• Molecules and Cells
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• v.38 no.2
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• pp.171-179
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• 2015

Prostatic acid phosphatase (PAP) expression increases proportionally with prostate cancer progression, making it useful in prognosticating intermediate to high-risk prostate cancers. A novel ligand that can specifically bind to PAP would be very helpful for guiding prostate cancer therapy. RNA aptamers bind to target molecules with high specificity and have key advantages such as low immunogenicity and easy synthesis. Here, human PAP-specific aptamers were screened from a 2'-fluoropyrimidine (FY)-modified RNA library by SELEX. The candidate aptamer families were identified within six rounds followed by analysis of their sequences and PAP-specific binding. A gel shift assay was used to identify PAP binding aptamers and the 6N aptamer specifically bound to PAP with a Kd value of 118 nM. RT-PCR and fluorescence labeling analyses revealed that the 6N aptamer bound to PAP-positive mammalian cells, such as PC-3 and LNCaP. IMR-90 negative control cells did not bind the 6N aptamer. Systematic minimization analyses revealed that 50 nucleotide sequences and their two hairpin structures in the 6N 2'-FY RNA aptamer were equally important for PAP binding. Renewed interest in PAP combined with the versatility of RNA aptamers, including conjugation of anti-cancer drugs and nano-imaging probes, could open up a new route for early theragnosis of prostate cancer.

• Molecules and Cells
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• v.42 no.10
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• pp.721-728
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• 2019

Non-structural protein 1 (NS1) of influenza virus has been shown to inhibit the innate immune response by blocking the induction of interferon (IFN). In this study, we isolated two single-stranded RNA aptamers specific to NS1 with $K_d$ values of $1.62{\pm}0.30nM$ and $1.97{\pm}0.27nM$, respectively, using a systematic evolution of ligand by exponential enrichment (SELEX) procedure. The selected aptamers were able to inhibit the interaction of NS1 with tripartite motif-containing protein 25 (TRIM25), and suppression of NS1 enabled retinoic acid inducible gene I (RIG-I) to be ubiquitinated regularly by TRIM25. Additional luciferase reporter assay and quantitative real-time PCR (RT-PCR) experiments demonstrated that suppression of NS1 by the selected aptamers induced IFN production. It is noted that viral replication was also inhibited through IFN induction in the presence of the selected aptamers. These results suggest that the isolated aptamers are strongly expected to be new therapeutic agents against influenza infection.

• Bulletin of the Korean Chemical Society
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• v.35 no.5
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• pp.1279-1284
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• 2014

The binding of TATA-binding protein (TBP) to the TATA-box containing promoter region is aided by many other transcriptional factors including TFIIA and TFIIB. The mechanistic insight into the assembly of RNA polymerase II preinitation complex (PIC) has been gained by either directly altering a function of target protein or perturbing molecular interactions using drugs, RNAi, or aptamers. Aptamers have been found particularly useful for studying a role of a subset of PIC on transcription for their ability to inhibit specific molecular interactions. One major hurdle to the wide use of aptamers as specific inhibitors arises from the difficulty with traditional assays to validate and determine specificity, affinity, and binding epitopes for aptamers against targets. Here, using a technique called the bio-layer interferometry (BLI) designed for a label-free, real-time, and multiplexed detection of molecular interactions, we studied the assembly of a subset of PIC, TBP binding to TATA DNA, and two distinct classes of aptamers against TPB in regard to their ability to inhibit TBP binding to TFIIA or TATA DNA. Using BLI, we measured not only equilibrium binding constants ($K_D$), which were overall in close agreement with those obtained by electrophoretic mobility shift assay, but also kinetic constants of binding ($k_{on}$ and $k_{off}$), differentiating aptamers of comparable KDs by their difference in binding kinetics. The assay developed in this study can readily be adopted for high throughput validation of candidate aptamers for specificity, affinity, and epitopes, providing both equilibrium and kinetic information for aptamer interaction with targets.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.88-92
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• 2005

