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Young-Rok Kim

Publications and source records attributed to Young-Rok Kim.

6 recordsLinked to original sources
PubMed2007

Nanopore sensor for fast label-free detection of short double-stranded DNAs.

Functionalizing surface enhanced the molecular sensing ability of a fabricated nanopore by increasing the translocation duration time for a short double-stranded DNA. The surface of nanopore was derivatized with gamma-aminopropyltriethoxysilane and the positively charged surface attracted DNA molecules when they were in the vicinity of nanopore. The translocation duration time of DNA increased due to the strong electrostatic interaction and it enabled us to detect a short double-stranded DNA (<1 kbp) that is under the size limit of a conventional solid state nanopore sensor. Both 539 and 910 bp double-stranded DNAs were analyzed with the surface functionalized nanopore and their translocation kinetics are presented in this work. The new feature of the surface modified nanopore that can detect short double-stranded DNA molecules could readily be applied for a rapid label-free diagnostic analysis in a Lab-On-a-Chip type DNA sensor.

Biosensing Techniques↗
PubMed2006

Real-time analysis of enzymatic surface-initiated polymerization using surface plasmon resonance (SPR).

The kinetics of enzymatic surface-initiated polymerization of PHB on gold surface has been examined by SPR and the resultant polymer layers characterized by AFM and FT-IR spectrometry. The immobilized enzyme catalyzed surface-initiated polymerization of 3HB-CoA, resulting in the formation of a polymer brush on the surface. The rate of polymer growth from the surface was monitored by SPR in real-time. Polymer growth as measured by the increase in the resonance angle showed no apparent lag phase during the polymerization reaction. SPR analysis also revealed that the thickness of the polymer film could be controlled by varying the initial enzyme density on the surface. The average thicknesses of the PHB film after polymerization reaction were 95, 45 and 15 nm for the surfaces that were treated with 0.5, 0.3 and 0.1*10(-6) M of enzyme, respectively. The binding of PHA synthase at different concentration to the mixed SAMs and subsequent polymerization.

Acyltransferases↗
PubMed2006

Nanoscale volcanoes: accretion of matter at ion-sculpted nanopores.

We demonstrate the formation of nanoscale volcano-like structures induced by ion-beam irradiation of nanoscale pores in freestanding silicon nitride membranes. Accreted matter is delivered to the volcanoes from micrometer distances along the surface. Volcano formation accompanies nanopore shrinking and depends on geometrical factors and the presence of a conducting layer on the membrane's back surface. We argue that surface electric fields play an important role in accounting for the experimental observations.

Journal Article↗
PubMed2004

Engineering of chimeric class II polyhydroxyalkanoate synthases.

PHA synthase is a key enzyme involved in the biosynthesis of polyhydroxyalkanoates (PHAs). Using a combinatorial genetic strategy to create unique chimeric class II PHA synthases, we have obtained a number of novel chimeras which display improved catalytic properties. To engineer the chimeric PHA synthases, we constructed a synthetic phaC gene from Pseudomonas oleovorans (phaC1Po) that was devoid of an internal 540-bp fragment. Randomly amplified PCR products (created with primers based on conserved phaC sequences flanking the deleted internal fragment) were generated using genomic DNA isolated from soil and were substituted for the 540-bp internal region. The chimeric genes were expressed in a PHA-negative strain of Ralstonia eutropha, PHB(-)4 (DSM 541). Out of 1,478 recombinant clones screened for PHA production, we obtained five different chimeric phaC1Po genes that produced more PHA than the native phaC1Po. Chimeras S1-71, S4-8, S5-58, S3-69, and S3-44 exhibited 1.3-, 1.4-, 2.0-, 2.1-, and 3.0-fold-increased levels of in vivo activity, respectively. All of the mutants mediated the synthesis of PHAs with a slightly increased molar fraction of 3-hydroxyoctanoate; however, the weight-average molecular weights (Mw) of the PHAs in all cases remained almost the same. Based upon DNA sequence analyses, the various phaC fragments appear to have originated from Pseudomonas fluorescens and Pseudomonas aureofaciens. The amino acid sequence analyses showed that the chimeric proteins had 17 to 20 amino acid differences from the wild-type phaC1Po, and these differences were clustered in the same positions in the five chimeric clones. A threading model of PhaC1Po, developed based on homology of the enzyme to the Burkholderia glumae lipase, suggested that the amino acid substitutions found in the active chimeras were located mostly on the protein model surface. Thus, our combinatorial genetic engineering strategy proved to be broadly useful for improving the catalytic activities of PHA synthase enzymes.

Acyltransferases↗
PubMedDate not supplied

Enzymatic surface-initiated polymerization: a novel approach for the in situ solid-phase synthesis of biocompatible polymer poly(3-hydroxybutyrate).

A novel system for surface-initiated enzymatic polymerization of a film of polyhydroxyalkanoate (PHA) on solid surfaces has been developed and characterized. PHAs are aliphatic polyesters produced by a variety of microorganisms as a reserve of carbon and energy, and their properties range from elastomers to thermoplastics, depending on their monomeric composition. The PHA synthase from Ralstonia eutropha H16 was expressed as a poly-histidine fusion in Escherichia coli and immobilized onto several solid substrates through a transition-metal complex, Ni(2+)-nitrilotriacetic acid. The immobilized PHA synthase catalyzed the surface-initiated polymerization of 3-(R)-hydroxybutyryl-CoA, forming a polymer film with a uniform thickness on the surface. In this work, we describe the patterned immobilization of the intact enzyme on silicon and subsequent enzymatic polymerization. The immobilized enzyme had a lower specific activity and did not exhibit a lag phase as compared to the soluble enzyme.

Acyltransferases↗