• Journal of Microbiology and Biotechnology
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• v.18 no.8
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• pp.1377-1385
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• 2008

The uracil-sensing domain in archaeal family B-type DNA polymerases recognizes pro-mutagenic uracils in the DNA template, leading to stalling of DNA polymerases. Here, we describe our new findings regarding the molecular, mechanism underpinning the stalling of polymerases. We observed that two successive deaminated bases were required to stall TNA1 and KOD1 DNA polymerases, whereas a single deaminated base was enough for stalling Pfu DNA polymerase, in spite of the virtually identical uracil-sensing domains. TNA1 and KOD1 DNA polymerases have a much higher extension rate than Pfu DNA polymerase; decreasing the extension rate resulted in stalling by TNA1 and KOD1 DNA polymerases at a single deaminated base. These results strongly suggest that these polymerases require two factors to stop DNA polymerization at a single deaminated base: the presence of the uracil-sensing domain and a relatively slow extension rate.

• Smart Structures and Systems
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• v.12 no.1
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• pp.73-95
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• 2013

Nine deoxyribonucleic acid (DNA) sequences were used to functionalize single-walled carbon nanotube (SWNT) sensors to detect the trace amount of methanol, acetone, and HCl in vapor. DNA 24 Ma (24 randomly arranged nitrogenous bases with one amine at each end of it) decorated SWNT sensor and DNA 24 A (only adenine (A) base with a length of 24) decorated SWNT sensor have demonstrated the largest sensing responses towards acetone and HCl, respectively. On the other hand, for the DNA GT decorated SWNT sensors with different sequence lengths, the optimum DNA sequence length for acetone and HCl sensing is 32 and 8, separately. The detection of methanol, acetone, and HCl have identified that DNA functionalized SWNT sensors exhibit great selectivity, sensitivity, and repeatability with an accuracy of more than 90%. Further, a sensor array composed of SWNT functionalized with various DNA sequences was utilized to identify acetone and HCl through pattern recognition. The sensor array is a combination of four different DNA functionalized SWNT sensors and two bare SWNT sensors (work as reference). This wireless sensing system has enabled real-time gas monitoring and air quality assurance for safety and security.

• Proceedings of the Polymer Society of Korea Conference
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• 2006.10a
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• pp.33-34
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• 2006

The graft copolymer consisting of poly(N-isopropylacrylamide) (PNIPAAm) and single-stranded DNA was prepared. Interestingly, the copolymer was found to form nanoparticles above physiological temperature. We found that non-crosslinking aggregation of the nanoparticles was induced by the hybridization of the surface-bound DNA with the full-match complementary DNA, but not with one-base mismatch. The core material is not restricted to PNIPAAm; DNA-functionalized gold nanoparticle was found to show a similar aggregation induced only by the fully-complementary DNA, resulting in rapid color change within 3 min at ambient temperature. This methodology is general in principle and applicable for wide variety of clinical gene diagnosis.

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
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• 2014.10a
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• pp.358-360
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• 2014

For the several decades, various nanomaterials are broadly used in industry and research. With the growth of nanotechnology, the study of nanotoxicity is being accelerated. Particularly, mercury ion is widely used in real life. Because the mercury is representative high toxic material, it is highly recommended to detect the mercury ion. In previous reported work, thymine-thymine mismatches (T-T) capture mercury ion and create very stable base pair ($T-Hg^{2+}-T$). Here, we performed the high sensitive sensing method for direct label free detection of mercury ions and DNA binding using Kelvin Probe Force Microscope (KPFM). In this method, 30 base pairs of thymine (T-30) is used for mercury specific DNA binding ($T-Hg^{2+}-T$). KPFM is able to detect the mercury ion because there is difference between bare T-30 DNA and mercury mediated DNA ($T-Hg^{2+}-T$).

• The Transactions of The Korean Institute of Electrical Engineers
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• v.57 no.2
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• pp.320-326
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• 2008

In this paper, we propose a new algorithm emulating the DNA characteristics for noise-tolerant pattern matching problem on digital system. The digital pattern matching becomes core technology in various fields, such as, robot vision, remote sensing, character recognition, and medical diagnosis in particular. As the properties of natural DNA strands allow hybridization with a certain portion of incompatible base pairs, DNA-inspired data structure and computation technique can be adopted to bio-signal pattern classification problems which often contain imprecise data patterns. The key feature of noise-tolerance of DNA computing comes from control of reaction temperature. Our hardware system mimics such property to diagnose cardiovascular disease and results superior classification performance over existing supervised learning pattern matching algorithms. The hardware design employing parallel architecture is also very efficient in time and area.

• Journal of Sensor Science and Technology
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• v.21 no.5
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• pp.359-366
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• 2012

Nanopore DNA sequencing is an emerging and promising technique that can potentially realize the goal of a low-cost and high-throughput method for analyzing human genome. Especially, solid-state nanopores have relatively high mechanical stability, simple surface modification, and facile fabrication process without the need for labeling or amplification of PCR (polymerized chain reaction) in DNA sequencing. For these advantages of solid-sate nanopores, the use of solid-state nanopores has been extensively considered for developing a next generation DNA sequencing technology. Solid-state nanopore sequencing technique can determine and count charged molecules such as single-stranded DNA, double-stranded DNA, or RNA when they are driven to pass through a membrane nanopore between two electrolytes of cis-trans chambers with applied bias voltage by measuring the ionic current which varies due to the existence of the charged particles in the nanopore. Recently, many researchers have suggested that nanopore-based sensors can be competitive with other third-generation DNA sequencing technologies, and may be able to rapidly and reliably sequence the human genome for under $1,000.

