• Bulletin of the Korean Chemical Society
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• v.34 no.3
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• pp.749-752
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• 2013

Trehalose-tethered monomeric and dimeric berberines were synthesized in 50% and 30% from the reaction of berberrubine with 6-tosyl-${\alpha}$,${\alpha}^{\prime}$-trehalose and 6,6'-ditosyl-${\alpha}$,${\alpha}^{\prime}$-trehalose, respectively, and fully characterized by MS (HR and ESI) and NMR ($^1H$, $^{13}C$, COSY and HSQC). Spectrophotometric and spectrofluorimetric titrations indicated that compared with berberine, trehalose-tethered monomeric berberine had comparable DNA-binding affinity toward calf-thymus DNA, whereas trehalose-spaced dimeric berberine exhibited higher DNA-binding affinity. The potential application of these conjugates is also briefly discussed.

• Korea-Australia Rheology Journal
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• v.19 no.3
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• pp.141-146
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• 2007

We examine the wall contact of a $3\;{\mu}m$ tethered DNA chain's free end under shear with a focus on developing schemes for double-tethering in the application of making scaffolds for molecular wires. At this scale our results are found to be highly dependent on small length scale rigidity. Chain-end-wall contact frequency, mean fractional extension deficit upon contact, and standard deviation in extension upon contact are examined for scaling with dimensionless flow strength, Wi. Predictions made using a one dimensional approximation to the Smoluchowski equation for a dumbbell and three dimensional dumbbell simulations produce extension deficit, standard deviation, and frequency scaling exponents of -1/3, -1/3, and 2/3, respectively whereas more fine-grained Kratky-Porod (KP) simulations produce scaling exponents of -0.48, -0.42, and 0.76. The contact frequency scaling of 2/3 is derived from the known results regarding cyclic dynamics Analytical scaling predictions are in agreement with those previously proposed for ${\lambda}-DNA$. [Ladoux and Doyle, 2000, Doyle et al., 2000]. Our results suggest that the differences between the dumbbell and the KP model are associated with the addition of chain discretization and the correct bending potential in the latter. These scaling results will aide future exploration in double tethering of DNA to a surface.

• Asian Journal of Atmospheric Environment
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• v.5 no.3
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• pp.172-180
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• 2011

The transfer of microorganisms is important process for ecosystems. Microorganisms in dryland can transport itself to wetland through atmospheric diffusion, but only few papers reported about the atmospheric bioaerosol present over dryland. We carried out the direct sampling using a tethered balloon over Dunhuang City, China's northwestern dryland. Bioaerosols were collected using a tethered balloon with a bioaerosol collector at 820 m above the ground (1,960 m above the sea level) around noon on August 17, 2007. The bioaerosols were cultured after the collection at Dunhuang Meteorological observatory. Two strains of molds were isolated using the Nutrient agar medium. About 400-bp 18S rRNA partial sequences were amplified by PCR and determined afterwards. The results of a homology search by 18S rRNA sequences of isolates in DNA databases (GenBank, DDBJ, and EMBL) and an observation of the form revealed that two bioaerosols in the convective mixed layer over Dunhuang City were Cladosporium sp. and Aspergillus sp.

• Molecules and Cells
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• v.45 no.1
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• pp.33-40
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• 2022

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.92.1-92.1
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• 2013

Molecular electronics has been the subject of intese research for many years because of the fundamental interest in molecular charge transport and potential applications, such as (bio)nanosensors and molecular memory devices. Molecular electronics requires a method for making reliable eletrical contacts to singlemolecules. To date, several approaches have been reported: scanning-probe microscopy, mechanical break junctions, nano patterning, and direct deposition of electrode on a self-assembled monolayers. However, most methods are laborious and difficult for large-scale application and more importantly, cannot control the number of moleucles in the junction. Recently, DNA has been used as a template for metallic nanostructures (e.g., Ag, Pd, and Au nanowires) through DNA metallization process. Furthermore, oligodeoxynucleotides have been tethered to organic molecules by using conventional organic reactions. Collectively, these techniques should provide an efficient route toward reliable and reproducible molecular electronic devices with large-scale fabrication. Therefore, I will present a paradigm for the fabrication of moleuclar electronic devices by using micrometer-sized DNA-singe organic molecule and DNA triblock structures.

