• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.287-293
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• 2005

Predicting RNA secondary structure as accurately as possible is very important in functional analysis of RNA molecules. However, different prediction methods and related parameters including terminal GU pair of helices, minimum length of helices, and free energy systems often give different prediction results for the same RNA sequence. Then, which structure is more important than the others? i.e. which combinations of the methods and related parameters are the optimal? In order to investigate above problems, first, three prediction methods, namely, random stacking of helical regions (RS), helical regions distribution (HD), and Zuker's minimum free energy algorithm (ZMFE) were compared by taking 1139 tRNA sequences from Rfam database as the samples with different combinations of parameters. The optimal parameters are derived. Second, Zuker's dynamic programming method for prediction of RNA secondary structure was revised using the above optimal parameters and related software BJRNAFold was developed. Third, the effects of short-range interaction were studied. The results indicated that the prediction accuracy would be improved much if proper short-range factor were introduced. But the optimal short-range factor was difficult to determine. A user-adjustable parameter for short-range factor was introduced in BJRNAFold software.

• Journal of Microbiology
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• v.42 no.1
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• pp.56-59
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• 2004

Together with the previous reports, my computer survey revealed that several bacteria contain six copies of the type group II intron IntA. The sequence analysis of IntAs showed the high level of homology in the nucleotide sequence (91.9-99.8%). The consensus sequence, 2,270 base pair long, was derived from the nucleotide sequences of all IntA members. The size of the open reading frame intA was 502 amino acids long, that is homologous to reverse transcriptase-like proteins encoded within the group II introns. It was reported that EPEC.IntA and Sf.IntA were inserted into IS911 and IS629, respectively. The sequence of the flanking region IntA was analyzed here. The data show the insertion of EC.IntA into IS629, the insertion of EHEC.IntA into IS3, the insertion of Yp.IntA into IS904-like sequence, and the insertion of EK12.IntA into IS911. Interestingly, these IS elements nested by IntAs were the members of IS3 family elements. The sequences of the IS3 members correspond to the OrfB with the DDE motif conserved in retroviral integrases. Alignment of the flanking sequences of IntAs revealed that the flanking regions -25 to + 10 of insertion sites, that are generally believed to be required for the retrohoming, were not strongly conserved. The data presented here suggests that the retrohoming pathway of IntA seems to differ from those of other group II introns.

• BMB Reports
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• v.38 no.6
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• pp.676-682
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• 2005

To date, no 8-oxoguanine-specific endonuclease-coding gene has been identified in Thermotoga maritima of the order Thermotogales, although its entire genome has been deciphered. However, the hypothetical protein Tm1821 from T. maritima, has a helix-hairpin-helix motif that is considered to be important for DNA binding and catalytic activity. Here, Tm1821 was overexpressed in Escherichia coli and purified using Ni-NTA affinity chromatography, protease digestion, and gel filtration. Tm1821 protein was found to efficiently cleave an oligonucleotide duplex containing 8-oxoguanine, but Tm1821 had little effect on other substrates containing modified bases. Moreover, Tm1821 strongly preferred DNA duplexes containing an 8-oxoguanine:C pair among oligonucleotide duplexes containing 8-oxoguanine paired with four different bases (A, C, G, or T). Furthermore, Tm1821 showed AP lyase activity and Schiff base formation with 8-oxoguanine in the presence of $NaBH_4$, which suggests that it is a bifunctional DNA glycosylase. Tm1821 protein shares unique conserved amino acids and substrate specificity with an 8-oxoguanine DNA glycosylase from the hyperthermophilic archaeon. Thus, the DNA recognition and catalytic mechanisms of Tm1821 protein are likely to be similar to archaeal repair protein, although T. maritima is an eubacterium.

• 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 $11.5({\pm}0.3)bp/turn$.

• Microbiology and Biotechnology Letters
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• v.25 no.6
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• pp.560-565
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• 1997

DNA fragment assembly is a major concem in shot-gun DNA sequencing project. It is to reconstruct a consensus DNA sequence from a collection of random oritented fragments. We developed a computer program that is useful for DNA fragment assembly. Inputs to the program are DNA fragment sequences including IUB-IUPAC bases. The program produces the most probable reconstruction ot the original DNA sequence as a text format or a PostScript format. The program consists of four phases: the first phase quickly eliminates fragment pairs that can not possibly overlap. In the second phase, the quality of overlap between each pair is calculated to a score. In the third phase, overlap pairs are sorted by their scores and consistency of the overlaps is checked. The last phase determines consensus sequences and displays them. The performance of fragment assembly program was tested on a set of DNA fragment sequences which were generated from long DNA sequences of GenBank by a fragmentation program.

