• Journal of Microbiology and Biotechnology
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• v.16 no.12
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• pp.2004-2007
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• 2006

An efficient method for the in vitro reassembly of homologous DNA sequences is presented. The proposed method involves obtaining single strands of homologous genes and hybridizing them to obtain partially hybridized heteroduplex DNA; cleaving the single-stranded regions of the heteroduplex DNA using S1 nuclease to generate double-strand DNA fragments; denaturing the double-strand DNA fragments to generate single-strand DNA fragments; conducting a series of polymerase chain reactions (PCR) using the single-strand DNA fragments as internal primers and a mixture of homologous DNA as templates to obtain elongated reassembled DNA; and finally, amplifying the reassembled DNA by a PCR using terminal primers. As a result, DNA reassembly could be achieved between homologous genes with a sequence similarity as low as 78%.

• BMB Reports
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• v.31 no.4
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• pp.384-390
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• 1998

DNA fragments (51-587 bp) were separated by capillary electrophoresis using entangled polymer, hydroxyethylcellulose, in uncoated fused silica capillary columns. The factors affecting the separation of DNA fragments with hydroxyethylcellulose media were evaluated, i.e., the concentration of buffer and entangled polymer, effects of additives (methanol, ethidium bromide, EDTA), temperature, and injection methods. Maximum performance was obtained by adding 5% methanol in 0.5% hydroxyethylcellulose solution at $30^{\circ}C$. Addition of methanol in polymer media increased the resolution of small size DNA fragments (< 100 bp). On the other hand, addition of ethidium bromide and EDTA, which are commonly used in conventional DNA separation, reduced the resolution of DNA fragments in the polymer solution. It turns out that the separation behavior of DNA in entangled polymer is more sensitive to the running condition compared to that in polyacrylamide gel-filled capillary, but the reproducibility of DNA separation in entangled polymer is reliable.

• BMB Reports
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• v.30 no.6
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• pp.426-430
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• 1997

The helical periodicity of the triple-stranded $(dT)_n{\cdot}(dA)_n{\cdot}(dT)_n$ sequence was determined by measuring gel-mobilities of bent DNA fragments containing the sequence. In the bent DNA fragments, a $GA_{22}G$ $CT_{22}C$ sequence was located between two bent DNA loci composed of six $A_{6}{\cdot}T_{6}$ repeats. and the DNA length between the bent DNA loci was varied by 1 base pair over a full helical turn. The gel mobility of each bent DNA fragment reflected the overall extent of DNA bending and varied with the DNA length between the two bent loci. Mobilities of the bent DNA fragments in 5% polyacrylamide gel were measured after preincubating the DNA fragments both in the presence and absence of $CT_{22}C$ oligonucleotide. By comparing the bent DNA fragments containing an intermolecular triplex structure with those of a genuine duplex structure in the gel mobilities, the helical periodicity of the $T_n{\cdot}A_n{\cdot}T_n$ triplex DNA was determined to be $11.5({\pm}0.3)bp/turn$.

• Journal of Life Science
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• v.8 no.3
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• pp.348-351
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• 1998

Common DNA fragments of the ${\beta}$-globin gene were observed from six races of the adult common carp: Hybrid-Yamato, Japanese wild type, Mirror, Suwa-Yamato, Scale German, and Saku-Yamato. Chromosomal DNAs isolated from the above six races were digested with restriction endonucleased EcoRI and PstI. The digested fragments were transferred onto nitrocellulose filter and hybridized with a probe of carp ${\beta}$-globin cDNA. Molecular sizes of the hybridized DNA fragments digested with EcoRI were 3.6Kb(Kilo base), 4.3Kb and 15Kb in Hybrid-Yamato, Japanese wild type, Mirror, Scale German and Saku-Yamato carp DNAs. In Scale German and Saku-Yamato carp DNAs, two and one more hybridized DNA fragments were observed, respectively. Molecular sizes of the hybridized DNA fragments digested with PstI were 2.2Kb, 6.5Kb, 7.8Kb and 9.2Kb in Hybrid-Yamato, 2.2Kb, 6.5Kb and 9.2Kb in Japanese wild type, 2.2Kb, 6.5Kb, 7.8Kb, and 13Kb in Mirror, 2,2Kb, 5,5Kb, 6.5Kb, 7.8Kb, 9.2Kb and13Kb in Scale German, and 2.2Kb, 5.5Kb, 6.5Kb, 9.2Kb and Saku-Yamato carp DNA. Therefore, depending on carps, three to six DNA fragments were hybridized with ${\beta}$-globin gene probe. Thus it indicated polymorphysm in the globin gene family of carp.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.6
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• pp.2989-2993
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• 2016

