• Journal of Photoscience
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• v.11 no.3
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• pp.133-139
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• 2004

The metal-ligand complex, $[Ru(phen)_2(dppz)]^{2+}$ (phen=1,10-phenanthroline, dppz=dipyrido[3,2-a:2',3'-c]phenazine) (RuPD), was used as a spectroscopic probe for studying nucleic acid dynamics. The RuPD complex displays a long lifetime and a molecular light switch property upon DNA binding due to shielding of its dppz ligand from water. To show the usefulness of this luminophore (RuPD) for probing nucleic acid dynamics, we compared its intensity and anisotropy decays when intercalated into the $tRNA^{val}$ and pBluescript (pBS) II SK(+) phagemid through a comparison with ethidium bromide (EB), a conventional nucleic acid probe. We used frequency-domain fluorometry with a blue light-emitting diode (LED) as the modulated light source. The mean lifetime for the $tRNA^{val}$ (<${\tau}$> = 166.5 ns) was much shorter than that for the pBS II SK(+) phagemid (<${\tau}$> = 481.3 ns), suggesting a much more efficient shielding from water by the phagemid. Because of their size difference, the anisotropy decay data showed a much shorter rotational correlation times for the $tRNA^{val}$ (99.9 and 23.6 ns) than for the pBS II SK(+) phagemid (968.7 and 39.5 ns). These results indicate that RuPD can be useful for studying nucleic acid dynamics.

• International Journal of Oral Biology
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• v.44 no.1
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• pp.8-13
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• 2019

Recently, the importance of on-site detection of pathogens has drawn attention in the field of molecular diagnostics. Unlike in a laboratory environment, on-site detection of pathogens is performed under limited resources. In this study, we tried to optimize the experimental conditions for on-site detection of pathogens using a combination of ultra-fast convection polymerase chain reaction (cPCR), which does not require regular electricity, and nucleic acid lateral flow (NALF) immunoassay. Salmonella species was used as the model pathogen. DNA was amplified within 21 minutes (equivalent to 30 cycles of polymerase chain reaction) using ultra-fast cPCR, and the amplified DNA was detected within approximately 5 minutes using NALF immunoassay with nucleic acid detection (NAD) cassettes. In order to avoid false-positive results with NAD cassettes, we reduced the primer concentration or ultra-fast cPCR run time. For singleplex ultra-fast cPCR, the primer concentration needed to be lowered to $3{\mu}M$ or the run time needed to be reduced to 14 minutes. For duplex ultra-fast cPCR, $2{\mu}M$ of each primer set needed to be used or the run time needed to be reduced to 14 minutes. Under the conditions optimized in this study, the combination of ultra-fast cPCR and NALF immunoassay can be applied to on-site detection of pathogens. The combination can be easily applied to the detection of oral pathogens.

• Journal of Microbiology
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• v.44 no.1
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• pp.72-76
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• 2006

Plasma-derived products are produced from plasma via fractionation and chromatography techniques, but can also be produced by other methods. In the performance of nucleic acid amplification tests (NAT) with plasma-derived products, it is necessary to include an internal control for the monitoring of all procedures. In order to avoid false negative results, we confirmed the usefulness of the bovine viral diarrhoea virus (BVDV) for use as an internal control in the detection of hepatitis C virus (HCV) RNA in plasma-derived products. These products, which were spiked with BVDV, were extracted and then NAT was performed. Specificity and sensitivity were determined via the adjustment of primer concentrations and annealing temperatures. BVDV detection allows for validation in the extraction, reverse transcription, and amplification techniques used for HCV detection in plasma-derived products.

• Proceedings of the Korean Information Science Society Conference
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• 2006.06a
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• pp.43-45
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• 2006

Unlike RNA interference, whose usage is limited to eukaryotic cells, Peptide Nucleic Acid (PNA) technique is applicable to both eukaryotic and prokaryotic cells. PNA has been proven to be an effective agent for blocking gene expressions and has several advantages over other antisense techniques. Here we developed a parallel computing software that provides the ideal sequences to design PNA oligos to prevent any off-target effects. We applied a new approach in our location-finding algorithm that finds a target gene from the whole genome sequence. Message Passing Interface (MPI) was used to perform parallel computing in order to reduce the calculation time. The software will help biologists design more accurate and effective antisense PNA by minimizing the chance of off-target effects.

• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3099-3102
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• 2010

A label-free DNA detection method was developed for a simple electrochemical DNA sensor with a short assay time. Self-assembled monolayers of peptide nucleic acid were used as a probe on gold electrodes. The formation of the self-assembled monolayers on the gold electrodes was successfully checked by means of cyclic voltammetry. The target DNA, hybridized with peptide nucleic acid, can be detected by the anodic peak current of ferrocene dendrimers, which interact electrostatically with the target DNA. This anodic peak current was measured by square wave voltammetry at 0.3 V to decrease the detection limit on the order of the nanomolar concentrations. As a result, the label-free electrochemical DNA sensor can detect the target DNA in concentrations ranging from 1 nM to $1\;{\mu}M$ with a detection limit of 1 nM.

