• The Korean Journal of Mycology
• /
• v.22 no.4
• /
• pp.366-377
• /
• 1994

The base composition of DNA of Aspergillus phoenicis, Rhizopus acidus and Candida albicans treated with cycloheximide and nalidixic acid during the culture was analyzed to compare with the control. The contents of base in the DNA were inhibited by cycloheximide, 20.4% of adenine, 43.1% of thymine, 40.9% of cytosine, 35.3% of guanine, 32.2% of purine, and 42.7% of pyrimidine for A. phoenicis. In R. acidus, 34.2% of adenine, 42.1% of thymine, 38.0% of cytosine, 18.1% of guanine, 24.1% of purine and 40.0% of pyrimidine were depressed by cycloheximide. In the antibiotic treatment of C. albicans, 58.3% of adenine, 58.5% of thymine, 58.1% of cytosine, 42.4% of guanine, 46.8% of purine and 58.8% of pyrimidine were inhibited to compare with the control. The nalidixic acid treatments were showed that, in A. phoenicis 41.6% of adenine, 47.1% of thymine, 59.3% of cytosine, 46.3% of guanine, 45.6% of purine and 57.2% of pyrimidine were inhibited. When R. acidus was treated with nalidixic acid, 59.1% of adenine, 54.7% of thymine, 35.3% of cytosine, 37.4% of guanine, 45.9% of purine and 44.9% of pyrimidine decreased. In treatment of nalidixic acid, the content of DNA was depressed 60.1% of adenine, 68.6% of thymine, 60.7% of cytosine, 40.0% of guanine, 45.8% of purine and 63.5% of pyrimidine for C. albicans In the DNA synthesis of three fungal cells, cycloheximide and nalidixic acid treatments were analyzed obviously that the biosynthesis of pyrimidine was depressed than that of purine. Therefore, it was showed that the DNA contents in the various fungal cells were inhibited remarkably in nalidixic acid treatment than cycloheximide.

• Proceeding of EDISON Challenge
• /
• 2015.03a
• /
• pp.151-155
• /
• 2015

The molecular interactions between the nucleic acid bases and water molecules are important in organism. Despite Adenine-Thymine Hoogsteen base pair and Guanine-Cytosine Watson-Crick base pair have been demonstrated to be most stable in a gas phase, the effect of water on the stability of these base pairs remains elusive. Here we report the structural and thermodynamic characteristics on possible Adenine-Thymine and Guanine-Cytosine base pairs in a gas phase as well as in an aqueous phase by using quantum mechanical method and statistical mechanical calculations. First, we optimized the direct base-pair interaction energies of four Adenine-Thymine base pairs (Hoogsteen base pair, reverse Hoogsteen base pair, Watson-Crick base pair, and reverse Watson-Crick base pair) and three Guanine-Cytosine base pairs (GC1 base pair, GC2 base pair, and Watson Crick base pair) in a gas phase at the $B3LYP/6-31+G^{**}$ level. Then, the effect of solvent was quantified by the electronic reorganization energy and the solvation free energy by statistical mechanical calculations. Thereby, we discuss the effect of water on the stability of Adenine-Thymine and Guanine-Cytosine base pairs, and argue why Adenine-Thymine Watson-Crick base pair and Guanine-Cytosine Watson-Crick base pair are most stable in an aqueous environment.

• Bulletin of the Korean Chemical Society
• /
• v.35 no.12
• /
• pp.3532-3534
• /
• 2014

In theoretical simulations of proton transfer in DNA, environmental factors nearly have not been considered. In our calculations, using QM/MM method on the basis of CP2K, proton transfer on adenine-thymine base pair is studied in water, at wide scope temperature, and under the external electric field. Our results indicate that the external electric field induces the proton transfer at room temperature, and its intensity and temperature have some effect on hole localization and proton transfer.

• Proceedings of the Korean Society of Potoscience Conference
• /
• 2006.06a
• /
• pp.44-44
• /
• 2006

• Bulletin of the Korean Chemical Society
• /
• v.29 no.1
• /
• pp.205-207
• /
• 2008

• Journal of the Korean Institute of Intelligent Systems
• /
• v.13 no.1
• /
• pp.37-44
• /
• 2003

In this paper, we investigated the performance of both DNA coding method and Genetic Algorithm(GA) in numeric pattern (from 0 to 9) recognition. The performance of the DNA coding method is compared to the that of the GA. GA searches effectively an optimal solution via the artificial evolution of individual group of binary string using binary coding, while DNA coding method uses four-type bases denoted by Adenine(A), Cytosine(C), Guanine(G) and Thymine(T). To compare the performance of both method, the same genetic operators(crossover and mutation) are applied and the probabilities of crossover and mutation are set the same values. The results show that the DNA coding method has better performance over GA. The reasons for this outstanding performance are multiple candidate solution presentation in one string and variable solution string length.