The commonest cancer in Egyptian females occurs in the breast cfDNA is a non-invasive marker for tumor detetion and prognostic assessment in many types of cancer including breast cancer. This study aimed to assess the role of cfDNA and its fragmentation pattern in breast cancer prognosis and treatment response. Forty female patients with malignant breast tumors and a comparable group of healthy blood donors were enrolled prospectively. cfDNA levels and fragmentation patterns were investigated after cfDNA extraction, gel electrophoresis and gel analysis. The percentage of breast cancer patients positive for cfDNA (92.5%) was significantly higher than that of controls (55%). Also, mean concentration of cfDNA was significantly higher than in the control group (P<0.05). Most Her-2 positive patients had long cfDNA fragments, this being significant as compared to Her-2 negative patients (P<0.05). Metastasis was also positively linked to significantly higher cfDNA (P<0.05) and the mean cfDNA integrity index was significantly higher in non-responders compared to treatment responders (P<0.05). In conclusion, both qualitative and quantitative aspects of cfDNA and its different fragments in breast cancer patients could be related to prognosis, metastasis and treatment response. Long cfDNA fragments could be particularly useful for prediction purposes.

• Environmental Mutagens and Carcinogens
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• v.22 no.3
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• pp.199-204
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• 2002

It has been known that Ganoderma lucidum and Lentinus edodes have anticancer activity and immune enhancing activity. These two mushrooms were grown in liquid culture and harvested. From these mycelia, DNA was isolated and EtBr-CsCl density gradient ultracentrifugation was performed to purify it further. Then mitochondrial DNA was isolated by bisbenzimide-CsCl density ultracentrifugaton. Mitochondrial DNA of Ganoderma lucidum was digested by restriction enzymes, EcoR I, Hind Ⅲ, and Pst I, then electrophoresed. It showed 12, 22, 4 fragments. Mitochondrial DNA of Lentinus edodes was digested by EcoR I. Electric pattern showed 6 fragments. 4 fragments had appeared by Pst 1 digested mitochondrial DNA. Hind ill couldn't digest mitochondrial DNA of Lentinus edodes. Mitochondrial DNA of fusants was isolated to compare to those of parents. The results showed that fusant P₂S₄has new, recombined mitochondrial DNA. But P₂S₄had the same DNA that Ganoderma lucidum had.

• Journal of fish pathology
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• v.19 no.2
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• pp.141-153
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• 2006

