• BMB Reports
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• v.42 no.11
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• pp.764-768
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• 2009

The tandem ubiquitin-interacting motif (UIM) domain located at the N-terminus of Receptor Associated Protein 80 (RAP80) plays a crucial role in ionizing radiation (IR)-induced DNA damage response. RAP80 translocates to sites of IR-induced DNA damage through interaction of its UIM domain with ubiquitinated H2A and Lys63-linked polyubiquitin chains. The exact mechanism, however, through which RAP80 associates with Lys63-linked polyubiquitin chains is not clear. Here, we show by in vitro GST-pull down assays that modifying the linker region between the tandem ubiquitin binding domains of RAP80 changes the binding affinity for Lys63-linked polyubiquitin chains and affects translocation to sites of DNA breaks. Based on these findings, we suggest that the length of the linker region between the tandem ubiquitin binding domains of RAP80 may be a key factor in the binding of RAP80 with Lys63-linked polyubiquitin chains as well as in the translocation of RAP80 to DNA break sites.

• Journal of Environmental Health Sciences
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• v.35 no.5
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• pp.343-354
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• 2009

Since Barker found associations between low birth weight and several chronic diseases later in life, the hypothesis of fetal origins of adult disease (aka, Barker Hypothesis) and epigenetics have been emerging as a new paradigm for geneenvironment interaction of chronic disease. Epigenetics is the study of heritable changes in gene silencing that occur without any change in DNA sequence. Gene expression can be regulated by several epigenetic mechanisms, including DNA methylation and histone modifications, which may be associated with chronic conditions, such as cancers, cardiovascular disease, and type-2 diabetes. One carbon metabolism which involves the transfer of a methyl group catalyzed by DNA methyltransferase is an important mechanism by which DNA methylation occurs in promoter regions and/or repetitive elements of the genome. Environmental factors may induce epigenetic modification through production of reactive oxygen species, alteration of methyltransferase activity, and/or interference with methyl donors. In this review, we introduce recent studies of epigenetic modification and environmental factors, such as heavy metals, environmental hormones, air pollution, diet and psychosocial stress. We also discuss epigenetic perspectives of early life environmental exposure and late life disease occurrence.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.299-302
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• 2013

Methylenetetrahydrofolate reductase (MTHFR) has been reported to be associated with DNA methylation, an epigenetic feature frequently found in gastric cancer. We conducted a case-control study to explore the association of MTHFR C677T polymorphisms with gastric cancer risk and its relation with the DNA methylation of COX-2, MGMT, and hMLH1 genes. Genotyping of P16, MGMT and HMLH1 was determined by methylation-specific PCR after sodium bisulfate modification of DNA, and genotyping of MTHFR C677T was conducted by TaqMan assays using the ABI Prism 7911HT Sequence Detection System. Folate intake was calculated with the aid of a questionnaire. Compared with the MTHFR 677CC genotype, the TT genotype was significantly associated with 2.08 fold risk of gastric cancer when adjusting for potential risk factors. Individuals who had an intake of folate above $310{\mu}g$/day showed protective effects against gastric cancer risk. The effect of MTHFR C677T polymorphisms on the risk of gastric cancer was modified by folate intake and methylation status of MGMT (P for interaction <0.05).

• KIPS Transactions on Computer and Communication Systems
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• v.9 no.11
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• pp.247-249
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• 2020

In the era of the 4th industrial revolution, the demand for convergence between ICT technologies is increasing in various fields. Accordingly, a new term that combines data, network, and artificial intelligence technology, DNA (Data, Network, AI) is in use. and has recently become a hot topic. DNA has various potential technology to be able to develop intelligent application in the real world. Therefore, this paper introduces the reviewed papers on the service image placement mechanism based on the logical fog network, the mobility support scheme based on machine learning for Industrial wireless sensor network, the prediction of the following BCI performance by means of spectral EEG characteristics, the warning classification method based on artificial neural network using topics of source code and natural language processing model for data visualization interaction with chatbot, related on DNA technology.

