a cytosine residue yielded an uracil residue in the ancient template, and results in the misincorporation of an adenine residue in PCR. This promotes a consistent substitution (cytosine thymine, guanine adenine) to original nucleotide sequences. Contamination with exogenous DNA is a major problem in aDNA analysis, and causes oversight as erroneous conclusion. This report represents serious problems that DNA modification and contamination are the main issues in result validation of aDNA analysis. Now, we introduce several criterions suggested to authenticate reliance of aDNA analysis by many researchers in this field.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.3
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• pp.358-363
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• 2008

The intracytoplasmic sperm injection (ICSI) procedure has recently been utilized to produce transgenic animals and may serve as an alternative to the conventional pronuclear microinjection in species such as pigs whose ooplasm is opaque and pronuclei are often invisible. In this study, the effects of sperm membrane disruption and electrical activation of oocytes on in vitro development and expression of transgene green fluorescent protein (GFP) in ICSI embryos were tested to refine this recently developed procedure. Prior to ICSI, sperm heads were treated with Triton X-100+NaCl or Triton X-100+NaCl+NaOH, to disrupt membrane to be permeable to exogenous DNA, and incubated with linearized pEGFP-N1 vector. To induce activation of oocytes, a single DC pulse of 1.3 kV/cm was applied to oocytes for $30{\mu}sec$. After ICSI was performed with the aid of a micromanipulator, in vitro development of embryos and GFP expression were monitored. The chemical treatment to disrupt sperm membrane did not affect the developmental competence of embryos. 40 to 60% of oocytes were cleaved after injection of sperm heads with disrupted membrane, whereas 48.6% (34/70) were cleaved without chemical treatment. Regardless of electrical stimulation to induce activation, oocytes were cleaved after ICSI, reflecting that, despite sperm membrane disruption, the perinuclear soluble sperm factor known to mediate oocyte activation remained intact. After development to the 4-cell stage, 11.8 (2/17, Triton X-100+NaCl+NaOH) to 58.8% (10/17, Triton X-100+NaCl) of embryos expressed GFP. The expression of GFP beyond the stage of embryonic genome activation (4-cell stage in the pig) indicates that the exogenous DNA might have been integrated into the porcine genome. When sperm heads were co-incubated with exogenous DNA following the treatment of Triton X-100+NaCl, GFP expression was observed in high percentage (58.8%) of embryos, suggesting that transgenic pigs may efficiently be produced using ICSI.

• Proceedings of the KSAR Conference
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• 2004.06a
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• pp.191-191
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• 2004

Transgenic animals are produced primarily by microinjecting exogenous DNA into the male pronuclei of a zygote. Microinjection method for gene transmitting is successful in mice but not efficient in farm animals, limiting it's general utility such as a large scale facility and labour. Based on our finding that sperm cells bind with exogenous DNA, sperm was used as a vector for producing transgenic animals to introduced green fluorescence protein(GFP) gene. (omitted)

• Toxicological Research
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• v.34 no.4
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• pp.297-302
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• 2018

Cells are constantly exposed to endogenous and exogenous chemical and physical agents that damage their genome by forming DNA lesions. These lesions interfere with the normal functions of DNA such as transcription and replication, and need to be either repaired or tolerated. DNA lesions are accurately removed via various repair pathways. In contrast, tolerance mechanisms do not remove lesions but only allow replication to proceed despite the presence of unrepaired lesions. Cells possess two major tolerance strategies, namely translesion synthesis (TLS), which is an error-prone strategy and an accurate strategy based on homologous recombination (homology-dependent gap repair [HDGR]). Thus, the mutation frequency reflects the relative extent to which the two tolerance pathways operate in vivo. In the present paper, we review the present understanding of the mechanisms of TLS and HDGR and propose a novel and comprehensive view of the way both strategies interact and are regulated in vivo.