• Korean Journal of Agricultural Science
• /
• v.46 no.4
• /
• pp.885-895
• /
• 2019

Plant biotechnologists have long dreamed of technologies to manipulate genes in plants at will. This dream has come true partly through the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, which now has been used to edit genes in several important crops. However, there are many restrictions in editing a gene precisely using the CRISPR/Cas9 technology because CRISPR/Cas9 may cause deletions or additions in some regions of the target gene. Several other technologies have been developed for gene targeting and precision editing. Among these, base editors might be the most practically and efficiently used compared to others. Base editors are tools which are able to cause a transition from cytosine into thymine, or from adenine into guanine very precisely on specific sequences. Cytosine base editors basically consist of nCas9, cytosine deaminase, and uracil DNA glycosylase inhibitor (UGI). Adenine base editors consist of nCas9 and adenine deaminase. These were first developed for human cells and have since also been applied successfully to crops. Base editors have been successfully applied for productivity improvement, fortification and herbicide resistance of crops. Thus, base editor technologies start to open a new era for precision gene editing or breeding in crops and might result in revolutionary changes in crop breeding and biotechnology.

• Journal of the Korean Chemical Society
• /
• v.24 no.4
• /
• pp.280-287
• /
• 1980

The interactions of chemical carcinogens, such as polycyclic aromatic hydrocarbons, dimethylaminoazobenzene (DAB) and its derivatives and heterocyclic compounds with tissue components, especially with deoxyribonucleic acid (DNA), were examined by means of simple Huckel method. Assuming that the formations of a loose molecular complex between the carcinogens and the tissue components are the first step of chemical carcinogenesis, the most proble orientation between the chemical carcinogens and adenine-thymine (A=T) pair or guanine-cytosine $(G\equivC)$ pair is determined. It has been found that, in the case of the formation of molecular complex between chemical carcinogens and A=T pair, the two atoms of K-region of the carcinogens and the atom of L-region in the proximity of their K-region are combined correspondingly with C-l' carbon atom in the sugar that is attached to thymine, N-1 nitrogen atom and C-5 carbon atom in the thymine part of A=T pair, while, in the case of that between the carcinogens and $G\equivC$ pair, the above three atoms of the carcinogens are combined correspondingly with C-8 carbon atom, N-9 nitrogen atom and N-3 nitrogen atom in the guanine part of $G\equivC$ pair.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2004.11a
• /
• pp.77-85
• /
• 2004

A significant portion (about 8% in human genome) of mammalian mRNA sequences contains AU(Adenine and Uracil) rich elements or AREs at their 3' untranslated regions (UTR). These mRNA sequences are usually stable. ARE motifs are assorted into three classes. The importance of AREs in biology is that they make certain mRNA unstable. We analyzed the occurrences of AREs and Alu, and propose a possible mechanism on how human mRNA could acquire and keep A REs at its 3' UTR originated from Alu repeats. Interspersed in the human genome, Alu repeats occupy 5% of the 3' UTR of mRNA sequences. Alu has poly-adenine (poly-A) regions at the end that lead to poly -thymine (poly-T) regions at the end of its complementary Alu. It has been discovered that AREs are present at the poly -T regions. In the all ARE's classes, 27-40% of ARE repeats were found in the poly -T region of Alu with mismatch allowed within 10% of ARE's length from the 3' UTRs of the NCBI's reference m RNA sequence database. We report that Alu, which has been reported as a junk DNA element, is a source of AREs. We found that one third of AREs were derived from the poly -T regions of the complementary Alu.

• Journal of Microbiology and Biotechnology
• /
• v.5 no.1
• /
• pp.1-5
• /
• 1995

A genomic DNA of alkaliphilic bacterium, Micrococcus sp. Y-l, was analysed using the physical mapping method of pulsed-field gel electrophoresis (PFGE). Five restriction enzymes of Sspl, Hpal, Xbal, Ndel or EcoRI, which recognize the Adenine-Thymine-rich sequences of genomic DNA, were used for the generation of few (7 to 20) distinctly separate fragments, with average sizes in the range of 200～500 kb. However, the sites for Notl and SfiI, 8 base-recognizing enzymes, were highly frequent. The genome size of this strain was determined to be 4 mega base pairs (Mb) from restriction fragments separated by PFGE. This is the first case of restriction mapping in alkaliphilic bacterium.