• Bulletin of the Korean Chemical Society
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• v.34 no.12
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• pp.3695-3702
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• 2013

A nickel(II) complex $[Ni(H_2biim)_2(H_2O)_2](ClO_4)_2{\cdot}H_2O$ (1) of biimidazole ligand has been synthesized and characterized (Where $H_2biim$ = 2,2'-biimidazole). The single crystal X-ray diffraction of the complex shows a dimeric structure with six coordinated psudo-octahedral geometry. The cyclic voltammograms of complex exhibited one quasireversible reduction wave ($E_{pc}=-0.61V$) and an irreversible oxidation wave ($E_{pa}=1.28V$) in DMF solution. The interaction of the complex with Calf-Thymus DNA (CT-DNA) has been investigated by absorption and fluorescence spectroscopy. The complex is an avid DNA binder with a binding constant value of $1.03{\times}10^5M^{-1}$. The results suggest that the nickel(II) complex bind to CT-DNA via intercalative mode and can quench the fluorescence intensity of EB bind to CT-DNA with $K_{app}$ value of $3.2{\times}10^5M^{-1}$. The complex also shown efficient oxidative cleavage of supercoiled pBR322 DNA in the presence of hydrogen peroxide as oxidizing agent. The DNA cleavage by complex in presence of quenchers; viz. DMSO, KI, $NaN_3$ and EDTA reveals that hydroxyl radical or singlet oxygen mechanism is involved. The complex showed invitro antimicrobial activity against four bacteria and two fungi. The antimicrobial activity was nearer to that of standard drugs and greater than that of the free ligand.

• Molecules and Cells
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• v.26 no.1
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• pp.5-11
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• 2008

Stalled DNA replication forks activate specific DNA repair mechanism called post-replication repair (PRR) pathways that simply bypass DNA damage. The bypassing of DNA damage by PRR prevents prolonged stalling of DNA replication that could result in double strand breaks (DSBs). Proliferating cell nuclear antigen (PCNA) functions to initiate and choose different bypassing pathways of PRR. In yeast, DNA replication forks stalled by DNA damage induces monoubiquitination of PCNA at K164, which is catalyzed by Rad6/Rad18 complex. PCNA monoubiquitination triggers the replacement of replicative polymerase with special translesion synthesis (TLS) polymerases that are able to replicate past DNA lesions. The PCNA interaction motif and/or the ubiquitin binding motif in most TLS polymerases seem to be important for the regulation of TLS. The TLS pathway is usually error-prone because TLS polymerases have low fidelity and no proofreading activity. PCNA can also be further polyubiquitinated by Ubc13/ Mms2/Rad5 complex, which adds an ubiquitin chain onto monoubiquitinated K164 of PCNA. PCNA polyubiquitination directs a different PRR pathway known as error-free damage avoidance, which uses the newly synthesized sister chromatid as a template to bypass DNA damage presumably through template switching mechanism. Mammalian homologues of all of the yeast PRR proteins have been identified, thus PRR is well conserved throughout evolution. Mutations of some PRR genes are associated with a higher risk for cancers in mice and human patients, strongly supporting the importance of PRR as a tumor suppressor pathway.

• Archives of Pharmacal Research
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• v.25 no.1
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• pp.11-24
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• 2002