• Food Engineering Progress
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• v.21 no.3
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• pp.191-200
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• 2017

There have been great efforts to develop a rapid and sensitive detection method to monitor the presence of pathogenic bacteria in food. While a number of methods have been reported for bacterial detection with a detection limit to a single digit, most of them are suitable only for the bacteria in pure culture or buffered solution. On the other hand, foods are composed of highly complicated matrices containing carbohydrate, fat, protein, fibers, and many other components whose composition varies from one food to the other. Furthermore, many components in food interfere with the downstream detection process, which significantly affect the sensitivity and selectivity of the detection. Therefore, isolating and concentrating the target pathogenic bacteria from food matrices are of importance to enhance the detection power of the system. The present review provides an introduction to the representative sample preparation strategies to isolate target pathogenic bacteria from food sample. We further describe the nucleic acid-based detection methods, such as PCR, real-time PCR, NASBA, RCA, LCR, and LAMP. Nucleic acid-based methods are by far the most sensitive and effective for the detection of a low number of target pathogens whose performance is greatly improved by combining with the sample preparation methods.

• The Plant Pathology Journal
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• v.35 no.2
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• pp.164-171
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• 2019

An assay for detecting Apple scar skin viroid (ASSVd) was developed based on nucleic acid sequence based amplification (NASBA) in combination with realtime detection during the amplification process using molecular beacon. The ASSVd specific primers for amplification of the viroid RNA and molecular beacon for detecting the viroid were designed based on highly conserved regions of several ASSVd sequences including Korean isolate. The assay had a detection range of $1{\times}10^4$ to $1{\times}10^{12}$ ASSVd RNA $copies/{\mu}l$ with reproducibility and precision. Following the construction of standard curves based on time to positive (TTP) value for the serial dilutions ranging from $1{\times}10^7$ to $1{\times}10^{12}$ copies of the recombinant plasmid, a standard regression line was constructed by plotting the TTP values versus the logarithm of the starting ASSVd RNA copy number of 10-fold dilutions each. Compared to the established RT-PCR methods, our method was more sensitive for detecting ASSVd. The real-time quantitative NASBA method will be fast, sensitive, and reliable for routine diagnosis and selection of viroid-free stock materials. Furthermore, real-time quantitative NASBA may be especially useful for detecting low levels in apple trees with early viroid-infection stage and for monitoring the influence on tree growth.

• International Journal of Oral Biology
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• v.46 no.1
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• pp.1-6
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• 2021

Since the outbreak of coronavirus disease 2019 (COVID-2019), the infection has spread worldwide due to the highly contagious nature of severe acute syndrome coronavirus (SARS-CoV-2). To manage SARS-CoV-2, the development of diagnostic assays that can quickly and accurately identify the disease in patients is necessary. Currently, nucleic acid-based testing and serology-based testing are two widely used approaches. Of these, nucleic acid-based testing with quantitative reverse transcription-PCR (RT-qPCR) using nasopharyngeal (NP) and/or oropharyngeal (OP) swabs is considered to be the gold standard. Recently, the use of saliva samples has been considered as an alternative method of sample collection. Compared to the NP and OP swab methods, saliva specimens have several advantages. Saliva specimens are easier to collect. Self-collection of saliva specimens can reduce the risk of infection to healthcare providers and reduce sample collection time and cost. Until recently, the sensitivity and accuracy of the data obtained using saliva specimens for SARS-CoV-2 detection was controversial. However, recent clinical research has found that sensitive and reliable data can be obtained from saliva specimens using RT-qPCR, with approximately 81% to 95% correspondence with the data obtained from NP and OP swabs. These data suggest that self-collected saliva is an alternative option for the diagnosis of COVID-19.

• Asian-Australasian Journal of Animal Sciences
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• v.11 no.3
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• pp.209-216
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• 1998

The paper presented here is aimed at increasing knowledge on purine metabolism in ruminants and hence the quantification of microbial cells entering the small intestine from urinaη excretion of purine derivatives. Nucleic acid metabolisms of micro-organisms in the rumen, digestion and absorption of nucleic acids entering the intestines, metabolisms of absorbed and endogenous purines involving de novo synthesis of nucleic acids in the ruminants host, and the relationship between absorbed and excreted purines are reviewed. Principal concerns about an amount of purine derivatives excreted in urine in relation to a change in purine-N: total-N ratios in rumen microbes that leave the rumen are discussed. The use of urinary excretion of purine derivatives as an indicator of the amount of microbial biomass leaving the rumen has to be done with some caution since it may be impossible to get a representative sample of microbes entering the intestine and thus yield estimates are relative rather than absolute.

• The Korean Journal of Food And Nutrition
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• v.23 no.3
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• pp.376-380
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• 2010

Mushrooms(Pleurotus ostreatus, Agaricus bisporus and Flammulina velutipes) are popular food sources in Korea, and have been reported as therapeutic foods, useful for preventing various diseases. In this study we researched HPLC conditions for the determination of nucleic acids in extracts of the three type of mushrooms. The method for nucleic acids analysis of mushrooms was developed using HPLC with UV detection. To determine the nucleic acids, mushroom extracts were extracted in hot water at $90^{\circ}C$ by reflux extraction for 1 hr. Then, the extracts were hydrolyzed by enzymes RP-1G and 50000G. The HPLC conditions were simple, rapid, and sensitive, and were applicable for the analysis of 4 nucleosides(cytidine, uridine, guanosine and inosine) and 3 mono-nucleotides(5'-CMP, 5'-UMP, and 5'-IMP) in the mushrooms. The nucleic acids in the mushrooms were cytidine, guanosine, inosine, uridine, 5'-CMP, 5'-IMP, and 5'-UMP. The analysis results for total nucleic acids in the mushroom extracts(Pleurotus ostreatus, Agaricus bisporus, and Flammulina velutipes) indicated levels of 25.28, 27.75, and 19.87 mg/g, respectively. In conclusion, this method can be used successfully for qualitative and quantitative analysis of nucleic acids in Pleurotus ostreatus, Agaricus bisporus, and Flammulina velutipes.