• Korean Journal of Microbiology
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• v.35 no.2
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• pp.115-120
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• 1999

Multiple Sequence Alignment of DNA and protem sequences is a imnport'mt tool in the study of molecular evolution, gene regulation. and prolein suucture-function relationships. Progressive pairwise alignment method generates multiple sequence alignment fast but not necessarily with optimal costs. Dynamic programming generates multiple sequence alig~~menl with optimal costs in most cases but long execution time. In this paper. we suggest genetlc algorithm lo improve the multiple sequence alignment generated from the cnlent methods, describe the design of the genetic algorithm, and compare the multiple sequence alignments from 0111 method and current methods.

• Journal of the Korean Chemical Society
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• v.42 no.5
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• pp.506-511
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• 1998

When the spermine, which is one of the polyamines containing cation in vivo, binds to DNA, it can increase the stability of DNA. At the same time, it can cause B-form to Z-form transformations of DNA. However, because we cannot determine the binding geometry of the spermine to DNA by using spectroscopic methods, nobody can show the accurate binding mechanism of a DNA-spermine complex. Thus, we used DAPI as a spectroscopic probe of spermine, which binding geometry was well known. At the result of base selective binding geometry of spermine to synthetic DNA, the concentration of spermine gets higher, it grows the hydrophobic environment of DAPI which bound the minor groove of adenine-thymine base pair. Simultaneously, spermine seems to bridge the backbones around the minor groove of $poly[d(A-T)_2]$. So that, the intensity of fluorescence spectrum of that shows sudden increasement. In guanine-cytocine base pair, $poly[d(G-C)_2]$, we can suppose that spermine bind to the major groove of that, shoving out the DAPI which is partially intercalated between the base pocket across the major groove of it. In both cases, spermine doesn't show the base selectivity against to DNA.

• Korean Journal of Medicinal Crop Science
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• v.14 no.3
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• pp.178-182
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• 2006

This study was conducted to investigate the variation in sequence, the base composition and the sequence similarity of 18S rDNA (18S ribosomal RNA coding region) in the 10 Polygonatum spp. collections. The entire 18S rDNA region of 10 Polygonatum spp. collections ranged from 913 bp to 914 bp. There were 8 variable sites in the entire 18S region, and they were attributable to nucleotide substitution and deletion. $T{\rightarrow}C$ transition happened in 4 sites, and $A{\rightarrow}G$ transition happened in 1 site. $C{\rightarrow}A$ transversion happened in 1 site, and deletion happened in 2 sites. Transition rates were five times that of transversion. Base compositions of 18S rDNA were $23.09{\sim}23.33%$ in adenine, $23.33{\sim}23.52%$ in guanine, $25.60{\sim}25.85%$ in thymine and $27.38{\sim}27.79%$ in cytosine. The A + T content of 18S rDNA of 10 Polygonatum spp. collections averages 48.99%, ranging from 48.80% to 49.18%, and the G + C content averages 51.01%, ranging from 50.82% to 51.20%. Pairwise sequence comparisons indicated that 18S rDNA sequence similarity ranged from 99.7% to 100%.

• Korean Journal of Ichthyology
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• v.12 no.1
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• pp.14-19
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• 2000

The sequences of two fragments of 18s ribosomal DNA were determined to elucidate relationship between Pungitius sinensis and P. kaibarae. The proportion of G+C pair is 54.85% to 55.15% in P. kaibarae populations and 52.76% in P. sinensis. Number of substitutions ranges from 10~18 among the populations of P. kaibarae and up to 165 between P. sinensis and P. kaibarae. The value of sequence divergence were 0.0118~0.0195 among the populations of P. kaibarae and 0.2136~0.2306 between P. sinensis and P. kaibarae. The result of pairwise comparison of the sequences indicate that phylogenetic relationship between P. sinensis and P. kaibarae was differentiated to specific level.

• The Korean Journal of Zoology
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• v.37 no.3
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• pp.439-451
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• 1994

미꾸리속 어류 2종의 유전적 차이를 알아보기 위하여 염색체 분석과 미토콘드리아 DNA(mtDNA) 분석을 실시하였다. 일반염색에 의한 핵형 분석 결과 미꾸리(2N=50)와 미꾸라지(2N=48)는 염색체수에 차이가 있었으며. N-banding 분석 결과 두 종간에는 인형성 부위의 위치와 크기에 차이가 있었다. C-handing 겪과 미꾸라지는 1번 염색체쌍 동원 체부위에 넓게 C-band플 갖고 있었다. 미꾸리속 어류 2종의 mtONA를 7개의 6-base cutting 제한효소로 처리하여 절편 양상을 비교. 분석한 결과 2종 공히 mtDNA의 genome 크기는 약 16.OKb였으며 fragment homology(F)에서 미꾸리의 종내 집단간의 F값은 0.674. 미꾸라지는 0.862로 유사하게 나타났으나, 종간 F값은 0.207(0.074-0.417)로 낮았다 염기치환율은 미꾸리가 p=0.021, 미꾸라지는 p=0.002로 미꾸라지가 미꾸리에 비해 매우 낮은 염기치환율을 보였고. 종간 평균 염기치환율은 p=0.104로 차이 를 나타냈다. MtDNA 분석과 핵형 분석 결과 미꾸라지는 Robertsonlan translocation의 결과 미꾸리로 부터 분화된 것으로 추정 되었다.

