• Proceedings of the Korean Information Science Society Conference
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• 2003.10b
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• pp.772-774
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• 2003

DNA/DNA의 연쇄 결합 반응에 대한 시뮬레이션을 열역학적 데이터를 이용하여 구현하였다. 1-Base의 non Watson-Crick 결합과, dangling end(결합이 이루어진 두개의 DNA strand 중 한쪽 끝이 다른 쪽 끝보다 길거나 짧은 경우)를 허용하는 nearest-neighbor model을 사용하여 구현된 이 모델에서는 한번의 hybridization만을 예측하는 것이 아니라 연속적인 결합 반응의 시뮬레이션이 가능하다. 이를 통해서 분자 알고리즘의 설계와 검증이 가능할 뿐만 아니라, cross-homology의 검사를 통한 시퀀스의 검증까지도 가능하다. 이러한 in silico 에서의 접근 방식은 효율적인 분자 알고리즘의 개발과 신뢰성 있는 시퀀스의 설계에 도움이 될 수 있다.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.181-190
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• 2019

In Escherichia coli, DicA protein is involved in cell division control. DicA protein is known to bind DNA better at $25^{\circ}C$ than at $37^{\circ}C$. However, the molecular cause of the temperature dependent binding is not clear. In this study, we investigated how DicA binds DNA and why its DNA binding activity depends on temperature. An unique in vivo DNA binding assay developed in this laboratory showed that unlike the homologous proteins such as RovA or SlyA, DicA uses its N-terminal domain for DNA binding. The in vivo DNA binding assay of DicA also demonstrated that the temperature-dependent DNA binding activity does not come from Cnu or H-NS that is known to bind DNA better at $25^{\circ}C$ than at $37^{\circ}C$. Electrophoretic Mobility Shift Assay (EMSA), when performed with purified DicA protein, did not show temperature-dependent DicA binding activity. However when EMSA was performed with crude protein from WT E. coli cells, temperature-dependent DicA binding activity was observed, suggesting that there is a factor(s) that confers temperature DNA binding activity of DicA in vivo.

• Korean journal of applied entomology
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• v.34 no.2
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• pp.100-105
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• 1995

A whole body extract (WBE), a crude nuclear fraction, of aphids was prepared and used to identify the proteins which bound specifically to 5'-upstream regions of the transcription initiation site of the aphid ribosomal RNA gene (rDNA). While DNA fragment (-263/-195) was bound by only one specific 53 kDa protein, two DNA fragments, A(-194/23) and B(-393/-264), were commonly bound by three proteins (52 kDa, 50 kDa and 40 kDa). It was also revealed that the formation of he DNA-protein complex requires a cation.

• Proceedings of the Korean Information Science Society Conference
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• 2003.04c
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• pp.476-478
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• 2003

1-Base의 non Watson-Crick 결합과, Dangling end(결합이 이루어진 두 개의 DNA strand 중 한쪽 끝이 다른 쪽 끝보다 짧은 경우)를 허용하는 nearest-neighbor model을 사용하여 DNA/DNA Hybridization 예측 시스템을 구현하였다. DNA 컴퓨팅을 기존의 실리콘 컴퓨터를 이용하여 접근하는 이러한 방법은 좀 더 효율적인 분자 알고리즘의 개발과 DNA 컴퓨팅에 사용될 수 있는 더욱 신뢰성 있는 DNA 시퀀스의 설계에 도움을 줄 수 있을 것이다.

• Korean Journal of Microbiology
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• v.43 no.4
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• pp.250-255
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• 2007

The RecA protein of Deinococcus radiodurans is essential for the extreme radiation resistance of this organism. The central steps involved in recombinational DNA repair require DNA-dependent ATP hydrolysis by recA protein. Key feature of RecA protein-mediated activities is the interactions with ssDNA and dsDNA. The ssDNA is the site where RecA protein filament formation nucleates and where initiation of DNA strand exchange takes place. The effect of sequence heterogeneity of ssDNA was examined in this experiment. The rate of homopolymeric synthetic ssDNA-dependent ATP hydrolysis was constant or nearly so over a broader range of pHs. For poly(dT)-dependent ATP or dATP hydrolysis, rates were generally faster, with a broader optimum between pH 7.0 and 8.0. Activities of RecA protein were affected by the ionic environment. The ATPase activity was shown to have different sensitivity to anionic species. The presence of glutamate seemed to slimulate the hydrolytic activity. Dr RecA protein was shown to require $Mg^{2+}$ ion greater than 2 mM for binding to etheno ssDNA and the binding stoichiometry of 3 nucleotide for RecA protein monomer.