Aptamer is the single-stranded oligonucleotide which binds to various target molecules such as proteins, peptides, lipids and small organic molecules with high affinity and specificity. DNA aptamers specific for the $17{\beta}-estradiol$ were selected by SELEX (Systematic Evolution of Ligands by EXponential enrichment) process from a random DNA library. These DNA aptamers have a high affinity to $17{\beta}-estradiol$ as an endocrine disrupting chemical. Nanowell and $200{\mu}m$ gold electrode were used as substrate for DNA aptamer immobilization and electrochemical analysis. Especially, nanowell gold electrode was fabricated by e-beam lithography. The size of single nanowell is 130nm and 40,000 nanowells were deposited on one gold electrode. The immobilization method was based on the interaction between the biotinylated aptamer and streptavidin deposited on gold electrode previously. Immobilization procedure was optimized by surface plasma resonance (SPR) and electrochemical analysis. After the immobilization of DNA aptamer on streptavidin modified gold electrode, $17{\beta}-estradiol$ solution was treated on aptamer immobilized gold electrode. The current of gold electrode was decreased by the binding of $17{\beta}-estradiol$ to DNA aptamer immobilized on gold electrode. However, in negative control experiments of 1-aminoanthraquinone and 2-methoxynaphthalene, the current was rarely decreased. And more sensitive data was obtained from nanowell gold electrode comparing with $200{\mu}m$ gold electrode.

• 한국어정보학회:학술대회논문집
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• 2016.10a
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• pp.189-194
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• 2016

본 연구는 다국어 감성사전 및 감성주석 코퍼스 구축 프로젝트인 MUSE 프로젝트의 일환으로 한국어 감성사전을 구축하기 위해 대표적인 영어 감성사전인 SentiWordNet을 이용하여 한국어 감성사전을 구축하는 방법의 의의와 한계점을 검토하는 것을 목적으로 한다. 우선 영어 SentiWordNet의 117,659개의 어휘중에서 긍정/부정 0.5 스코어 이상의 어휘를 추출하여 구글 번역기를 이용해 자동 번역하는 작업을 실시하였다. 그 중에서 번역이 되지 않거나, 중복되는 경우를 제거하고, 언어학 전문가들의 수작업으로 분류해낸 결과 3,665개의 감성어휘를 획득할 수 있었다. 그러나 이마저도 병명이나 순수 감성어휘로 보기 어려운 사례들이 상당수 포함되어 있어 실제 이를 코퍼스에 적용하여 감성어휘를 자동 판별했을 때에 맛집 코퍼스에서의 재현율(recall)이 긍정과 부정에서 각각 47.4%, 37.7%, IT 코퍼스에서 각각 55.2%, 32.4%에 불과하였다. 이와 더불어 F-measure의 경우, 맛집 코퍼스에서는 긍정과 부정의 값이 각각 62.3%, 38.5%였고, IT 코퍼스에서는 각각 65.5%, 44.6%의 낮은 수치를 보여주고 있어, SentiWordNet 기반의 감성사전은 감성사전으로서의 역할을 수행하기에 충분하지 않은 것으로 나타났다. 이를 통해 한국어 감성사전을 구축할 때에는 한국어의 언어적 속성을 고려한 체계적인 접근이 필요함을 역설하고, 현재 한국어 전자사전 DECO에 기반을 두어 보완 확장중인 SELEX 감성사전에 대해 소개한다.

• Journal of Microbiology and Biotechnology
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• v.27 no.11
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• pp.2037-2043
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• 2017

The surface protein hemagglutinin (HA) mediates the attachment of influenza virus to host cells containing sialic acid and thus facilitates viral infection. Therefore, HA is considered as a good target for the development of diagnostic tools for influenza virus. Previously, we reported the isolation of single-stranded aptamers that can distinguish influenza subtype H1 from H5. In this study, we describe a method for the selective electrical detection of H1 using the isolated aptamer as a molecular probe. After immobilization of the aptamer on Si wafer, enzyme-linked immunosorbent assay (ELISA) and field emission scanning electron microscopy (FE-SEM) showed that the immobilized aptamer bound specifically to the H1 subtype but not to the H5 subtype. Assessment by cyclic voltammetry (CV) also demonstrated that the immobilized aptamer on the indium thin oxide-coated surface was specifically bound to the H1 subtype only, which was consistent with the ELISA and FE-SEM results. Further measurement of CV using various amounts of H1 subtype provided the detection limit of the immobilized aptamer, which showed that a nanomolar scale of target protein was sufficient to produce the signal. These results indicated that the selected aptamer can be an effective probe for distinguishing the subtypes of influenza viruses by monitoring current changes.