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.176.2-176.2
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• 2003

Transcription factors (TF) can bind tightly to specific DNA lesions formed by some anticancer agents. The formation these TF:(drug-modified DNA) complex may disrupt expression of genes critical for cell survival, and it was proved to be one of biochemical mechanisms of anticancer activity. Based on this model, we have designed programmable DNA Alkylating agents that can also attract TF, especially nuclear receptors. As a model compound, we designed drug molecules, RA-mustard and Am580-mustard, that enable to bind both retinoic acid receptor (RAR) and DNA by using molecular modeling techniques, and synthesized them by connecting chlorambucil and ligand for RAR with a linker unit. (omitted)

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3658-3662
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• 2010

A new bis-Ru(II) complex, in which two [Ru(1,10-phenanthroline)$_2$dipyrido[3,2-a:2',3'-c]phenazine]$^{2+}$ were tethered by a 1,3-bis(4-pyridyl)propane linker, was synthesized and its binding mode and stoichiometry to DNA was investigated by optical spectroscopy including linear dichroism (LD) and fluorescence intensity measurement. The magnitude of the negatively reduced LD signal of the bis-Ru(II) complex in the dipyrido[3,2-a:2',3'-c]phenazine (DPPZ) ligand absorption region appeared to be similar compared to that in the DNA absorption region, which is considered to be a diagnostic for DPPZ ligand intercalation. The binding stoichiometry measured from its LD magnitude and enhanced fluorescence intensity corresponds to one ligand per three DNA bases, effectively violating the nearest neighbouring site exclusion model for classical DNA intercalation. This observation is in contrast with monomer analogue [Ru(1,10-phenanthroline)$_2$dipyrido[3,2-a:2',3'-c]phenazine]$^{2+}$, which is saturated at the DPPZ ligand to DNA base ratio of 0.25, or one DPPZ ligand per four nucleobases.

• Applied Science and Convergence Technology
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• v.24 no.5
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• pp.190-195
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• 2015

Here, we demonstrated a $Pb^{2+}$ detecting aptasensor using $Pb^{2+}$-sensitive DNAzyme-conjugated gold nanorods (GNRs). Fluorescent DNA substrates that were initially quenched by GNRs, are released in response to $Pb^{2+}$ ions to give a substantial fluorescence signal. The GNR-tethered DNAzyme is reusable at least three times with a LOD of 50 nM.

• BMB Reports
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• v.43 no.11
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• pp.732-737
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• 2010

RNA interference is a post-transcriptional silencing mechanism triggered by the bioavailability and/or exogenous introduction of double-stranded RNA (dsRNA) into cells. Here we describe a novel method for the synthesis of siRNA in a single vessel. The method employs in vitro transcription and a single-stranded DNA (ssDNA) template and design, which incorporates upon self-annealing, two promoters, two templates, and three loop regions. Using this method of synthesis we generated efficacious siRNAs designed to silence both exogenous and endogenous genes in mammalian cells. Due to its unique design the single-stranded template is easily amenable to adaptation for attachment to surface platforms for synthesis of siRNAs. A siRNA synthesis platform was generated using a 3' end-biotinylated ssDNA template tethered to a streptavidin coated surface that generates stable siRNAs under multiple cycles of production. Together these data demonstrate a unique and robust method for scalable siRNA synthesis with potential application in RNAi-based array systems.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1615-1620
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• 2010

Bis-[dipyrido[3,2-$\alpha$:2',3'-c]phenazine)$_2$(1,10-phenanthroline)$_2Ru_2$]$^{2+}$ complexes (bis-Ru(II) complexes) tethered by linkers of various lengths were synthesized and their binding properties to DNA investigated by normal absorption and linear dichroism spectra, and fluorescence techniques in this study. Upon binding to DNA, the bis-Ru(II) complex with the longest linker (1,3-bis-(4-pyridyl)-propane), exhibited a negative $LD^r$ signal whose intensity was as large as that in the DNA absorption region, followed by a complicate $LD^r$ signal in the metal-to-ligand charge transfer region. The luminescence intensity of this bis-Ru(II) complex was enhanced. The observed $LD^r$ and luminescence results resembled that of the [Ru(1,10-phenanthroline)$_2$ dipyrido[3,2-$\alpha$:2',3'-c]phenazine]$^{2+}$ complex, whose dipyrido[3,2-$\alpha$:2',3'-c]phenazine (dppz) ligand has been known to intercalate between DNA bases. Hence, it is conclusive that both dppz ligands of the bis-Ru(II) complex intercalate. The binding stoichiometry, however, was a single intercalated dppz per ~ 2.3 bases, which violates the "nearest binding site exclusion" model for intercalation. The length between the two Ru(II) complexes may be barely long enough to accommodate one DNA base between the two dppz ligands, but not for two DNA bases. When the linker was shorter (4,4'-bipyridine or 1,2-bis-(4-pyridyl)-ethane), the magnitude of the LD in the dppz absorption region, as well as the luminescence intensity of both bis-Ru(II) complexes, was half that of the bis-Ru(II) complex bearing a long linker. This observation can be elucidated by a model whereby one of the dppz ligands intercalates while the other is exposed to the aqueous environment.