• Bulletin of the Korean Chemical Society
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• 제34권11호
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• pp.3471-3473
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• 2013

• 대한화학회지
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• 제65권2호
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• pp.121-124
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• 2021

RNA molecules which bind to the G-rich sequence in the 5'-UTR RNA which plays an important role in expression of N-ras, were selected. The secondary structures of five selected RNA aptamers including primer sequence were found by the CLC RNA workbench ver. 4.2 program (www.clcbio.com) and investigated with RNA structural probes such as RNase T1 which has specificity for a G in single-stranded region, RNase V1 specific for double strand and nuclease S1 specific for single strand. The generalized secondary structure model was proposed and characterized. It was composed of a central long double strand region flanked by single strand region at both end sides. The double strand region had an internal single-strand region and bulges. The single strand loop in the right side was composed of four or five nucleotides.

• BMB Reports
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• 제29권2호
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• pp.133-136
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• 1996

The affinity cleavage reagent Methidiumpropyl-EDTA-Iron(II) is applied to the structural analysis of 5S rRNA. Analysis of cleavage sites induced by MPE-Fe(II) on 5S rRNA shows that MPE intercalates easily between the unstable base pairs or into the bulges, thereby it strongly cuts the nucleosides nearby. The stable helical stems A, B, D and E as well as loop d are weakly cut. Most of the single-stranded loops are not cleaved. Based on the cleavage pattern of the 5S rRNA by MPE-Fe(II) and RNase V1, we suggest that MPE-Fe(II) may be used as a potential chemical probe in searching for the unstable helical regions of RNA, and for the sequences that appear to be involved in folding and distorting 5S rRNA.

• Bulletin of the Korean Chemical Society
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• 제27권2호
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• pp.224-230
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• 2006

Escherichia coli transcription termination factor Rho catalyzes the unwinding of RNA/DNA duplex in reactions that are coupled to ATP binding and hydrolysis. We report here the kinetic mechanism of presteady state ATP binding and hydrolysis by the Rho-RNA complex. Presteady state chemical quenched-flow technique under multiple turnover condition was used to probe the kinetics of ATP binding and hydrolysis by the Rho-RNA complex. The quenched-flow presteady state kinetics of ATP hydrolysis studies show that three ATPs are bound to the Rho-RNA complex with a rate of $4.4\;{\times}\;10^5M^{-1}s^{-1}$, which are subsequently hydrolyzed at a rate of $88s^{-1}$ and released during the initiation process. Global fit of the presteady state ATP hydrolysis kinetic data suggests that a rapid-equilibrium binding of ATP to Rho-RNA complex occurs prior to the first turnover and the chemistry step is not reversible. The initial burst of three ATPs hydrolysis was proposed to be involved in the initialization step that accompanies proper complex formation of Rho-RNA. Based on these results a kinetic model for initiation process for Rho-RNA complex was proposed relating the mechanism of ATP binding and hydrolysis by Rho to the structural transitions of Rho-RNA complex to reach the steady state phase, which is implicated during translocation along the RNA.

• 한국자기공명학회논문지
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• 제21권3호
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• pp.109-113
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• 2017

The hepatitis C virus (HCV) internal ribosome entry site (IRES) is an RNA structure located in the 5'-UTR of the HCV RNA genome. The HCV IRES consists of four domains I, II, III, and IV, where domains II - IV are recognized by 40S ribosomal subunit and the domain III is bound to eukaryotic initiation factor 3 (eIF3) for translation initiation. Here, we have characterized the tertiary interaction between an L-/K- rich peptide and the HCV IRES domain IV. To probe the peptide binding interface in RNA, we synthesized $^{13}C$- and $^{15}N$-double labeled RNA and the binding site was identified by using the chemical shift perturbation (CSP) NMR methods. Our results showed that the peptide binds to the upper stem of the IRES domain IV, indicating that the tertiary interaction between the IRES domain IV and the peptide would disrupt the initiation of translation of HCV mRNA by blocking the start codon exposure. This study will provide an insight into the new peptide-based anti-viral drug design targeting HCV IRES RNA.

