• The Plant Pathology Journal
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• 제37권3호
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• pp.291-298
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• 2021

False smut caused by Ustilaginoidea virens is an important rice fungal disease that significantly decreases its production. In the recent past, conventional methods have been developed for its detection that is time-consuming and need high-cost equipments. The research and development in nanotechnology have made it possible to assemble efficient recognition interfaces in biosensors. In this study, we present a simple, sensitive, and selective oxidized graphene-based geno-biosensor for the detection of rice false smut. The biosensor has been developed using a probe DNA as a biological recognition element on paper electrodes, and oxidized graphene to enhance the limit of detection and sensitivity of the sensor. Probe single-stranded DNA (ssDNA) and target ssDNA hybridization on the interface surface has been quantitatively measured with the electrochemical analysis tools namely, cyclic voltammetry, and linear sweep voltammetry. To confirm the selectivity of the device, probe hybridization with non-complementary ssDNA target has been studied. In our study, the developed sensor was able to detect up to 10 fM of target ssDNA. The paper electrodes were employed to produce an effective and cost-effective platform for the immobilization of the DNA and can be extended to design low-cost biosensors for the detection of the other plant pathogens.

• 미생물학회지
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• 제26권2호
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• pp.88-92
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• 1988

The isolation and characterization of a new type II methylase, BmaI methylase, from Bacillus macerans ATCC 8244 were described. BmaI methylase was isolated by procedures of ammonium sulfate fractionation, DEAE-cellulose chromatography and phosphocellulose chromatography. Two types of methylases were present in this strain and only one of the two was a site specific BmaI methylase. The pBR322 DNA methylated by BmaI methylase was not cleaved by BmaI endonuclease, and pBR322 DNA cleaved by BmaI endonuclease was not methylated by BmaI methylase. The optimal pH for the BmaI methylase activity was 7.5, and optimal NaCl concentration was about 50 mM. BmaI methylase could methylate single-stranded M13mp18 DNA.

• Molecules and Cells
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• 제40권2호
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• pp.143-150
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• 2017

Homologous recombination (HR) is necessary for maintenance of genomic integrity and prevention of various mutations in tumor suppressor genes and proto-oncogenes. Rad51 and Rad54 are key HR factors that cope with replication stress and DNA breaks in eukaryotes. Rad51 binds to single-stranded DNA (ssDNA) to form the presynaptic filament that promotes a homology search and DNA strand exchange, and Rad54 stimulates the strand-pairing function of Rad51. Here, we studied the molecular dynamics of Rad51 and Rad54 during the cell cycle of HeLa cells. These cells constitutively express Rad51 and Rad54 throughout the entire cell cycle, and the formation of foci immediately increased in response to various types of DNA damage and replication stress, except for caffeine, which suppressed the Rad51-dependent HR pathway. Depletion of Rad51 caused severe defects in response to postreplicative stress. Accordingly, HeLa cells were arrested at the G2-M transition although a small amount of Rad51 was steadily maintained in HeLa cells. Our results suggest that cell cycle progression and proliferation of HeLa cells can be tightly controlled by the abundance of HR proteins, which are essential for the rapid response to postreplicative stress and DNA damage stress.

• BMB Reports
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• 제31권2호
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• pp.149-155
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• 1998

The N199H variant of the EcoRI endonuclease has about twice the catalytic activity of the wild-type. A comparison of their biochemical characteristics, using synthetic oligonucleotides 5'-dAAAACTTAAGAAAAAAAAAAA-3' (KA) and 5'-dTTTTTGAATTCTTTTTTTTTT-3' (KT), helps to define the cleavage reaction pathway of these enzymes. Both EcoRI and EcoRI variant N199H were found to cleave singlestranded KA or KT about three times faster than the double-stranded forms, although the KT oligonucleotide was more susceptible. Using the ssDNA substrate in kinetic analyses, lower $K_m$ values were obtained for the N199H variant than for the wild-type at low (50 mM), as well as high (200 mM), sodium chloride concentrations. This difference between the endonucleases is attributed to a grealter accessibility for tbe substrate by the variant, and also a higher affinity for the DNA backbone. It also appears that the relative activities of the two enzymes, particularly at high ionic strength, are proportional to their populations in the monomeric enzyme form. That is, according to gel filtration data, half of the N199H molecules exist as monomers in 200 mM NaCl, whereas those of the wild-type are mainly dimeric. Consequently, the Asp199 residue of the EcoRI endonuclease may be implicated in the protein-protein interaction leading to dimerization, as well as in coupling to DNA substrates. In summary, it is proposed that active monomeric endonuclease molecules, derived from the dimeric enzyme, recognize and form a complex with a single stranded form of the DNA substrate, which then undergoes nucleophilic substitution and cleavage.

• 생명과학회지
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• 제15권6호
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• pp.935-940
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• 2005

Coumarine이 부착된 인산결합 단백질 (PBP-MDCC)의 형광변화가 뉴클레오사이드 삼인산 가수분해과정에서 배출된 무기 인산의 양을 측정하기 위해 관찰되었다. PBP-MDCC 정제후, 형광 방출 스펙트럼은 형광세기가 PBP-MDCC의 몰비을로 약 $70\%$까지 직선형태로 증가하는 것을 보였다. 형광 신호와 인산 기준물질과의 상호관계 측정이 인산 농도-형광세기 표준곡선을 구하기 위하여 stopped-flow 기구에서 행하여졌다. dTTP 가수분해로 부터 나오는 에너지를 이용하여 이중나선 DNA를 풀어주는 단백질인 T7박테리오파지 나선효소를 dPTT라 반응 시켰을 때, 형광변화를 배출된 인산의 양으로 전환할 수 있었다. 인산 배출 결과는 단일가닥 Ml3 DNA가 T7나선 효소에 의한 dTTP가수분해반응을 여러배 증가시키는 것을 보인다. 뉴클레오타이드 삼인산 가수분해 반응에 있어서 종말점 분석 대신에, PBP-MDCC에 의한 연속적인 인산 배출 분석이 배출된 인산을 측정하는데 있어서 쉽고 편리한 방법임을 보였다.

