Department of Chemical and Biomolecular Engineering
Korea Advanced Institute of Science and Technology

Faculty

Hyun Gyu Park (박현규)

Professor

Tel : +82-42-350-3932
Fax : +82-42-350-3910
E-mail : hgpark@kaist.ac.kr
Homepage : http://bcbd.kaist.ac.kr
Education
- 1996 : KAIST (Ph.D. in Chem. Eng.)
- 1992 : KAIST (M.S. in Chem. Eng.)
- 1990 : KAIST (B.S. in Chem. Eng.)


Employment and Professional Experience
- August 1992 - Feb. 1993 : Visiting Scholar at Dept. of Biochem. Eng. Univ. of Iowa, USA.
- Feb. 1, 1996 – Mar. 19, 2002 : Senior Researcher at Samsung Advanced Institute of Technology
- April 1, 2002 – Feb. 28, 2006 : Assistant professor at Dept. of Chemical & Biomolecular Eng. KAIST
- Mar. 1, 2006 – present : Associate professor at Dept. of Chemical & Biomolecular Eng. KAIST
- Editorial Board Member, The Open Catalysis Journal (ISSN 1876-214X, Bentham Open), (2008~present)
- Editorial Board Member, Biotechnology Journal (ISSN 1860-6768, WILEY), (2010~present)
- Editorial Board Member, American Journal of Analytical Chemistry (Scientific Research Publishing), (2010~present)


Research interests
- Nucleic acid bioengineering
- Microarray technology (DNA and cell chips)
- Electrochemical technology for molecular diagnostics
- Nanobiotechnology & enzyme engineering


Selected Publications
1. Jae Yang Song, Hyun Gyu Park*, Sung-Ouk Jung and Jae Chan Park, “Diagnosis of HNF-1α mutations on a PNA zip- code microarray by single base extension”, Nucleic Acids Research, 33(2), e19-e26 (2005).
2. Yun Kyung Jung, Tae Won Kim, Jumi Kim, Jong-Man Kim* and Hyun Gyu Park* “Universal colorimetric detection of nucleic acids based on polydiacetylene (PDA) liposomes”, Advanced Functional Materials, 18(5), 701-708 (2008).
3. Yun Kyung Jung, Tae Won Kim, Cheulhee Jung, Dae-Yeon Cho and Hyun Gyu Park* “A polydiacetylene (PDA) microchip, based on a biotin-streptavidin (STA) interaction for the diagnosis of pathogen infections”, Small, 4(10), 1778-1784 (2008).
4. Hyo young Mun, Agnishwar Girigoswami, Cheulhee Jung, Dae-Yeon Cho, Hyun Gyu Park*, “SNPs detection by a single-strand specific nuclease on a PNA zip-code microarray”, Biosensors and Bioelectronics, 24(6), 1706-1711 (2009).
5. Byoung Yeon Won, Sung Chul Shin, Won-young Chung, Sujeong Shin, Dae-Yeon Cho and Hyun Gyu Park*, “Mismatch DNA-specific enzymatic cleavage employed in a new method for the electrochemical detection of genetic mutations”, Chemical Communications, (28), 4230-4232 (2009).
6. Rongzhan Fu, Taihua Li and Hyun Gyu Park*, “An ultrasensitive DNAzyme-based colorimetric strategy for nucleic acid detection”, Chemical Communications, (39), 5838-5840 (2009).
7. Moon Il Kim, Byung Jo Yu, Min-Ah Woo, Daeyeon Cho, Jonathan S. Dordick, June Hyoung Cho, Byung-Ok Choi and Hyun Gyu Park*, “Multiplexed amino acid array utilizing bioluminescent Escherichia coli auxotrophs”, Analytical Chemistry, 82(10), 4072-4077 (2010).
8. Taihua Li, Rongzhan Fu and Hyun Gyu Park*, “Pyrrolo-dC based fluorescent aptasensors for the molecular recognition of targets”, Chemical Communications, 46(19), 3271-3273 (2010).
9. Cheulhee Jung, Ji Won Chung, Un Ok Kim, Min Hwan Kim and Hyun Gyu Park*, “An isothermal target and probe amplification (iTPA) method, based on a combination of an isothermal chain amplification (ICA) technique and a FRET cycling probe technology (CPT)”, Analytical Chemistry, 82(14), 5937-5943 (2010).
10. Ki Soo Park, Cheulhee Jung, and Hyun Gyu Park*, “Illusionary polymerase activity triggered by metal ions: use for molecular logic-gate operations”, Angewandte Chemie International Edition, 49(50), 9757–9760 (2010). (Highlighted as an inside cover article)

Biochip & Biodevice Laboratory
Nucleic acid bioengineering, Biochips & Biosensor, Electrochemical diagnosis, Nanobiotechnology & Enzyme engineering