• Microbiology and Biotechnology Letters
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• v.22 no.2
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• pp.134-142
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• 1994

The neucleotide sequences of the xylA gene encoding $\beta $-xylosidase of Bacillus stearothermophilus and is its flanking regions were datermined. Three open reading frame(ORFs) were found, one of which(ORF1) appeared to code for the $\beta $-xylosidase. The 1830 base pair ORF1 encoded 609 amino acids starting from a TTG initiation codon. The molecular weight deduced from the nucleotide sequence(68 KD) was in agreement with that estimated by SDS-polyacrylamide gel electrophoresis of the purified enzyme(66 KD). The Shine-Dalgarno sequence(5'-AGGAGG-3') was found 11 bp upstream of the initiation codon. Further 15 bp upstream, there observed a potential transcription initiation signals. The putative -10 sequence(CATAAT) and -35 sequence(TTGTTA) coresponded closely to the consensus sequences for Bacillus subtilis RNA polymerase with major sigma factor. The guanine-plus-cytosine content of the coding region of the xylA gene was 56mol% while that of the third position of the codons was 63 mol%. Based on the comparison with the amino acid sequences of several other carbohydrate degrading enzymes, two conserved regions, possibly participating in the catalytic mechamism of $\beta $-xylosidase xylA, were identified in 278-298 and 329-350 regions of the translated xylA gene. The nucleotide sequence of the xylA was found to exhibit no homology to any other genes so far reproted.

• Bulletin of the Korean Chemical Society
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• v.29 no.10
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• pp.1937-1940
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• 2008

The P1 duplex of Tetrahymena group I ribozyme is the important system for studying the conformational changes in folding of ribozyme. The formation of the P1 duplex between IGS and substrate RNA and the catalytic activity of ribozyme require a variety of metal ions such as $Mg^{2+}$ and $Mn^{2+}$. In order to investigate the effect of the $Mg^{2+}$ concentration on the conformation of the P1 duplex, the NMR study was performed as a function of $Mg^{2+}$ concentration. This study revealed that the less stable AU-rich region formed duplex at $50{^{\circ}C}$ under high $Mg^{2+}$ concentration condition but melts out under low $Mg^{2+}$ concentration condition. It was also found that in the active conformation under 10 mM $MgCl_2$ condition, the unstable central G${\cdot}$U wobble pair maintains the significant base pairing up to $50{^{\circ}C}$. This study provides the information of the unique feature of the P1 duplex structure and the roll of $Mg^{2+}$ ion on the formation of the active conformation.

• Genomics & Informatics
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• v.5 no.2
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• pp.68-76
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• 2007

Due to the increasing interest in SNPs and mutational hot spots for disease traits, it is becoming more important to define and understand the relationship between SNPs and their flanking sequences. To study the effects of flanking sequences on SNPs, statistical approaches are necessary to assess bias in SNP data. In this study we mainly applied Markov chains for SNP sequences, particularly those located in intronic regions, and for analysis of in-del data. All of the pertaining sequences showed a significant tendency to generate particular SNP types. Most sequences flanking SNPs had lower complexities than average sequences, and some of them were associated with microsatellites. Moreover, many Alu repeats were found in the flanking sequences. We observed an elevated frequency of single-base-pair repeat-like sequences, mirror repeats, and palindromes in the SNP flanking sequence data. Alu repeats are hypothesized to be associated with C-to-T transition mutations or A-to-I RNA editing. In particular, the in-del data revealed an association between particular changes such as palindromes or mirror repeats. Results indicate that the mechanism of induction of in-del transitions is probably very different from that which is responsible for other SNPs. From a statistical perspective, frequent DNA lesions in some regions probably have effects on the occurrence of SNPs.

• Fisheries and Aquatic Sciences
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• v.18 no.1
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• pp.109-113
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• 2015

Three leptocephali (22.2, 22.7, 56.0 mm in total length) collected from the East/Japan Sea were identified by morphological and genetic analyses as belonging to the genus Scolecenchelys (Anguilliformes, Ophichthidae). Morphologically, the specimens were characterized by 148-158 myomeres, 10 gut swellings, dorsal fin origin above middle of the body, and 6 postanal melanophores between the anus and the caudal margin. An analysis of an 849-base pair 12S rRNA sequence of mitochondrial DNA showed that sequences are concordant with those of adult Scolecenchelys fuscogularis (genetic distance = 0.001). Furthermore total number of myomeres is consistent with the total number of vertebrae in adult S. fuscogularis. This study provides the first description of the morphological characteristics of S. fuscogularis leptocephali and their variations with size. The Korean name of S. fuscogularis is "Ga-neun-mul-baem", established by Ji et al. (2012).

• Journal of the Korean Chemical Society
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• v.38 no.1
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• pp.21-25
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• 1994

The proton affinities of substituted imidazoles, relevant to the binding of lexitropsins that contain imidazole ring to the base pair (G-C sequence) of minor groove of DNA, are studied with the aid of EHT calculations. It is shown that proton affinity of imidazole substituted at position $\alpha$ to the basic nitrogen is slightly larger than that of imidazole substituted at N for the methylimidazole. Proton affinities of N-substituted imidazoles are found to be larger than those of imidazoles substituted at position ${\alpha}$ for a selected set of the other derivatives. As predicted the proton affinity increases when electron-donating group is attached at position N of imidazole.