• 한국자기공명학회논문지
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• 제23권3호
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• pp.61-66
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• 2019

RNAs exhibit distinct structural and dynamic features required for proper function. The hydrogen-bonded imino protons of RNAs are a probe of the conformational transition and dynamic feature. MicroRNAs originate from primary transcripts containing hairpin structures. The levels of mature miR156 influence the flowering time of plants. To understand the molecular mechanism of biological function of $miR156:miR156^*$ duplex, we performed hydrogen exchange study on the model RNAs mimicking two phenotypes of $miR156:miR156^*$, $miR156:miR156^*$ (m-miR156a) and $miR156:miR156^*$ (m-miR156g) duplexes. This study found that the internal bulge of m-miR156a destabilized the neighboring base-pairs, whereas the bulge structure of m-miR156g did not affect the thermal stabilities of the neighboring base-pairs.

• Tuberculosis and Respiratory Diseases
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• 제46권3호
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• pp.338-349
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• 1999

연구배경: 호중구는 급성염증이 있을 때 존재하는 제일 많은 세포로서 폐의 염증이 있을 때에도 말초혈액에서부터 이동됨과 동시에 활성화된 호중구에서 분비하는 단백분해효소, 산화물 및 여러 가지 cytokine등에 의해 염증이 더욱 심해지고 호중구의 이동이 더욱 증가되는 것으로 알려져 있다. 호중구의 이동을 증가시키는 물질로 현재까지 LTB4, PAF, C5a, fMLP, TNF, IL-8 등이 밝혀져 있으며 특히 IL-8은 chemokine이라고 부르는 조그만 cytokine에 속하며 GRO/MGSA는 IL-8과 같은 C-X -C subgroup에 속하는 단백질로서 이 유전인자는 PF-4, IL-8등과 같은 chromosome 4q12-q21에 위치한다. IL-8이 호중구의 이동 및 활성화에 강력한 영향을 미치는 것은 잘 증명되어 있지만 같은 C-X-C subgroup에 속하며 최근에 발견된 GRO/MGSA의 기능 및 발현과정 등에 대해서는 잘 밝혀져 있지 않다. 내피세포는 TNF$\alpha$나 IL-1$\beta$ 등의 자극을 받으면 호중구의 유착을 돕는 접착분자 및 IL-8등의 생성이 증가되는등 염증반응에 능동적인 역할을 한다고 밝혀지고 있다. 저자들은 인체의 제대정맥에서 내피세포를 분리하여 TNF나 IL-1로 자극을 가하였을때 호중구의 이동을 증가시키는 IL-8이나 GRO/MGSA mRNA의 발현과 분비가 일어나는지 또한 호중구 화학주성에 미치는 각각의 기여도를 비교, 관찰하고자 하였다. 방 법: 제대정맥에서 내피세포를 분리, 배양하고 여기에 TNF-$\alpha$ IL-1$\beta$ 등을 0.2, 2, 20 ${\mu}g/ml$ 농도로 자극을 가하고 1, 4, 8, 24 시간이 경과하여 IL-8 및 GRO/MGSA mRNA의 발현을 RT-PCR로 관찰하고, 배양상층액내 IL-8 및 GRO/MGSA의 양을 ELISA로 측정하였으며 상층액의 호종구 화학주성 활성화도를 Neuro Probe 48 well chemotactic chamber를 이용하여 측정하였다. 결 과: 제대정맥 내피세포에 TNF-$\alpha$ 및 IL-1$\beta$로 자극하였을 때 내피세포에서의 IL-8 mRNA는 1 시간후부터, GRO/MGSA mRNA의 발현은 4 시간후부터 각각 관찰되었으며 TNF-$\alpha$ 및 IL-1$\beta$의 자극농도에 따른 뚜렸한 차이는 없었다. TNF-$\alpha$ 및 IL-1$\beta$로 자극한 내피세의 배양상층액에서 측정한 IL-8도 1시간후부터 현저히 증가되었고 GRO/MGSA의 양은 4시간후부터 현저히 증가되어 있었다. TNF-$\alpha$ 및 IL-1$\beta$로 자극한 내피세포의 배양상층액의 호중구 화학주성활성화도는 각각으로 1시간 자극 후에 현저히 증가되어 있었다. 결 론: 이상의 결과에서 제대정맥 내피세포를 TNF-$\alpha$ 및 IL-1$\beta$로 자극시 IL-8 및 GRO/MGSA mRNA 발현 및 단백이 분비되며, 특히 IL-8은 1시간 후에 GRO/MGSA는 4 시간후에 각각 증가되고 호중구화학주성활성화는 1시간후부터 최고치로 증가됨을 관찰하여, GRO/MGSA보다는 IL-8 이 호종구유주인자로서의 중요한 역할을 할것으로 생각된다.