• Bulletin of the Korean Chemical Society
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• 제31권7호
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• pp.2011-2014
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• 2010

The fluorescence intensity of a single-stranded oligonucleotide containing a fluorene-labeled deoxyuridine $(U^{Fl})$ unit increases by only 1.5-fold upon formation of its perfectly matched duplex. To increase the fluorescence signal during hybridization, we positioned a quencher strand containing a deoxyguanine (dG) nucleobase, functioning as an internal quencher, opposite to the $U^{Fl}$ unit to reduce the intrinsic fluorescence upon hybridization with a probe. From an investigation of the optimal length of the quencher strand and the effect of the neighboring base sequence, we found that a short strand (five-nucleotide) containing all natural nucleotides and dG as an internal quencher was effective at reducing the intrinsic fluorescence of a linear beacon; it also exhibited high total discrimination factors for the formation of perfectly matched and single base-mismatched duplexes. Such assays that function based on clear changes in fluorescence in response to single-base nucleotide mutations would be useful tools for accelerating diagnoses related to various diseases.

• BMB Reports
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• 제42권1호
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• pp.53-58
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• 2009

The methyl-directed mismatch repair (MMR) mechanism has been extensively studied in vitro and in vivo, but one of the difficulties in determining the biological relationships between the MMR-related proteins is the tendency of MutL to self-aggregate. The properties of a stable MutL homologue were investigated using a thermostable MutL (TmL) from Thermotoga maritima MSB8 and whose size exclusion chromatographic and crosslinking analyses were compatible with a dimeric form of TmL. TmL underwent conformational changes in the presence of nucleotides and single-stranded DNA (ssDNA) with ATP binding not requiring ssDNA binding activity of TmL, while ADPnP-stimulated TmL showed a high ssDNA binding affinity. Finally, TmL interacted with the T. maritima MutS (TmS), increasing the affinity of TmS to mismatched DNA base pairs and suggesting that the role of TmL in the formation of a mismatched DNA-TmS complex may be a pivotal observation for the study of the initial MMR system.

• Journal of Microbiology and Biotechnology
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• 제25권10호
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• pp.1768-1771
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• 2015

Human Fen1 protein (hFen1) plays an important role in Okazaki fragment processing by cleaving the flap structure at the junction between single-stranded (ss) DNA and doublestranded (ds) DNA, an intermediate formed during Okazaki fragment processing, resulting in ligatable nicked dsDNA. It was reported that hChlR1, a member of the cohesion establishment factor family, stimulates hFen1 nuclease activity regardless of its ATPase activity. In this study, we found that cohesion establishment factors cooperatively stimulate endonuclease activity of hFen1 in in vivo mimic condition, including replication protein-A-coated DNA and high salt. Our findings are helpful to explain how a DNA replication machinery larger than the cohesion complex goes through the cohesin ring structure on DNA during S phase in the cell cycle.

• Clinical and Experimental Pediatrics
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• 제48권12호
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• pp.1295-1309
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• 2005

Nowadays, the nutritional deficits are rarely seen in Korea. However, an increased availability of the highly palatable energy dense, nutrient-poor foods increases the risks of obesity and deficits of vitamins and minerals in the general population. Also, optimum intake of vitamins and minerals, which varies with age and genetic back ground, might not suffice the poor, young, obese, and elderly people. Young girls and individuals participating in weight reductions and aesthetic components are prone to micronutrient deficiencies because they restrict food intake and specific micronutrient rich foods. An inadequate intake of vitamins or minerals is associated with reduced physical performance and exercise capacity, increased obesity, decreased cognitive function, increased DNA damages such as single- and double-stranded breaks or oxidative DNA lesions, and accelerated aging process and increased neuronal damages with mitochondrial oxidative decay. Most of these deleterious effects of the deficit could be prevented by a one tablet of multivitamins with a good balanced diet. High dose B vitamins are frequently administered to overcome the metabolic inadequacy to the people with the less functional enzymes with increased Km values for their coenzymes due to the single gene mutation or due to the single nucleotide polymorphisms. And some certain antioxidant vitamins are also used in large quantities to overcome the oxidative stress and to repair the damages. In this review, new nutritional concepts of some vitamins and minerals, which are widely used and useful for the children, will be discussed.

• BMB Reports
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• 제34권5호
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• pp.428-433
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• 2001

A defect in uvsC of Aspergillus nidulans caused high methyl methansulfonate (MMS)-sensitivity, hyporecombination, and a lack of UV induced mutation. The uvsC gene of Aspergillus nidulans shares a sequence similarity with the RAD51 gene of Saccharomyces cerevisiae. In this study, in vitro and in vivo tests were conducted in order to determine whether or not the UVSC protein had functional similarities to RAD51, the recombination enzyme in yeast. The purified recombinant UVSC protein, following expression in Escherichia coli, showed binding activity to single-stranded DNA (ssDNA), when both ATP and magnesium are present. In addition, ATPase activity was also demonstrated and its activity was stimulated in the presence of ssDNA. The UVSC protein that was expressed under the ADH promoter in S. cerevisiae suppressed in part the sensitivity to MMS of the rad51 null mutant. Similarly, when the uvsC cDNA was expressed from the nmt promoter, the MMS sensitivity of the rhp51 null mutant of Schizosaccharomyces pombe was partially complemented. These results indicate that the A. nidulans UVSC protein is a functional homologue of the RAD51 protein.