• BMB Reports
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• v.53 no.9
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• pp.453-457
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• 2020

The right-handed double-helical structure of DNA (B-DNA), which follows the Watson-Crick model, is the canonical form of DNA existing in normal physiological settings. Even though an alternative left-handed structure of DNA (Z-DNA) was discovered in the late 1970s, Z-form nucleic acid has not received much attention from biologists, because it is extremely unstable under physiological conditions, has an ill-defined mechanism of its formation, and has obscure biological functions. The debate about the physiological relevance of Z-DNA was settled only after a class of proteins was found to potentially recognize the Z-form architecture of DNA. Interestingly, these Z-DNA binding proteins can bind not only the left-handed form of DNA but also the equivalent structure of RNA (Z-RNA). The Z-DNA/RNA binding proteins present from viruses to humans function as important regulators of biological processes. In particular, the proteins ADAR1 and ZBP1 are currently being extensively re-evaluated in the field to understand potential roles of the noncanonical Z-conformation of nucleic acids in host immune responses and human disease. Despite a growing body of evidence supporting the biological importance of Z-DNA/RNA, there remain many unanswered principal questions, such as when Z-form nucleic acids arise and how they signal to downstream pathways. Understanding Z-DNA/RNA and the sensors in different pathophysiological conditions will widen our view on the regulation of immune responses and open a new door of opportunity to develop novel types of immunomodulatory therapeutic possibilities.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.367-373
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• 2013

The ruthenium(II) ferrocenyl heterocyclic thiosemicarbazone complexes of the type $[RuCl(CO)(EPh_3)]_2L$ (where E = P/As; L = binucleating monobasic tridendate thiosemicarbazone ligand) have been investigated. Strutural features were determined by analytical and spectral techniques. Binding of these complexes with CT-DNA by absorption spectral study indicates that the ruthenium(II) complexes form adducts with DNA and has intrinsic binding constant in the range of $3.3{\times}10^4-1.2{\times}10^5M^{-1}$. The complexes exhibit a remarkable DNA cleavage activity with CT-DNA in the presence of hydrogen oxide and the cleavage activity depends on dosage.

• Korean Journal of Microbiology
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• v.32 no.2
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• pp.102-108
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• 1994

Autonomously replicating sequence Binding Factor 1(ABF1) is a DNA-binding protein that specifically recognizes the $RTCRYN_5ACG$ at many sites in the yeast genome including the promoter element, mating-type silencer and ARS. To express the intact full-length ABF1 gene in E. coli, the ABF1 gene has been cloned into pMAL-c2 and His-61, Leu-353 and Leu-360 were substituted with other amino acid. ABF1 fusion proteins of wild type ABF1 and H61A, L353R and L360R nutants were purified by amylose resin affinity chromatography. Fusion protein of MBP and ABF1 was digested by Factor Xa and Characterized by gel retardation assay and complementation test. As aresult, we suggested that other DNA binding motif except atypical inc-finger motif is in the middle region of ABF1.

• Molecules and Cells
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• v.27 no.1
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• pp.47-54
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• 2009

A cDNA clone for a transcript preferentially expressed during an early phase of flooding was isolated from Nicotiana tabacum. Nucleotide sequencing of the cDNA clone identified an open reading frame that has high homology to the previously reported glycine-rich RNA-binding proteins. The open reading frame consists of 157 amino acids with an N-terminal RNA-recognition motif and a C-terminal glycine-rich domain, and thus the cDNA clone was designated as Nicotiana tabaccum glycine-rich RNA-binding protein-1 (NtGRP1). Expression of NtGRP1 was upregulated under flooding stress and also increased, but at much lower levels, under conditions of cold, drought, heat, high salt content, and abscisic acid treatment. RNA homopolymer-binding assay showed that NtGRP1 binds to all the RNA homopolymers tested with a higher affinity to poly r(G) and poly r(A) than to poly r(U) and poly r(C). Nucleic acid-binding assays showed that NtGRP1 binds to ssDNA, dsDNA, and mRNA. NtGRP1 suppressed expression of the fire luciferase gene in vitro, and the suppression of luciferase gene expression could be rescued by addition of oligonucleotides. Collectively, the data suggest NtGRP1 as a negative modulator of gene expression by binding to DNA or RNA in bulk that could be advantageous for plants in a stress condition like flooding.