• Proceedings of the KSAR Conference
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• 2001.03a
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• pp.56-56
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• 2001

The exogenous gene transfer by intracytoplasmic sperm injection (ICSI) procedure has been recently used to produce transgenic mice and pigs. Sperm-mediated DNA transfer has the potential to markedly simplify the generation of transgenic animals. This method may serve as an alternative to the pronucleus injection of DNA for the production of transgenic pigs. Therefore, in this study, we investigated the expression of transgene after co-injection of spermatozoon or sperm head with green fluorescent protein (GFP) gene into in vitro matured porcine oocytes. Spermatozoon and sperm head, that was obtained by sonication, were treated with 0.03% Triton X-100 to remove the membrane. They were preincubated with linearized pEGFP-N1 for 1 min, and then embryos cultured NCSU23 medium for 2.5 days after co-injected of sperm and DNA. We monitored expression of GFP in embryos under epifluorescent microscope. The remove of sperm membrane did not alter the developmental competence of embryos after ICSI. At 7 days following injection, the rates of blastocysts following injection of intact sperm (15.0%), and of sperm with disrupted membrane (14.2%) were higher than that following IVF (10.0%). Porcine oocytes injected with sperm which co-cultured with DNA concentration of 1, 0.1, and 0.01 ng were 60, 65.7 and 75% and 18.5, 37.4 and 22.2% for rates of cleavage and GFP expression, respectively. In vitro matured porcine oocytes injected with sperm and isolated sperm head resulted in 69 and 59.7% of cleavage rates, respectively The rates of embryo GFP expressed did not significantly different between sperm (20.4%) and sperm head (20.0%) injection. The transgenic embryos with the clusters of positive blastomeres were observed under fluorescent microscope. Most of embryos expressed GFP gene showed mosaicism. They showed GFP expression at 1/4, 2/4 and 3/4 of blastomeres at the 4-cell stage. Among these 4-cell embryos, the expression rate of 1/4 blastomere group (54.6%) was higher than the other groups (15.3-30.7%). These results indicate that membrane disrupted sperm could attach with exogenous DNA, and that this procedure may be useful to introduce foreign gene into porcine oocytes. Therefore, our data suggest that the ICSI car be a useful tool to efficiently produce transgenic pig as well as other mammals.

• Biomolecules & Therapeutics
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• v.15 no.3
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• pp.192-198
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• 2007

Emodin (1,3,8-trihydroxy-6-methylanthraquinone) is a major constituent of rhubarb. Although it has been claimed to have a wild spectrum of therapeutic value, its side effects, especially in human kidney cells have not been well characterized. In this study, we have carried out in vitro genetic toxicity test of emodin and microarray analysis of differentially expressed genes in response to emodin. The result of Ames test showed mutations with emodin treatment in base substitution strain TA1535 both with and without exogenous metabolic activation. Likewise, emodin showed mutations in frame shift TA98 both with and without exogenous metabolic activation. The result of COMET assay in L5178Y cells with emodin treatment showed DNA damage both with and without exogenous metabolic activation. Emodin did not increase micronuclei in CHO cells both with and without exogenous metabolic activation. 150 Genes were selected as differentially expressed genes in response to emodin by microarray analysis and these genes would be candidate biomarkers of genetic toxic action of emodin.

• Biomolecules & Therapeutics
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• v.15 no.3
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• pp.199-204
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• 2007

Carbamates have excellent insecticidal activities against a broad spectrum of insects. They possess knocking-down, fast-killing, and systemic effects, however, they are toxic to mammals. In this study, we have carried out in vitro genetic toxicity test of methylcarbamate and microarray analysis of differentially expressed genes in response to methylcarbamate. Methylcarbamate did not show mutations in base substitution strain TA1535 both with and without exogenous metabolic activation. Methylcarbamate did not show mutations in frame shift TA98 both with and without exogenous metabolic activation. Methylcarbamate showed DNA damage based on single cell gel/comet assay in L5178Y cells both with and without exogenous metabolic activation. Methylcarbamate did not increase micronuclei in CHO cells both with and without exogenous metabolic activation. Microarray analysis of gene expression profiles in L5178Y cells in response to methylcarbamate selected differentially expressed 132 genes that could be candidate biomarkers of genetic toxic action of methylcarbamate.