The antitumor antibiotic (+)-CC-1065 can alkylate N3 of guanine in certain sequences. A previous high-field $^1H$ NMR study on the$(+)-CC-1065d[GCGCAATTG*CGC]_2$ adduct ($^*$ indicates the drug alkylation site) showed that drag modification on N3 of guanine results in protonation of the cross-strand cytosine [Park, H-J.; Hurley, L. H. J. Am. Chem. Soc.1997, 119,629]. In this contribution we describe a further analysis of the NMR data sets together with restrained molecular dynamics. This study provides not only a solution structure of the (+)-CC-1065(N3- guanine) DNA duplex adduct but also new insight into the molecular basis for the sequence- specific interaction between (+)-CC-1065 and N3-guanine in the DNA duplex. On the basis of NOESY data, we propose that the narrow minor groove at the 7T8T step and conformational kinks at the junctions of 16C17A and 18A19T are both related to DNA bending in the drugDNA adduct. Analysis of the one-dimensional $^1H$ NMR (in $H_2O$) data and rMD trajectories strongly suggests that hydrogen bonding linkages between the 8-OH group of the (+)-CC-1065 A-sub-unit and the 9G10C phosphate via a water molecule are present. All the phenomena observed here in the (+)-CC-1065(N3-guanine) adduct at 5'$-AATTG^*$are reminiscent of those obtained from the studies on the (+)-CC-1065(N3-adenine) adduct at $5'-AGTTA^*$, suggesting that (+)-CC-1065 takes advantage of the conformational flexibility of the 5'-TPu step to entrap the bent structure required for the covalent bonding reaction. This study reveals a common molecular basis for (+)-CC-1065 alkylation at both $5'-TTG^*$ and $5'-TTA^*$, which involves a trapping out of sequence-dependent DNA conformational flexibility as well as sequence-dependent general acid and general base catalysis by duplex DNA.

• Molecules and Cells
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• v.44 no.2
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• pp.79-87
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• 2021

Chromatin dynamics is essential for maintaining genomic integrity and regulating gene expression. Conserved bromodomain-containing AAA+ ATPases play important roles in nucleosome organization as histone chaperones. Recently, the high-resolution cryo-electron microscopy structures of Schizosaccharomyces pombe Abo1 revealed that it forms a hexameric ring and undergoes a conformational change upon ATP hydrolysis. In addition, single-molecule imaging demonstrated that Abo1 loads H3-H4 histones onto DNA in an ATP hydrolysis-dependent manner. However, the molecular mechanism by which Abo1 loads histones remains unknown. Here, we investigated the details concerning Abo1-mediated histone loading onto DNA and the Abo1-DNA interaction using single-molecule imaging techniques and biochemical assays. We show that Abo1 does not load H2A-H2B histones. Interestingly, Abo1 deposits multiple copies of H3-H4 histones as the DNA length increases and requires at least 80 bp DNA. Unexpectedly, Abo1 weakly binds DNA regardless of ATP, and neither histone nor DNA stimulates the ATP hydrolysis activity of Abo1. Based on our results, we propose an allosteric communication model in which the ATP hydrolysis of Abo1 changes the configuration of histones to facilitate their deposition onto DNA.

• Interaction and multiscale mechanics
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• v.6 no.4
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• pp.395-409
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• 2013

Molecular dynamics (MD) systems are highly nonlinear and nonlocal, and the conventional model order reduction methods are ineffective for MD systems. The RBF-POD method (Lee and Chen, 2013) employed a radial basis function (RBF) approximated potential energies and inter-atomic forces of MD systems under the framework of the proper orthogonal decomposition (POD) method for the reduced-order modeling of MD systems. In this work, we focus on the numerical procedures of the RBF-POD method and demonstrate how to apply this approach to the modeling of ds-DNA molecules under stretching and bending conditions.

• Journal of Radiation Protection and Research
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• v.45 no.1
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• pp.11-15
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• 2020

Background: There have been various studies to investigate the mechanisms of DNA damage from low-energy electrons. To understand the mechanism of these strand breaks, it is necessary to investigate the dissociation mechanism of the DNA constituents, that is, bases, sugars, and phosphates. Materials and Methods: We studied the dissociation of thymine base upon interaction with low-energy electrons. For this experiment, thymine powder was pressed onto the indium base and irradiated by 5 eV electrons. Results and Discussion: Non-irradiated and irradiated thymine samples were compared and analyzed using the X-ray photoelectron spectroscopic technique to analyze the dissociation patterns of the molecular bonds after low-energy electron irradiation of thymine. Conclusion: With 5 eV electron irradiation, C-C and N-C = O bonds are the primary dissociations that occur in thymine molecules.