• BMB Reports
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• v.41 no.7
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• pp.511-515
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• 2008

The nucleocapsid (NC) protein of the Human Immunodeficiency Virus-1 plays a key role in viral genomic packaging by specifically recognizing the Psi($\Psi$) RNA sequence within the HIV-1 genome RNA. Recently, a novel cell-based assay was developed to probe the specific interactions in vivo between the NC and $\Psi$-RNA using E.coli cells (J. Virol. 81: 6151-55, 2007). In order to examine the extendibility of this cell-based assay to RNAs other than $\Psi$-RNA, this study tested the RNA aptamers isolated in vitro using the SELEX method, but whose specific binding ability to NC in a living cellular environment has not been established. The results demonstrate for the first time that each of those aptamer RNAs can bind specifically to NC in a NC zinc finger motif dependent manner within the cell. This confirms that the cell-based assay developed for NC-$\Psi$interaction can be further extended and applied to NC-binding RNAs other than $\Psi$-RNA.

• Annual Conference on Human and Language Technology
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• 2016.10a
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• pp.189-194
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• 2016

본 연구는 다국어 감성사전 및 감성주석 코퍼스 구축 프로젝트인 MUSE 프로젝트의 일환으로 한국어 감성사전을 구축하기 위해 대표적인 영어 감성사전인 SentiWordNet을 이용하여 한국어 감성사전을 구축하는 방법의 의의와 한계점을 검토하는 것을 목적으로 한다. 우선 영어 SentiWordNet의 117,659개의 어휘중에서 긍정/부정 0.5 스코어 이상의 어휘를 추출하여 구글 번역기를 이용해 자동 번역하는 작업을 실시하였다. 그 중에서 번역이 되지 않거나, 중복되는 경우를 제거하고, 언어학 전문가들의 수작업으로 분류해 낸 결과 3,665개의 감성어휘를 획득할 수 있었다. 그러나 이마저도 병명이나 순수 감성어휘로 보기 어려운 사례들이 상당수 포함되어 있어 실제 이를 코퍼스에 적용하여 감성어휘를 자동 판별했을 때에 맛집 코퍼스에서의 재현율(recall)이 긍정과 부정에서 각각 47.4%, 37.7%, IT 코퍼스에서 각각 55.2%, 32.4%에 불과하였다. 이와 더불어 F-measure의 경우, 맛집 코퍼스에서는 긍정과 부정의 값이 각각 62.3%, 38.5%였고, IT 코퍼스에서는 각각 65.5%, 44.6%의 낮은 수치를 보여주고 있어, SentiWordNet 기반의 감성사전은 감성사전으로서의 역할을 수행하기에 충분하지 않은 것으로 나타났다. 이를 통해 한국어 감성사전을 구축할 때에는 한국어의 언어적 속성을 고려한 체계적인 접근이 필요함을 역설하고, 현재 한국어 전자사전 DECO에 기반을 두어 보완 확장중인 SELEX 감성사전에 대해 소개한다.

• Journal of Microbiology and Biotechnology
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• v.34 no.2
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• pp.289-295
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• 2024

We have developed an aptamer that specifically binds to Porphyromonas gingivalis to reduce the cellular damage caused by P. gingivalis infection and applied it as a biosensor. P. gingivalis is one of the major pathogens causing destructive periodontal disease among the periodontal microorganisms constituting complex biofilms. Porphyromonas gingivalis G-protein (PGP) known to play an important role in the transmission of germs was used as a target protein for the screening of aptamer. The aptamer that has binds to the G-protein of P. gingivalis, was screened and developed through the Systemic Evolution of Ligands by Exponential Energy (SELEX) method. Modified-Western blot analysis was performed with the aptamer which consisted of 38 single-stranded DNA to confirm the selectivity. ELONA (enzyme linked oligonucleotide assay) used to confirm that the aptamer was sensitive to PGP even at low concentration of 1 ㎍/ml. For the rapid detection of P. gingivalis, we constructed a surface plasmon resonance biosensor with SPREETA using the PGP aptamer. It was confirmed that PGP could be detected as low concentration as at 0.1 pM, which is the minimum concentration of aptamer sensor within 5 min. Based on these results, we have constructed a SPREETA biosensor based on aptamer that can bind to P. gingivalis G-protein. It can be used as an infection diagnosis system to rapidly diagnose and analyze oral diseases caused by P. gingivalis.