• Molecules and Cells
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• v.45 no.1
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• pp.33-40
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• 2022

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

• Journal of Microbiology
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• v.35 no.1
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• pp.40-46
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• 1997

The pWHM220 cosmid with a 24-kb insert cloned from Streptomyces albus ATCC 21838 induces the biosynthesis of a polysther antibiotic similar to salinomycin in Streptomyces invidans. We have analyzed this region by DNA sequencing as well as Southern blot hybridization with type I and type II polyketide synthase (PKS) probes. Surprisingly, we found another set of type II SKS genes only 10-kb from the original PKS genes, salABCDE. The DNA sequence revealed two complete open reading frames (ORFs) named salB2 and salC2, and one partial ORF that does not resemble any known DNA or deduced protein sequence. The salC2 should code for chain length determining factor while the deduced amino acid sequence encoded by salB2 exhibits high similarity to .betha.-ketoacyl synthase from different PKS gene clusters. The highest identity was found for .betha.-keetoacyl synthases from S. argillaceus (MtmP. 59.1% identity), the mithramycin producer and from S. venezuelae ISP5230 (JadA, 52.3% identity), the jadomycin producer. The SalC2 protein clearly resembles its counterparts in order aromatic PKS gene clusters that are believed to influence the length of the polyketide chain. The highest identities observed were to that of S. argillaceus (MtmK, 62.3%) and S. venezuelae ISP 5230 (JadB, 55.1%) proteins, Moreover, the deduced amino acid sequences of the salB2 and salC2 products were 29.0% identical.

• Journal of Plant Biotechnology
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• v.31 no.3
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• pp.225-230
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• 2004

We employed single cell gel electrophoresis method (comet assay) to analyze the degree of nucleus-DNA damage in the leaves of red pepper (Capsicum annuum L.) seedlings exposed to $^{60}$ CO v-radiation stress. Nucleus-DNA damage was measured as the ratio of tail length (T) to head length (H) in individual comet image isolated from pepper leaf cell. The T/H ratio of control-cells and treated-cells at 50 or 100 Gy were 1.28 and 3.54 or 3.39, respectively, suggesting that nuclei of pepper cells were severely damaged in the integrity of DNA strand by the treatment of enhanced v-radiation. The percentage of head-DNA in control-cells was 76.8%, whereas those of 50 and 100 Gy treated-cells were 55.9% and 59.9%, respectively. Pretreatment of low dose (4 to 20 Gy) radiation to seeds decreased DNA-damage in the leaves of seedlings treated with high dose radiation at 50 or 100 Gy. In this experiment, we developed a sensitive, reliable and rapid method for evaluating genotoxic effect in the nuclei of plant cells by employing comet assay.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.7
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• pp.897-902
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• 2004

PSMC5 subunit, which belongs to the 26S proteasomal subunit family, plays an important role in the antigen presentation mediated by MHC class I molecular. Full-length cDNA of porcine PSMC5 was isolated using the in silico cloning and rapid amplification of cDNA ends (RACE). Amino acid was deduced and the primary structure was analyzed. Results revealed that the porcine PSMC5 gene shares the high degree of sequence similarity with its mammalian counterparts at both the nucleotide level and the amino acid level. The RT-PCR was performed to detect the porcine PSMC5 expression pattern in seven tissues and the result showed that high express level was observed in spleen, lung, marrow and liver while the low express level was in muscle. The full-length genomic DNA sequence of porcine PSMC5 gene was amplified by PCR and the genomic structure revealed that this gene was comprised by 12 exons and 11 introns. Best alignment of the cDNA and genomic exon DNA sequence presents 4 mismatches and this information potentially bears further study in gene polymorphisms.

• Horticultural Science & Technology
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• v.29 no.2
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• pp.123-129
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• 2011

To identify unintended vertical gene-transfer rates from the developed transgenic plants, rapid and unequivocal techniques are needed to identify event-specific markers based on flanking sequences around the transgene and to distinguish zygosity such as homo- and hetero-zygosity. To facilitate evaluation of zygosity, a polymerase chain reaction technique was used to analyze a transgenic pepper line B20 (homozygote), P915 wild type (null zygote), and their F1 hybrids, which were used as transgene contaminated plants. First, we sequenced the 3'-flanking region of the T-DNA (1,277 bp) in the transgenic pepper event B20. Based on sequence information for the 3'- and 5'-flanking region of T-DNA provided in a previous study, a primer pair was designed to amplify full length T-DNA in B20. We successfully amplified the full length T-DNA containing 986 bp from the flanking regions of B20. In addition, a 1,040 bp PCR product, which was where the T-DNA was inserted, was amplified from P915. Finally, both full length T-DNA and the 1,040 bp fragment were simultaneously amplified in the F1 hybrids; P915 ${\times}$ B20, Pungchon ${\times}$ B20, Gumtap ${\times}$ B20. In the present study, we were able to identify zygosity among homozygous transgenic event B20, its wild type P915, and hemizygous F1 hybrids. Therefore, this novel zygosity identification technique, which is based on PCR, can be effectively used to examine gene flow for transgenic pepper event B20.