Genomic DNA samples isolated from two geographical crayfish (Cambaroides similis) populations in the inland of the Korean Peninsula, at Jeonju (Jeonju crayfish; JJC) and Jeongup (Jeongup crayfish; JUe), were PCR-amplified repeatedly. The six arbitrarily selected primers OPC-03, OPC-06, OPC-09, URP-02, URP07 and URP-09 generated the common, specific, and polymorphic fragments. The sizes of DNA fragments also varied widely, from 100 bp - 2,600 bp. Here, 521 fragments were identified in the JJC population, and 354 in the JUC population: 6 primers generated 60 specific fragments (60/521 fragment, 11.5%) in the JJC population, and 90 (90/354 fragments, 25.4%) in the JUC population. These primers produced 42 polymorphic fragments (8.1%) in the DC population, and 18 (5.1%) in the mc population. Especially these results demonstrate that the primers detected numerous specific fragments. Especially, the decamer primer OPC-06 generated inter-population-common DNA fragments, approximately 400 and 800 bp, respectively, in both the JJC and JUC populations. The universal primer URP-02 also generated inter-population-identical DNA fragments, approximately 350 bp and 600 bp, between the two geographical crayfish populations. Based on the average bandsharing values of all samples, the bandsharing value of individuals within the JJC population was much higher than in the JUC population. The bandsharing value between individuals no. 10 and no. 15 was 0.683, which was the highest between the two geographical populations. The dendrogram obtained by the six primers indicates two genetic clusters: cluster I (CRAYFISH 01 - CRAYFISH II), and cluster 2 (CRAYFISH 12 - CRAYFISH 22). The genetic distance between the two geographical populations ranged from 0.053 to 0.605. Ultimately, the longest genetic distance displaying significant molecular differences was found to exist between individuals in the two crayfish populations, between individuals CRAYFISH no. 02 of Jeonju and CRAYFTSH no. 15 of Jeongup (genetic distance = 0.605).

• Microbiology and Biotechnology Letters
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• v.38 no.2
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• pp.136-143
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• 2010

DNA fragments encoding the ketosynthase (KS) domain of polyketide synthase (PKS) genes were amplified using polymerase chain reaction (PCR) from 9 strains of Sorangium cellulosum isolated in Korea, cloned into a plasmid vector and sequenced. A total of 83 cloned DNA fragments were analyzed, and similar fragments were excluded, leaving 43 independent DNA fragments encoding the KS domains. The predicted amino acid sequences of 32 fragments were 70%-100% identical to the amino acid sequences of already known PKS genes, while the remaining 11 fragments were $\leq$67% or less identical to the known sequences, suggesting that these genes are novel PKS genes.

• KSBB Journal
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• v.17 no.1
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• pp.106-109
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• 2002

Gel electrophoresis of DNA is a well known technique in molecular biology. This technique is simple, rapid to perform, and capable of adequately separating fragments of DNA. A number of mixtures of DNA fragments ("DNA size markers") are frequently employed in a purpose of extrapolating the sizes or the amount of DNA molecules during gel electrophoresis. DNA size markers are constructed by digesting plasmid DNA, bacteriophage DNA, or recombinant DNA molecules with one or more restriction enzymes. However, liquid suspension containing DNA size marker needs to be kept at a low temperature during storage and shipping. In an attempt to maintain the DNA samples at room temperature for extended period of time, lyophilization of DNA with addition of nuclease inhibitor was studied. Gel loading buffer was also added to the lyophilized DNA to provide additional convenience such that DNA size marker was the "ready-to-use" followed by simply reconstituting with distilled water.

• Journal of Plant Biology
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• v.39 no.2
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• pp.85-92
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• 1996

Small GTP-binding proteins are divided into three major group: Ras, Rho and Ypt/Rab. They have the conserved regions designed G1 to G5 that are critical in GDP/GTP exchange, GTP-induced conformational change and GTP hydrolysis. We isolated and characterized genomic DNA or cDNAfragments encoding G1 to G3 domains of small GTP-binding protein Rab and Rho from several plant species using two different PCR-based cloning strategies. Seven rab DNA fragments were isolated from 4 different plants, mung-bean, tobacco, rice and pepper using two degenerate primers corresponding to the GTP-binding domain G1 and G3 in small GTP-binding proteins. The amino acid sequences among these rab DNA fragments and other known small GTP-binding proteins shows that they belong to the Ypt/Rab family. Six rho DNA fragments were isolated from 5 different plants, mung-bean, rice, Arabidopsis, Allium and Gonyaulax using the nested PCR method that involves four degenerate primers corresponding to the GTP-binding domain G1, G3 and G4. The rho DNA fragments cloned show more than 90% homology to each other. Sequence comparison between plant and other known Rho family genes suggests that they are closely related (67 to 82% amino acid identity). Sequence analysis and southern blot analysis of rab and rho in mung-bean suggest than thses genes are encoded by multigene family in mung-bean.