Professional Education


  • Bachelor of Science, Seoul National University, Chemistry (2003)
  • Doctor of Philosophy, Stanford University, CHEM-PHD (2009)

Stanford Advisors


Journal Articles


  • Microfluidic Platforms for Single-Cell Analysis ANNUAL REVIEW OF BIOMEDICAL ENGINEERING, VOL 12 Zare, R. N., Kim, S. 2010; 12: 187-201

    Abstract

    Microfluidics, the study and control of the fluidic behavior in microstructures, has emerged as an important enabling tool for single-cell chemical analysis. The complex procedures for chemical cytometry experiments can be integrated into a single microfabricated device. The capability of handling a volume of liquid as small as picoliters can be utilized to manipulate cells, perform controlled cell lysis and chemical reactions, and efficiently minimize sample dilution after lysis. The separation modalities such as chromatography and electrophoresis within microchannels are incorporated to analyze various types of intracellular components quantitatively. The microfluidic approach offers a rapid, accurate, and cost-effective tool for single-cell biology. We present an overview of the recent developments in microfluidic technology for chemical-content analysis of individual cells.

    View details for DOI 10.1146/annurev-bioeng-070909-105238

    View details for Web of Science ID 000281447400008

    View details for PubMedID 20433347

  • SINGLE-MOLECULE SPECTROSCOPY USING MICROFLUIDIC PLATFORMS METHODS IN ENZYMOLOGY, VOL 472: SINGLE MOLECULE TOOLS, PT A: FLUORESCENCE BASED APPROACHES Kim, S., Zare, R. N. 2010; 472: 119-132

    Abstract

    Microfluidics serves as a convenient platform for single-molecule experiments by providing manipulation of small amounts of liquids and micron-sized particles. An adapted version of capillary electrophoresis (CE) on a microchip can be utilized to separate chemical species with high resolution based on their ionic mobilities (i.e., charges and sizes), but identification of separated species is not trivial, especially for complex mixtures of sticky biomolecules. We describe here how to use a surfactant mixture system for CE on a poly(dimethylsiloxane) (PDMS) microchip, capture separated peaks within a 50-pl chamber using microvalves, analyze the fluorescence signals with correlation spectroscopy to extract molecular diffusion characteristics, and to identify the biomolecular clusters in a model immunocomplex system.

    View details for DOI 10.1016/S0076-6879(10)72013-9

    View details for Web of Science ID 000279058600007

    View details for PubMedID 20580962

  • FRET-based measurement of GPCR conformational changes. Methods in molecular biology (Clifton, N.J.) Granier, S., Kim, S., Fung, J. J., Bokoch, M. P., Parnot, C. 2009; 552: 253-268

    Abstract

    The C-termini of G protein-coupled receptors (GPCRs) interact with specific kinases and arrestins in an agonist-dependent manner suggesting that conformational changes induced by ligand binding within the transmembrane domains are transmitted to the C-terminus. Förster resonance energy transfer (FRET) can be used to monitor changes in distance between two protein domains if each site can be specifically and efficiently labeled with a donor or acceptor fluorophore. In order to probe GPCR conformational changes, we have developed a FRET technique that uses site-specific donor and acceptor fluorophores introduced by two orthogonal labeling chemistries. Using this strategy, we examined ligand-induced changes in the distance between two labeled sites in the beta(2) adrenoceptor (beta(2)-AR), a well-characterized GPCR model system. The donor fluorophore, LumioGreen, is chelated by a CCPGCC motif [Fluorescein Arsenical Helix or Hairpin binder (FlAsH) site] introduced through mutagenesis. The acceptor fluorophore, Alexa Fluor 568, is attached to a single reactive cysteine (C265). FRET analyses revealed that the average distance between the intracellular end of transmembrane helix (TM) six and the C-terminus of the beta(2)-AR is 62 A. This relatively large distance suggests that the C-terminus is extended and unstructured. Nevertheless, ligand-specific conformational changes were observed (1). The results provide new insight into the structure of the beta(2)-AR C-terminus and ligand-induced conformational changes that may be relevant to arrestin interactions. The FRET labeling technique described herein can be applied to many GPCRs (and other membrane proteins) and is suitable for conformational studies of domains other than the C-terminus.

    View details for DOI 10.1007/978-1-60327-317-6_18

    View details for PubMedID 19513655

  • Use of a mixture of n-dodecyl-beta-D-maltoside and sodium dodecyl sulfate in poly(dimethylsiloxane) microchips to suppress adhesion and promote separation of proteins ANALYTICAL CHEMISTRY Huang, B., Kim, S., Wu, H., Zare, R. N. 2007; 79 (23): 9145-9149