■ Nucleic acid bioengineering 

1. Novel isothermal/quantitative nucleic acid amplification methods for ultra-high sensitive detection of biomolecules 

The invention of the PCR technique has made a tremendous impact on the areas of biological research and diagnostics since it can be used to generate quantities of nucleic acids needed for detection and measurements. However, the need for a temperature cycling instrument limits applications of PCR in point-of-care testing (POCT) environments. In order to overcome this limitation, we have developed a powerful isothermal amplification method (ICA) as part of a quantitative amplification technology (iTPA) that combines ICA and FRET cycling probe technology (CPT). By creating a rationally designed amplification mechanism, ICA amplifies target DNA highly enough to detect down to 100 copies under isothermal conditions. To achieve the iTPA, dual amplification of both the target and the FRET probe is efficiently utilized to bring about high sensitivity. The observations made in this study clearly demonstrate that even a single copy level of C. trachomatis pathogen can be reliably quantified. Furthermore, combining a target and signaling probe amplification method (iTPA) with a colorimetric detection method (GCA), we have successfully developed a novel and efficient assay for the direct colorimetric diagnosis of C. trachomatis pathogen as low as 100 copies under isothermal conditions. The methods do not require an expensive thermo-cycler or other instrumentation and are remarkably simple and convenient. The proposed approaches are thus thought to be promising for application in portable sensor systems such as micro-fluidic devices or POCT diagnostic kits.

2. Metal ion aptamer-based target detection and logic gate 

In recent years, an intense interest has grown in the interactions of nucleic acids with metal ions. Examples of such novel interactions include the specific binding of aptamers with metal ions and selective incorporation of metal ions as cofactors to promote the catalytic activities of nucleic acid enzymes (deoxyribozymes or ribozymes). In addition, it has been observed that certain metal ions like Hg2+, Ag+, Cu2+, Ni2+, and Co2+ specifically bind to nucleosides or ligandosides to form metal ion-mediated base pairs. We focus on the specific interactions of the mismatched base pairs (thymine-thymine (T-T) or cytosine-cytosine (C-C)) with the respective metal ions (Hg2+ or Ag+) and develop a new strategy in which a polymerase enzyme is controlled to accomplish an unnatural extension reaction even at the mismatched site of a primer with template DNA. The validity of this novel concept was systematically demonstrated by using Hg2+ and Ag+ to intentionally trigger an unusual illusionary polymerase activity at respective T-T and C-C mismatched primers. By utilizing this concept, we have successfully constructed a molecular scale logic gate system that uses Hg2+ or Ag+ as inputs and DNA amplification as an output. To the best of our knowledge, this is the first time that key logic gates, which use PCR amplification as an output and metal ions as triggers, have been described. We believe that this novel concept might serve as tools for the identification of metal ions (Hg2+ or Ag+) and also be extended to develop new single nucleotide polymorphism (SNP) genotyping strategy.

◈ The significance of this work derives from the following features.

☞ Being different from previous efforts in which interactions of nucleic acids with metal ions were studied, the current

     investigation probed these interactions in combination with polymerase activity. The work has led to the discovery

     that the illusionary activity of a polymerase can be intentionally triggered by using Hg2+ and Ag+ ions via their

     interaction with the respective mismatched base pairs T-T and C-C. This phenomenon results in an unusual

     polymerase amplification reaction.

☞ By utilizing this concept, a novel strategy to construct molecular scale logic gates was developed by rationally

     designing primers and selecting the type of DNA polymerase employed. The novel strategy is both simple and cost

     effective because it only requires incorporation of a single mismatched base (T and C) at the 3’ end of the primer and

     the use of metal ions (Hg2+ and Ag+) as inputs. In contrast, previously reported strategies for the construction of logic

     gates, which operate by specific metal ion regulation of the catalytic activity of deoxyribozymes, typically rely on

     complicated designs for gate switching and frequently require expensive RNA or chimeric DNA as operational

     substrates. These requirements significantly limit the utility of the older strategies.

3. DNAzyme 

Artificial DNAzymes (also called deoxyribozyme or catalytic DNA) are widely used as signal transduction components of biosensors because one DNAzyme molecule is able to catalyze many cycles of a specific reaction generating amplified readout signals. Among the DNAzymes acting as amplifying labels, a binary peroxidase DNAzyme attracted special efforts, which is composed of two single-stranded guanine-rich DNA strands self-assembling into G-quadruplex structure with hemin. Due to its ability to catalyze the generation of colorimetric or chemiluminescence signals, the binary peroxidase DNAzyme has been employed in many strategies for the detection of nucleic acids, small molecules, and proteins. Recently, we developed a novel ultrasensitive colorimetric detection method for nucleic acids. This method relies on a unique enzyme-mediated isothermal amplification strategy to realize triplex amplification effects on the readout signals: the target DNA recycling, the amplified generation of active DNAzymeMBs, and the DNAzyme-based signal amplification. This new isothermal colorimetric DNA detection method possesses ultra-high sensitivity with a detection limit down to 10 attomole range which was the lowest detection limit among the previous reports for peroxidase DNAzyme-based detection methods.

