Erratum

Shuo Ren 대한화학회 2019 Bulletin of the Korean Chemical Society Vol.40 No.12

Label-free Detection of the Transcription Initiation Factor Assembly and Specific Inhibition by Aptamers

Shuo Ren,유안유안장,Hye Rim Yoon,Sun Woo Hong,신동혁,이상호,이동기,진문수,Irene M. Min,김소연 대한화학회 2014 Bulletin of the Korean Chemical Society Vol.35 No.5

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 (KD), which were overall in close agreement with those obtained by electrophoretic mobility shift assay, but also kinetic constants of binding (kon and koff), 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.

Synthesis of UV active 2-methylisoborneol for water pollutant detection

Ren, Shuo,Sampath, Vasu,Rhee, Young Ho,Kim, Soyoun Springer-Verlag 2009 Toxicology and Environmental Health Sciences Vol.1 No.3

Trends in Three-dimensional Biochips

Shuo Ren,윤혜림,김소연 한국바이오칩학회 2008 BioChip Journal Vol.2 No.3

In the past decade we have witnessed a rapid development in nano biotechnology that has yielded highthroughput and large-scale analysis within a miniaturized and parallel assay system. The biochip is a powerful emerging technology for biomedical, diagnostical, therapeutical, toxicological, and environmental applications. There are diverse sensing mediators used for biochips, including DNA, RNA, and protein, and moreover, even living cells are being studied. Recently, a large variety of biochip materials have been developed. Here, we will give an overview of the trends in three-dimensional biochip materials, particularly focusing on gel materials in biochip applications. We will review some unique methods and remaining challenges.

Label-free Detection of the Transcription Initiation Factor Assembly and Specific Inhibition by Aptamers

Ren, Shuo,Jiang, Yuanyuan,Yoon, Hye Rim,Hong, Sun Woo,Shin, Donghyuk,Lee, Sangho,Lee, Dong-Ki,Jin, Moonsoo M.,Min, Irene M.,Kim, Soyoun Korean Chemical Society 2014 Bulletin of the Korean Chemical Society Vol.35 No.5

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.

Selection of DNA Aptamers Against Botulinum Neurotoxin E for Development of Fluorescent Aptasensor

Shuo Ren,신혜수,Vinayakumar Gedi,Pooja Dua,이동기,김소연 대한화학회 2017 Bulletin of the Korean Chemical Society Vol.38 No.3

Botulinum neurotoxins (BoNTs) produced by Clostridium botulinum are the deadliest toxins known to mankind with a potential of possible bioterrorism agents. Due to the high-potential harm of these toxins, a sensitive and real-time monitoring capable detection systems are required for the early stage detection. In this study, a novel sol–gel-based SELEX was used to isolate single-stranded nucleic acids (ssDNA) aptamers against purified BoNT type E toxoid (BoNTE) using a chemically synthesized random N40 ssDNA library. The bound aptamer sequences after five rounds were analyzed using next-generation sequencing and the resulted high-frequency aptamers were characterized using biolayer interferometry. Among the tested, aptamer BT5.6 showed low nanomolar binding affinity (KD, 53.3 nM) toward BoNTE. As a proof of concept, the aptamer was utilized in a graphene oxide-based detection platform. In summary, we screened and identified a ssDNA aptamer with high affinity toward BoNTE, which, we believe can be used for development of sensitive detection systems.

N-Acetyltransferase 2 Gene Polymorphisms are Associated with Susceptibility to Cancer: a Meta-analysis

Tian, Fang-Shuo,Shen, Li,Ren, Yang-Wu,Zhang, Yue,Yin, Zhi-Hua,Zhou, Bao-Sen Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.14

N-acetyltransferase 2 (NAT2) is a polymorphic enzyme that plays an important role in the metabolism of various potential carcinogens. In recent years, a number of studies have been carried out to investigate the relationship between the rs1799930 and rs1799931 polymorphism in NAT2 and cancer risk in multiple populations for different types of cancer. However, the results were not consistent. Therefore, we performed a meta-analysis to further explore the relationship between NAT2 polymorphism and the risk of cancer. A total of 21 studies involving 15, 450 subjects for rs1799930 and 13, 011 subjects for rs1799931 were included in this meta-analysis. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess strength of associations. We also evaluated the publication bias and performed a sensitivity analysis. Overall, our results showed an apparent significant association between the NAT2 rs1799930 polymorphism and cancer susceptibility in Asians (GA vs. GG: OR=1.22, 95% CI=1.03-1.45; dominant model: OR=1.22, 95% CI=1.03-1.43) and population-based controls (GA vs. GG: OR=1.10, 95% CI=1.01-1.19; dominant model: OR=1.09, 95% CI=1.01-1.18). In contrast, a significant association was observed between the NAT2 rs1799931 G>A polymorphism and decreased cancer susceptibility in overall meta-analysis (AA vs. GG: OR=0.55, 95% CI=0.33-0.93; GA vs. GG: OR=1.00, 95% CI=0.88-1.14; dominant model: OR=0.97, 95% CI=0.86-1.10; recessive model: OR=0.56, 95% CI=0.34-0.94) and the Asian group (AA vs. GG: OR=0.50, 95% CI=0.26-0.94; recessive model, OR=0.50, 95% CI=0.27-0.94). We found that the NAT2 rs1799930 may be a risk factor, while the NAT2 rs1799931 polymorphism is associated with a decreased risk of cancer and is likely a protective factor against cancer development.