• Journal of Dairy Science and Biotechnology
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• v.42 no.1
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• pp.18-22
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• 2024

In this study, we performed whole-genome sequencing of Levilactobacillus brevis KL251 (KL251) isolated from kimchi. The KL251 genome, characterized by a circular chromosome spanning 2,345,062 base pairs with a GC content of 45.78%, was analyzed. KL251 contains 2,275 coding DNA sequences (CDSs), 56 transfer RNAs (tRNAs), and 4 ribosomal RNAs (rRNAs). Genes associated with gamma-aminobutyric acid (GABA) production and CRISPR-Cas systems were identified and could potentially be used for GABA synthesis and defense against foreign DNA. Additionally, the presence of functional genes involved in isoprenoid biosynthesis, glutathione generation, and redox sensing showed that cellular metabolism and stress responses were important characteristics of this genome. These genomic findings suggest that the KL251 strain could potentially have several applications, including food fermentation, probiotics, dairy product starters, and the development of health-enhancing products.

• The Korea Journal of Herbology
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• v.28 no.6
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• pp.9-14
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• 2013

Objectives : Cnidii Fructus is prescribed as the fruit of Cnidium monnieri (L.) Cusson or Torilis japonica (Houtt.) DC. in Korea pharmacopoeia. Although there are differences in the composition of useful components, two species have been used without distinction. In order to discriminate them, DNA sequencing and taste pattern analysis were used in this study. Methods : Primers ITS 1 and ITS 4 were used to amplify the intergenic transcribed spacer(ITS) region of nuclear ribosomal DNA from seven T. japonica and six C. monnieri samples. Taste pattern of samples were measured by using taste-sensing system SA402B equipped with five foodstuff sensors(CT0, C00, AAE, CA0, and AE1). The five initial taste(sourness, bitterness, astringency, umami, and saltiness) and three aftertaste(aftertaste of bitterness, astringency, and umami) of two species were compared. Results : According to the results of ITS region sequence analysis, two species showed 94 base pairs differences. The similarity of two sequences was 85%. From the taste pattern analysis, sourness, bitterness, aftertaste of bitterness(aftertaste-B), and umami showed a different pattern. Especially, bitterness and aftertaste-B of C. monnieri were significantly higher than T. japonica. In addition, two species were shown to have two markedly different clustering by these two flavors. Conclusion : T. japonica and C. monnieri were effectively discriminated using DNA sequencing and taste pattern analysis. These methods can be used to identify the origin of traditional medicine in order to maintain therapeutic efficacy.

• Fisheries and Aquatic Sciences
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• v.12 no.4
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• pp.265-275
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• 2009

G Protein-coupled receptors (GPCRs) mediating wide ranges of physiological responses is one of the most attractive targets for drug development. Rhodopsin, a dim-light photoreceptor, has been extensively used as a model system for structural and functional study of GPCRs. Fish have rhodopsin finely-tuned to their habitats where the intensity and the wavelength of lights are changed depending on its water-depth. To study the detailed molecular characteristics of GPCR architecture and to understand the fishery light-sensing system, genes encoding rod opsins were isolated from fishes living under different photic environments. Full-length rod opsin genes were obtained by combination of PCR amplification and DNA walking strategy of genomic DNA isolated from olive flounder, P. olivaceus, Japanese eel, A. japonica, and Common carp C. carpio. Deduced amino acid sequences showed a typical feature of rod opsins including the sites for Schiffs base formation (Lys296) and its counter ion (Glu113), disulfide formation (Cys110 and Cys187), and palmitoylation (Cys322 and Cys323) although Cys322 is replaced by Phe in Japanese eel. Comparison of opsins by amino acid sequence alignment indicated the closest similarity between P. olivaceus and H. hippoglossus (94%), A. japonica and A. anguilla (98%), and C. carpio and C. auratus (95%), respectively.

• Interdisciplinary Bio Central
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• v.4 no.3
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• pp.10.1-10.12
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• 2012

Introduction: We investigated frameshift suppressor tRNAs previously reported to use five-base anticodon-codon interactions in order to provide a collection of frameshift suppressor tRNAs to the synthetic biology community and to develop modular frameshift suppressor logic devices for use in synthetic biology applications. Results and Discussion: We adapted eleven previously described frameshift suppressor tRNAs to the BioBrick cloning format, and built three genetic logic circuits to detect frameshift suppression. The three circuits employed three different mechanisms: direct frameshift suppression of reporter gene mutations, frameshift suppression leading to positive feedback via quorum sensing, and enzymatic amplification of frameshift suppression signals. In the course of testing frameshift suppressor logic, we uncovered unexpected behavior in the frameshift suppressor tRNAs. The results led us to posit a four-base binding hypothesis for the frameshift suppressor tRNA interactions with mRNA as an alternative to the published five-base binding model. Conclusion and Prospects: The published five-base anticodon/codon rule explained only 17 of the 58 frameshift suppression experiments we conducted. Our deduced four-base binding rule successfully explained 56 out of our 58 frameshift suppression results. In the process of applying biological knowledge about frameshift suppressor tRNAs to the engineering application of frameshift suppressor logic, we discovered new biological knowledge. This knowledge leads to a redesign of the original engineering application and encourages new ones. Our study reinforces the concept that synthetic biology is often a winding path from science to engineering and back again; scientific investigations spark engineering applications, the implementation of which suggests new scientific investigations.