    Abstract

    Dynamic modification of poly(dimethylsiloxane) channels using a mixture of n-dodecyl-beta-D-maltoside (DDM) and sodium dodecyl sulfate (SDS) is able to suppress analyte adsorption and control electroosmotic flow (EOF). In this mixed surfactant system, the nonionic surfactant DDM functions as a surface blocking reagent, whereas the anionic surfactant SDS introduces negative charges to the channel walls. Changing the DDM/SDS mixing ratio tunes the surface charge density and the strength of EOF. Using 0.1% (w/v) DDM and 0.03% (w/v) SDS, Alexa Fluor 647 labeled streptavidin can be analyzed according to the charges added by the fluorophores. Protein molecules with different numbers of fluorophores are well resolved. DDM and SDS also form negatively charged mixed micelles, which act as a separation medium. The low critical micellar concentration of DDM/SDS mixed micelles also allows the use of SDS at a nondenaturing concentration, which enables the analysis of proteins in their native state. The immunocomplex between a membrane protein, beta2 adrenergic receptor, and anti-FLAG antibody has been fully separated using 0.1% (w/v) DDM and 0.03% (w/v) SDS. We have also analyzed the composition of light-harvesting protein-chromophore complexes in cyanobacteria.

    View details for DOI 10.1021/ac071544n

    View details for Web of Science ID 000251311900047

    View details for PubMedID 17948969

  • Structure and conformational changes in the C-terminal domain of the beta(2)-adrenoceptor - Insights from fluorescence resonance energy transfer studies JOURNAL OF BIOLOGICAL CHEMISTRY Granier, S., Kim, S., Shafer, A. M., Ratnala, V. R., Fung, J. J., Zare, R. N., Kobilka, B. 2007; 282 (18): 13895-13905

    Abstract

    The C terminus of the beta(2)-adrenoceptor (AR) interacts with G protein-coupled receptor kinases and arrestins in an agonist-dependent manner, suggesting that conformational changes induced by ligands in the transmembrane domains are transmitted to the C terminus. We used fluorescence resonance energy transfer (FRET) to examine ligand-induced structural changes in the distance between two positions on the beta(2)-AR C terminus and cysteine 265 (Cys-265) at the cytoplasmic end of transmembrane domain 6. The donor fluorophore FlAsH (Fluorescein Arsenical Helix binder) was attached to a CCPGCC motif introduced at position 351-356 in the proximal C terminus or at the distal C terminus. An acceptor fluorophore, Alexa Fluor 568, was attached to Cys-265. FRET analyses revealed that the average distances between Cys-265 and the proximal and distal FlAsH sites were 57 and 62A(,) respectively. These relatively large distances suggest that the C terminus is in an extended, relatively unstructured conformation. Nevertheless, we observed ligand-specific changes in FRET. All ligands induced an increase in FRET between the proximal C-terminal FlAsH site and Cys-265. Ligands that have been shown to induce arrestin-dependent ERK activation, including the catecholamine agonists and the inverse agonist ICI118551, led to a decrease in FRET between the distal FlAsH site and Cys-265, whereas other ligands had no effect or induced a small increase in FRET. Taken together the results provide new insight into the structure of the C terminus of the beta(2)-AR as well as ligand-induced conformational changes that may be relevant to arrestin-dependent regulation and signaling.

    View details for DOI 10.1074/jbc.M611904200

    View details for Web of Science ID 000246060300079

    View details for PubMedID 17347144

  • Microfluidic separation and capture of analytes for single-molecule spectroscopy LAB ON A CHIP Kim, S., Huang, B., Zare, R. N. 2007; 7 (12): 1663-1665

    Abstract

    A complex mixture of fluorescently labeled biological molecules is separated electrophoretically on a chip and the constituent molecules are confined in a sub-nanolitre microchamber, which allows analysis by various single-molecule techniques.

    View details for DOI 10.1039/b713103h

    View details for Web of Science ID 000251121000013

    View details for PubMedID 18030384

  • Phospholipid biotinylation of polydimethylsiloxane (PDMS) for protein immobilization LAB ON A CHIP Huang, B., Wu, H. K., Kim, S., Kobilka, B. K., Zare, R. N. 2006; 6 (3): 369-373

    Abstract

    Polydimethylsiloxane (PDMS) surfaces can be functionalized with biotin groups by adding biotinylated phospholipids to the PDMS prepolymer before curing. The addition of beta-D-dodecyl-N-maltoside (DDM) in the solution blocks non-specific protein binding on these functionalized PDMS surfaces. We characterize the surface by measuring fluorescently labeled streptavidin binding. Single molecule tracking shows that the phospholipids are not covalently linked to PDMS polymer chains, but the surface functionalization is not removed by washing. We demonstrate the immobilization of biotinylated antibodies and lectins through biotin-avidin interactions.

    View details for DOI 10.1039/b515840k

    View details for Web of Science ID 000235993800005

    View details for PubMedID 16511619

  • Coating of poly(dimethylsiloxane) with n-dodecyl-beta-D-maltoside to minimize nonspecific protein adsorption LAB ON A CHIP Huang, B., Wu, H. K., Kim, S., Zare, R. N. 2005; 5 (10): 1005-1007

    Abstract

    Poly(dimethylsiloxane)(PDMS) surface is coated with n-dodecyl-beta-D-maltoside, which reduces the nonspecifically adsorbed protein on the PDMS surface to the single molecule level.

    View details for DOI 10.1039/b509251e

    View details for Web of Science ID 000232003200001

    View details for PubMedID 16175253