■ Microarray technology 

Of several microarray-based methods, zip-code microarray technology offers many promising opportunities due to its unique advantages over the conventional technology. The unique and distinct short oligonucleotides that are designed for the purpose of addressing complementary target sequences on arrays are known as zip-code sequences. Most attractive feature of this approach is that once developed, the zip-code microarray can be used for different sets of human genetic mutations. Recently, by combining zip-code microarray and new assay platforms using several kinds of enzymes, we have developed various strategies for the detection of genetic mutations of MODY and BRCA. For instance, zip-code microarray systems based on single base extension (SBE), ligation chain reaction (LCR) and single strand specific nuclease assay (SSS) have been developed and their diagnostic utilities were successfully verified by correctly diagnosing various human genetic mutations in MODY and BRCA genes.

Genitourinary infectious diseases are known to occur frequently among human beings and some of them have high possibility to pass into chronic diseases. However, current treatments are carried out without exact identification of infected pathogens and antibiotic resistances, causing overdose of multiple antibiotics. For the efficient diagnosis and treatment, we developed the DNA chip to reliably identify 14 pathogens simultaneously, causing the sexually transmitted diseases. The DNA chip developed is expected to have superior performance in terms of efficiency, specificity, sensitivity, and cost-effectiveness.

■ Electrochemical technology 

We are developing various electrochemical detection methods for genetic diagnosis. First, novel electrochemical strategies to detect nucleic acids were developed utilizing neutral charge property of peptide nucleic acid (PNA) or unique binding property of DNA intercalating agent. Second, a new detection method of DNA mutation or SNP genotyping was developed based on mismatched DNA-specific cleavage activity of CEL I endonuclease. These results developed by our group will serve as the basis for advanced electrochemical strategies for genetic diagnosis. In addition, we are currently developing the electrochemical real time PCR method.

1. Nanobiosensor 

Magnetic nanoparticles (MNPs), which were generally recognized to be biologically and chemically inert, have recently been reported to show intrinsic peroxidase activity (Gao et al., Nat. Nanotechnol. 2, 577-583, 2007). In order to accelerate and widen the utility of MNPs as next-generation alternatives to peroxidases, we have developed a nanostructured multi-catalyst system that consists of MNPs and an oxidative enzyme simultaneously entrapped in large pore sized mesoporous silica for convenient colorimetric detection of biologically important target molecules.

The results of the investigations demonstrate that the multi-catalyst system, incorporating various oxidases such as glucose oxidase, cholesterol oxidase, galactose oxidase, or pyruvate oxidase, has high selectivities and sensitivities for the detection of the corresponding target molecules along with excellent reusabilities and highly enhanced stabilities. Since the current system enabled rapid visual detection of target molecule in a quite reliable and cost-effective manner together with long-term stability, it should find practical applications in facility-limited or POCT-environments. It is envisaged that future applications of this technology will range from biosensors to multi-catalyst reactors.

2. Cell-based biosensor 

Determining amino acid concentrations is of broad interest in numerous aspects of biological research, clinical diagnosis and medicine, food technology, etc. In particular, measurement of free amino acid concentrations in physiological fluids such as blood, cerebrospinal fluid (CSF), and urine has been used as biochemical indicators of newborn errors of metabolism (aminoacidopathies), nutritional status, and therapeutic monitoring. Thus, there is significant incentive to develop a new approach to enable more convenient, reliable, and economical detection of amino acid concentrations.

Along these lines, we have developed a solid-phase multiplexed amino acid diagnostic array, which comprises 16 different amino acid E. coli auxotrophs yielding rapid, specific, and sensitive cell growth as a direct response to the concentration of corresponding amino acids.

To enhance the resulting cell-based signal, bioluminescence-based measurement of cell density was employed. As a result, an amino acid specific, concentration-dependent luminescence response is produced. The clinical validity of this approach was verified by reliably determining the concentrations of amino acids in newborn human blood specimens. Such an approach may also be extended to other rapid cell-based sensing of simple metabolites that are relevant to other clinical disorders, including homocysteine, galactose, various vitamins, folic acid, and lipids.

3. Polydiacetylene (PDA)-based colorimetric biosensor 

Colorimetric biosensors possess an inherent advantage in that they do not require any instrumentation or power supply, making them ideal for low-resource settings. Among the many approaches that have been developed, polydiacetylene (PDA) is particularly interesting because it yields a significant chromatic change from blue to red in response to a variety of external stimuli such as temperature, pH and molecular recognition. We have developed the colorimetric method for the detection of nucleic acids, based on ionic interactions by PDA liposomes. Amine-modified PDA sensors showed a dramatic color change from blue to red upon the addition of nucleic acids amplified by using the polymerase chain reaction (PCR) due to the stimuli caused by ionic interactions between the positively charged PDA and negatively charged phosphate backbone of the nucleic acids. By using the PDA-based colorimetric sensor, nucleic acids amplified by common PCR reaction, whose typical concentration is around 100 nM, was readily detected. Since implementation of this universal colorimetric method is simple, rapid and does not require any sophisticated instrumentation, it should find its great applications in the area of genetic diagnosis.