Cell-SELEX Based Identification of an RNA Aptamer for Escherichia coli and Its Use in Various Detection Formats

Dua, Pooja,Ren, Shuo,Lee, Sang Wook,Kim, Joon-Ki,Shin, Hye-su,Jeong, OK-Chan,Kim, Soyoun,Lee, Dong-Ki Korean Society for Molecular and Cellular Biology 2016 Molecules and cells Vol.39 No.11

Escherichia coli are important indicator organisms, used routinely for the monitoring of water and food safety. For quick, sensitive and real-time detection of E. coli we developed a 2'F modified RNA aptamer Ec3, by Cell-SELEX. The 31 nucleotide truncated Ec3 demonstrated improved binding and low nano-molar affinity to E. coli. The aptamer developed by us out-performs the commercial antibody and aptamer used for E. coli detection. Ec3(31) aptamer based E. coli detection was done using three different detection formats and the assay sensitivities were determined. Conventional Ec3(31)-biotin-streptavidin magnetic separation could detect E. coli with a limit of detection of $1.3{\times}10^6CFU/ml$. Although, optical analytic technique, biolayer interferometry, did not improve the sensitivity of detection for whole cells, a very significant improvement in the detection was seen with the E. coli cell lysate ($5{\times}10^4CFU/ml$). Finally we developed Electrochemical Impedance Spectroscopy (EIS) gap capacitance biosensor that has detection limits of $2{\times}10^4CFU/mL$ of E. coli cells, without any labeling and signal amplification techniques. We believe that our developed method can step towards more complex and real sample application.

A cross-contamination-free SELEX platform for a multi-target selection strategy

이상욱,강지혜,Shuo Ren,로렐토마스,김소연,정옥찬 한국바이오칩학회 2013 BioChip Journal Vol.7 No.1

Multi-target aptamer selection, known as multiplex systematic evolution of ligands by exponential enrichment (SELEX), is rapidly drawing interest because of its potential to enable high-speed, highthroughput aptamer selection. The parallelization of chemical processes by integrating microfluidic unit operations is a key strategy for developing a multiplex SELEX process. One of the potential problems with on-chip multiplexing chemical processes is crosscontamination. In order to avoid this, we propose a microfluidic network platform that uses pneumatic valves to allow the serial loading and incubation of aptamers with sol-gel entrapped target proteins. After target binding inside the sol-gels, the cross-contamination-free parallel elution of specifically bound aptamers is performed. The platform allows selective binding with five different targets immobilized in sol-gel spots. When eluting bound species, cross-contamination is avoided by sealing the adjacent elution chambers from each other using the pneumatic microvalves. Consequently, we demonstrate specific aptamer binding to the respective protein target and subsequent aptamer elution without any cross-contamination. This proof of concept opens the way to increased automation and microscale parallel processing of the SELEX methodology.

Study on the Fracture Toughness of Polypropylene-Basalt Fiber-Reinforced Concrete

Ninghui Liang,Lianxi Ren,Shuo Tian,Xinrong Liu,Zuliang Zhong,Zhiyun Deng,Ru Yan 한국콘크리트학회 2021 International Journal of Concrete Structures and M Vol.15 No.5

To study the hybrid effects of polypropylene fiber and basalt fiber on the fracture toughness of concrete, 13 groups of notched concrete beam specimens with different fiber contents and mass ratios were prepared for the three-point bending test. Based on acoustic emission monitoring data, the initiation cracking load and instability load of each group of specimens were obtained, and the fracture toughness parameters were calculated according to the double- K fracture criterion. The test results show that the basalt fiber-reinforced concrete has a greater increase in initial fracture toughness, and the toughness of coarse polypropylene fiber-reinforced concrete is more unstable. Moreover, after the coarse polypropylene fiber content reaches 6 kg/m³ and the basalt fiber content reaches 3 kg/m³, increasing the content will not significantly improve the fracture toughness of the concrete. The polypropylene-basalt fiber will produce positive and negative effects when mixed, and the mass ratio of 2:1 was optimal. Finally, the fitting analysis revealed that the fracture process of polypropylene-basalt fiber-reinforced concrete (PBFRC) can be objectively described by the bilinear softening constitutive curve improved by Xu and Reinhardt.