• Proceedings of the Korean Information Science Society Conference
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• 2004.04b
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• pp.307-309
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• 2004

급성 심근경색 진단용 DNA 컴퓨팅 시스템 모듈로서, 트로포닌 I (troponin I, Tnl). 트로포닌 T (troponin T, TnT). 미오글로빈 (myoglobin), C-반응 단백질 (C-reactive protein, CRP) 과 각각 결합할 수 있는 네 가지 종류의 앱타머틀 선정하고, 이의 개발을 시도하여, 그 중 첫 번째로 C-반응 단백질-결합 앱타머를 SELEX 기법을 이용하여 선별해내었다. 또한, 선별된 앱타머 염기서열에 기초하여 각각 10-mer 길이의 FDNA 와 QDNA 를 제작하고, 표적 단백질 (CRP) 과 혼합시켜 형광발현 변화의 추이를 살펴보았다. 앱타머 및 FDNA. QDNA 가 결합할 경우에는 형광감쇄효과가 발생하므로, 형광감쇄효과가 일어나지 않은 경우에 비하여 현저하게 형광측정값이 저조하게 나타나는 현상을 확인할 수 있었다. 향후 연구로, 나머지 세 가지 종류의 앱타머를 SELEX기법을 이용하여 선별해내고. 기확보된 C-반응 단백질-결합 앱타머 모듈과 함께 논리회로를 구성하는 DNA 컴퓨팅 칩을 제작할 예정이다.

• Journal of Life Science
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• v.12 no.1
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• pp.55-60
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• 2002

The differentiation of skeletal muscle precursor cells in culture is marked by the transcriptional activation of muscle-specific genes and the morphological differentiation of myoblast into multinucleate myotube. In this study, we examined the effect of TSA (Trichostatin A) on WF-kB DNA binding activity and muscle cell fusion in the process of myogenesis. Under TSA treatment, C2C12 myoblast could not fuse to myotube and its NF-kB DNA binding activity was also blocked. To investigate whether these phenomenons were affected by TSA in direct or not, differentiation media (DM) used to differentiate cells without TSA was concentrated and added to C2C12 myoblast with TSA simultaneously. C2C12 myoblast was fused to myotube and NF-kB DNA binding activity was recovered. These results suggest that TSA affects on the differentiation of myoblast, perhaps through several factors, by inhibiting myoblst fusion and blocking NF-kB DNA binding activity.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.02a
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• pp.391-392
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• 2013

반도체 집적회로의 고집적화 및 고성능화를 위한 기본 소자(MOSFET)의 미세화 및 단위공정의 물리적 한계를 극복하기 위해 기존의 Top-down 방식에서 buttom-up 방식의 공정에 대한 연구가 진행되고 있다. 그 중 nanoparticles를 이용한 나노소자 제작 연구가 이루어지고 있다. 하지만 이러한 nanoparticles를 이용한 나노소자의 제작에 있어서 원하는 위치에 nanoparticles를 배열하고 정렬하는데 어려움을 겪고 있다. 이 문제를 해결하기 위해서 자기조립 특성을 가지고 있는 DNA분자와 기능화를 통하여 표면에 positive charge를 띄고있는 Gold nanoparticles를 상호결합 시키는 실험을 하였다. Au-DNA nanowire는 backbone에 있는 phosphate부분에서 negative charge를 띠고 있는 DNA와 positive charge를 띠고 있는 Gold nanoparticles가 결합하는 원리로 형성된다. 그렇지만 Gold particles를 표면이 아닌 DNA에만 붙이는 것은 아직 해결해야 할 부분으로 남아있다. 본 연구에서는 이 문제를 해결하기 위하여 pH 조절을 통하여 기능화된 Gold particles의 charge의 변화를 주고 이를 Zeta potential 측정기로 측정한 후에 이 particles와 DNA를 결합시켜서 FE-SEM과 AFM 으로 확인하는 실험을 하였다.

• Applied Biological Chemistry
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• v.36 no.6
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• pp.547-552
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• 1993

Soybean nuclear extracts and S-100 were prepared to examine the soybean embryo factors which bind to the upstream region of soybean ${\beta}-conglycinin$ ${\alpha}'$ subunit gene. SEF3(soybean embryo factor 3), which is presumed to be a trans-acting factor for the expression of the gene, was detected in gel mobility shift assay using the DNA probe containing two AACCCA hexanucleotides. DNA probe containing CATGCAT or AACACA was used to find any other soybean embryo factor interacting with the upstream region of ${\beta}-Conglycinin$ ${\alpha}'$ subunit gene. It was found that there was no common DNA binding protein detected both in nuclear extracts and S-100. The relative levels of SEF3 binding activity both in nuclear extracts and S-100 of maturing soybean seeds were determined. SEF3 activity of nuclear extracts was first detected around 20 days after pollination and significantly increased around 32 days after pollination.

• 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.