• Journal of KIISE:Databases
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• v.36 no.6
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• pp.455-465
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• 2009

Suffix trees are widely used in similar sequence matching for DNA. They have several problems such as time consuming, large space usages of disks and memories and data skew, since DNA sequences are very large and do not fit in the main memory. Thus, in the paper, we present a space efficient indexing method called SENoM, allowing us to build trees without merging phases for the partitioned sub trees. The proposed method is constructed in two phases. In the first phase, we partition the suffixes of the input string based on a common variable-length prefix till the number of suffixes is smaller than a threshold. In the second phase, we construct a sub tree based on the disk using the suffix sets, and then write it to the disk. The proposed method, SENoM eliminates complex merging phases. We show experimentally that proposed method is effective as bellows. SENoM reduces the disk usage less than 35% and reduces the memory usage less than 20% compared with TRELLIS algorithm. SENoM is available to query efficiently using the prefix tree even when the length of query sequence is large.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.30 no.1
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• pp.88-94
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• 1997

The mitochondrial DNA (mtDNA) restriction fragment length polymorphi는 (RFLPs) of five populations were analyzed to delineate the stocks of Penaeus chinensis (Osbeck) in the Yellow Sea. Comparison of P. chinensis with P. japonicus to clarify the nucleotide divergence between two species was also carried out. Based on the fragment patterns, three composite haplotypes were analyzed in P. chinensis mtDNA as four naplotypes were in P. japonicus. Most individuals of each P. chinensis population are shared by one dominant haplotype. Another two haplotypes haying variations at the C/a I and hull sites were also distributed evenly in the Korean and Chinese populations. It is suggested that the gene exchange occurring between populations in the Yellow Sea is frequent. Average length of the mtDNA molecule was estimated to be about 16.44 kb in P. chinensis and 16.31 kb in P. japonicus, Sequence divergence (p) of mtDNA between two species estimated by using Upholt's (1977) fomula was $13.7\%$.

• The KIPS Transactions:PartB
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• v.14B no.6
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• pp.461-472
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• 2007

The emphasis in genome projects has Been moving towards the sequence analysis in order to extract biological "meaning"(e.g., evolutionary history of particular molecules or their functions) from the sequence. Especially. palindromic or direct repeats that appear in a sequence have a biophysical meaning and the problem is to recognize interesting patterns and configurations of words(strings of characters) over complementary alphabets. In this paper, we propose an algorithm to identify variable length palindromic pairs(longer than a threshold), where we can allow gaps(distance between words). The algorithm is called palindrome algorithm(PA) and has O(N) time complexity. A palindromic pair consists of a hairpin structure. By composing collected palindromic pairs we build n-pair palindromic patterns. In addition, we dot some of the longest pairs in a circle to represent the structure of a DNA sequence. We run the algorithm over several selected genomes and the results of E.coli K12 are presented. There existed very long palindromic pair patterns in the genomes, which hardly occur in a random sequence.

• Korean Journal of Veterinary Research
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• v.32 no.3
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• pp.389-398
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• 1992

Molecular cloning was carried out on the Danish strain of bovine viral diarrhea virus(BVDV) to construct strategy for the diagnostic tools and effective vaccine of BVD afterwards. A recombinant DNA clone(No. 29) was established successfully from cDNA for viral RNA tailed with adenine homopolymer at 3'-end. $^{32}P$-labeled DNA probes of 300~1,800bp fragments, originating from the clone 29, directed specific DNA-RNA hybridization results with BVDV RNA. Recombinant DNA of the clone 29 was about 5,200bp representing 41.6% of the full length of Danish strain's RNA, and restriction sites were recognized for EcoR I, Sst I, Hin d III and Pst I restriction enzymes in the DNA fragment.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2001.12a
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• pp.225-228
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• 2001

DNA computing has been applied to the problem of getting an optimal solution since Adleman's experiment. DNA computing uses strings with various length and four-type bases that makes more useful for finding a global optimal solutions of the complex multi-modal problems. This paper presents DNA coding method for finding optimal solution of the multi-modal function and compares the efficiency of this method with the genetic algorithms (GA). GA searches effectively an optimal solution via the artificial evolution of individual group of binary string and DNA coding method uses a tool of calculation or Information store with DNA molecules and four-type bases denoted by the symbols of A(Ademine), C(Cytosine), G(Guanine) and T(Thymine). The same operators, selection, crossover, mutation, are applied to the both DNA coding algorithm and genetic algorithms. The results show that the DNA based algorithm performs better than GA.