• Bulletin of the Korean Chemical Society
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• v.32 no.3
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• pp.947-955
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• 2011

The complexes [Pd(bpy)(Hex-dtc)]$NO_3$ and [Pt(bpy)(Hex-dtc)]$NO_3$ (bpy is 2,2'-bipyridine and Hex-dtc is hexyldithiocarbamato ligands) were synthesized and characterized by elemental analysis and spectroscopic studies. The cytotoxicity assay of the complexes has been performed on chronic myelogenous leukemia cell line, K562, at micromolar concentration. Both complexes showed cytotoxic activity far better than that of cisplatin under the same experimental conditions. The binding parameters of the complexes with calf thymus DNA (CT-DNA) was investigated using UV-visible and fluorescence techniques. They show the ability of cooperatively intercalating in CT-DNA. Gel filtration studies demonstrated that platinum complex could cleave the DNA. In the interaction studies between the Pd(II) and Pt(II) complexes with CT-DNA, several binding and thermodynamic parameters have been determined, which may provide deeper insights into the mechanism of action of these types of complexes with nucleic acids.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1260-1262
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• 2013

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1300-1302
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• 2013

• Bulletin of the Korean Chemical Society
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• v.31 no.5
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• pp.1314-1318
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• 2010

The $[Ru(tpy)_2]Cl_2$ (tpy:2,2':6',2"-terpyridine) complex was synthesized and its structure was confirmed by $^1H$-NMR and elemental analysis. Its binding mode toward DNA was compared with the well-known $[Ru(bpy)_3]Cl_2$ (bpy:2,2-bipyridyl), using isotropic absorption, linear dichroism(LD) spectroscopy, and an energy minimization study. Compared to $[Ru(bpy)_3]^{2+}$, the $[Ru(tpy)_2]^{2+}$ complex exhibited very little change in its absorption pattern, especially in the MLCT band, upon binding to DNA. Furthermore, upon DNA binding, both Ru(II) complexes induced a decrease in the LD magnitude in the DNA absorption region. The $[Ru(tpy)_2]^{2+}$ complex produced a strong positive LD signal in the ligand absorption region, which is in contrast with the $[Ru(bpy)_3]^{2+}$ complex. Observed spectral properties led to the conclusion that the interaction between the ligands and DNA bases is negligible for the $[Ru(tpy)_2]^{2+}$ complex, although it formed an adduct with DNA. This conclusion implies that both complexes bind to the surface of DNA, most likely to negatively charged phosphate groups via a simple electrostatic interaction, thereby orienting to exhibit the LD signal. The energy minimization calculation also supported this conclusion.

• Journal of Plant Biology
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• v.39 no.4
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• pp.279-286
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• 1996

To know the changes of rbcL mRNA level by illumination, Northern hybridization analysis was performed with maize (Zea mays L.cv. Golden X Bantam). The average level of rbcL. mRNA in the light-grown shoots was 3.1 times higher than that of the dark-grown shoots after 6 to 10 growth days. The maximum difference of rbcL mRNA level between the dark-grown and the light-grown shoots was 5.1 folds. These results indicate that accumulation of rbcL mRNAin maize shoots is induced by light. Since the transcriptional DNA binding proteins and their cognate promoter elements, we carried out gel-retardation assays to elucidate the specific binding proteins on the rbcL promoter. It was found that plastid proteins of light-grown shoots bound to the R2 DNA fragment (-33 to -229) and R3 DNA fragment (-230 to -418 from ATG) of the rbcL promoter. From the results of competitive binding assays and heat or protease treatments, it was demonstrated that the bindings were sequence-specific DNA-protein interactions. Therefore, it could be concluded that the rbcL promoter region has at least two specific recognition sites for plastid proteins.

• Journal of Life Science
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• v.16 no.6
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• pp.1052-1059
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• 2006

The heat shock response is induced by environmental stress, pathophysiological state and non-stress conditions and wide spread from bacteria to human. Although translations of most proteins are stopped under a heat shock response, heat shock proteins (HSPs) are produced to protect cell from stress. When heat shock response is induced, conformation of HSF1 was changed from monomer to trimer and HSF1 specifically binds to DNA, which was called a heat shock element(HSE) within the promoter of the heat shock genes. Human HSF1(hHSFl) contains five cysteine(Cys) residues. A thiol group(R-SH) of Cys is a strong nucleophile, the most readily oxidized and nitrosylated in amino acid chain. This consideration suggests that Cys residues may regulate the change of conformation and the activity of hHSF1 through a redox-dependent thiol/disulfide exchange reaction. We want to construct role of five Cys residues of hHSF by redox reagents. According to two studies, Cys residues are related to trimer formation of hHSF1. In this study, we want to demonstrate the correlation between structural change and DNA-binding activity of HSF1 through forming disulfide bond and trimerization. In this results, we could deduce that DNA binding activity of DNA binding domain wasn't affected by redox for always expose outside to easily bind to DNA. DNA binding activity of wild-type HSF's DNA binding domain was affected by conformational change, as conformational structure change (trimerization) caused DNA binding domain.