• The Korean Journal of Zoology
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• v.11 no.3
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• pp.83-84
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• 1968

An attempt was made to estimate the possible homology between human and bacterial DNA by the method of DNA-agar gel hybridization. HeLa DNA was embedded in the agar and $^14C-DNA$ Xanthomonas pelargonii was used as bacterial DNA for the sheared fragments. No homology between human and bacterial DNA was detected. If homology exists at all, it can be estimated from the sensitivity of the method and assuming some 1,000 nucleotide pairs per cistron, the not more than $2\times10^5$ base pairs or 200 bacterial cistrons would be preserved in human DNA, corresponding to less than 0.01 per cent of the total human genome.

• Korean Journal of Microbiology
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• v.24 no.2
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• pp.79-85
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• 1986

We have determined the sequence of $tRNA^{Arg}$ of A. nidulans partially by enzymatic rapid RNA sequencing technique. The sequence was 5'GGCCGGCUGGCCCAAXUGGCAAGGXUCUGAXUACGAAXCAGGAGAUUGCACXXXXXGAGCXXUXXGUCGGUCACCA3' The cloverleaf structure was made from above data. As a result, the anticodon sequence was identified as ACG. This result was confirmed with charging test. The complete sequence was proposed by supplementing the DNA sequence to and by assigning the position of minor bases to this RNA sequence.

• Korean Journal of Ecology and Environment
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• v.33 no.3 s.91
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• pp.206-212
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• 2000

Since some cyanobacterial isolates under selective culturing conditions are lacking of characteristic specialized cells or showing altered morphology, the morpho-taxonomic criteria are not accurate enough to discriminate between species. Instead of morphological parameters, a method based on the single or the combination of repetitive oligonucleotides in a single PCR, repetitive oligonucleotides-primed PCR (ROP-PCR), was applied to generate DNA profiles for members of the cyanobacterial genera Anabaena and Oscillatoria, both of which are responsible for causing poisonous blooms in various freshwater systems. ROP-PCR performed on 10 isolates of the cyanobacteria with ERIC and REP sequences from gram-negative bacteria, STRR1A and LTRR sequences derived from cyanobacterial genome, and eukaryotic repetitive sequences, led to the identification of distinct genotypes, and provided specific and repeatable DNA fingerprints for cyanobacterial isolates. Grouping analysis of cyanobacterial isolates showed a signifiant difference depending on the primer used in PCR.

• Microbiology and Biotechnology Letters
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• v.17 no.6
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• pp.600-605
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• 1989

For the purpose of isolation of the Zymomonas mobilis DNA fragments showing promoter activity in Escherichia coli, a promoter screening vector, PCMT215 was constructed by transferring a promoterless chloramphenicol acetyltransferase (CAT) gene of pYEJ001 into pMT21 which contains $\beta$-lactamase gene and multiple cloning sites. A library of Z, mobilis Sau3AI DNA fragments was constructed in E. coli using the newly constructed pCMT215. Fourteen clones showing resistance to chloramphenicol ranging in concentration from 30 to 750 $\mu$g/$m\ell$ were selected. From five clones of them, the Z. mobilis DNA fragments expressing CAT gene of the recombinant plasmids were sequenced and then sites of transcriptional initiation were identified. The nucleotide sequences of the cloned DNA shared AT rich regions, poly A's or T's stretches and palindromic regions. The positions of transcriptional initiation for CAT gene occurred at more than one site spaced over by 4 to 190 base pairs on the cloned fragments in E. coli.

• Journal of Life Science
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• v.14 no.6 s.67
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• pp.913-919
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• 2004

Mitochondrial DNA mutations have been reported in recent years in association with sensorineural hering loss. The purpose of this study is to identify the association between the noise-induced sensorineural hearing loss and the A to G mutation at nucleotide 3243, 1555, 7445 of mitochondrial DNA. Study subjects were established by history and chart review, and audiological and clinical data were obtained. Blood was sampled from 214 normal controls, 102 noise-induced hearing loss, and 28 sensorineural hearing loss. The DNA of these individuals were extracted, and mitochondrial DNA fragments were analyzed by polymerase chain reaction. Subsequently, the coding sequence of mitochondrial DNA 3243, 1555, 7445 were sequenced, and compared to the normal sequence, and all sequence variations were analyzed by restriction enzymes. Mitochondrial DNA mutations $(3243A{\rightarrow}G,\;1555A{\rightarrow}4G,\;7445A{\rightarrow}G)$ were not detected by polymerase chain reactions in any patients with noise-induced hearing loss, sensorineural hearing loss, and normal controls. The DNA sequencing of PCR products did not revealed an A to G substitution at nucleotide 3243, 1555, 7445 of mitochondrial DNA. The noise-induced sensorineural hearing loss was not associated with mitochondrial DNA mutation $(3243A{\rightarrow}G,\;1555A{\rightarrow}4G,\;7445A{\rightarrow}G)$.