chemistry
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Technology Detecting RNase Activity
(Ph.D. candidate Chang Yeol Lee)
A KAIST research team of Professor Hyun Gyu Park at Department of Chemical and Biomolecular Engineering developed a new technology to detect the activity of RNase H, a RNA degrading enzyme. The team used highly efficient signal amplification reaction termed catalytic hairpin assembly (CHA) to effectively analyze the RNase H activity. Considering that RNase H is required in the proliferation of retroviruses such as HIV, this research finding could contribute to AIDS treatments in the future, researchers say.
This study led by Ph.D. candidates Chang Yeol Lee and Hyowon Jang was chosen as the cover for Nanoscale (Issue 42, 2017) published in 14 November.
The existing techniques to detect RNase H require expensive fluorophore and quencher, and involve complex implementation. Further, there is no way to amplify the signal, leading to low detection efficiency overall. The team utilized CHA technology to overcome these limitations. CHA amplifies detection signal to allow more sensitive RNase H activity assay.
The team designed the reaction system so that the product of CHA reaction has G-quadruplex structures, which is suitable to generate fluorescence. By using fluorescent molecules that bind to G-quadruplexes to generate strong fluorescence, the team could develop high performance RNase H detection method that overcomes the limitations of existing techniques. Further, this technology could screen inhibitors of RNase H activity.
The team expects that the research finding could contribute to AIDS treatment. AIDS is disease caused by HIV, a retrovirus that utilizes reverse transcription, during which RNA is converted to DNA. RNase H is essential for reverse transcription in HIV, and thus inhibition of RNase H could in turn inhibit transcription of HIV DNA.
Professor Park said, “This technology is applicable to detect various enzyme activities, as well as RNase H activity.” He continued, “I hope this technology could be widely used in research on enzyme related diseases.”
This study was funded by Global Frontier project and Mid-career Researcher Support project of the Ministry of Science and ICT.
2017.11.28 View 6772 -
Nuclease-Resistant Hybrid Nanoflowers
An eco-friendly method to synthesize DNA-copper nanoflowers with high load efficiencies, low cytotoxicity, and strong resistance against nucleases has been developed by Professor Hyun Gyu Park in the Department of Chemical and Biomolecular Engineering and his collaborators.
The research team successfully formed a flower-shaped nanostructure in an eco-friendly condition by using interactions between copper ions and DNA containing amide and amine groups. The resulting nanoflowers exhibit high DNA loading capacities in addition to low cytotoxicity.
Flower-shaped nanocrystals called nanoflowers have gained attention for their distinct features of high surface roughness and high surface area to volume ratios. The nanoflowers have been used in many areas including catalysis, electronics, and analytical chemistry.
Of late, research breakthroughs were made in the generation of hybrid inorganic-organic nanoflowers containing various enzymes as organic components. The hybridization with inorganic materials greatly enhanced enzymatic activity, stability, and durability compared to the corresponding free enzymes.
Generally, the formation of protein nanocrystals requires high heat treatment so it has limitations for achieving the high loading capacities of intact DNA.
The research team addressed the issue, focusing on the fact that nucleic acids with well-defined structures and selective recognition properties also contain amide and amine groups in their nucleobases. They proved that flower-like structures could be formed by using nucleic acids as a synthetic template, which paved the way to synthesize the hybrid nanoflowers containing DNA as an organic component in an eco-friendly condition.
The team also confirmed that this synthetic method can be universally applied to any DNA sequences containing amide and amine groups. They said their approach is quite unique considering that the majority of previous works focused on the utilization of DNA as a linker to assemble the nanomaterials. They said the method has several advantageous features. First, the ‘green’ synthetic procedure doesn’t involve any toxic chemicals, and shows low cytotoxicity and strong resistance against nucleases. Second, the obtained nanoflowers exhibit exceptionally high DNA loading capacities.
Above all, such superior features of hybrid nanoflowers enabled the sensitive detection of various molecules including phenol, hydrogen peroxide, and glucose. DNA-copper nanoflowers showed even higher peroxidase activity than those of protein-copper nanoflowers, which may be due to the larger surface area of the flower- shaped structures, creating a greater chance for applying them in the field of sensing of detection of hydrogen peroxide.
The research team expects that their research will create diverse applications in many areas including biosensors and will be further applied into therapeutic applications.
Professor Park said, “The inorganic component in the hybrid nanoflowers not only exhibits low cytotoxicity, but also protects the encapsulated DNA from being cleaved by endonuclease enzymes. Using this feature, the nanostructure will be applied into developing gene therapeutic carriers.”
This research was co-led by Professor Moon Il Kim at Gachon University and KAIST graduate Ki Soo Park, currently a professor at Konkuk University, is the first author. The research was featured as the front cover article of the Journal of Materials Chemistry B on March 28, Issue 12, published by the Royal Society of Chemistry.
The research was funded by the Mid-Career Researcher Support Program of the National Research Foundation of Korea and the Global Frontier Project of the Ministry of Science, ICT & Future Planning.
(Figure: (A) Schematic illustration of the formation of nuclease-resistant DNA–inorganic nanoflowers. (B) SEM images showing time-dependent growth of DNA-nanoflowers. The concentration of A-rich ssDNA (Table S1, ESI†) was 0.25 mM.)
2017.04.14 View 9147 -
13 KAIST Faculty Named as Inaugural Members of Y-KAST
The Korean Academy of Science and Technology (KAST) launched the Young Korean Academy of Science and Technology (Y-KAST) and selected 73 scientists as its inaugural members on February 24. Among them, 13 KAIST faculty were recognized as the inaugural members of Y-KAST.
Y-KAIST, made up of distinguished mid-career scientists under the age of 45, will take the leading role in international collaboration as well as innovative agenda-making in science and technology.
The inaugural members include Professor Hyotcherl Ihee of the Department of Chemistry and Dr. Sung-Jin Oh of the Center for Mathematical Challenges at the Korea Institute for Advanced Study (KIAS), affiliated with KAIST. Professor Ihee is gaining wide acclaim in the fields of physics and chemistry, and in 2016, Dr. Oh was the youngest ever awardee of the Presidential Award of Young Scientist.
The other Y-KAIST members are as follows: Professors Haeshin Lee of the Department of Chemistry; Mi Young Kim, Byung-Kwan Cho, and Ji-Joon Song of the Department of Biological Sciences; Song-Yong Kim of the Department of Mechanical Engineering; Sang-il Oum of the Department of Mathematical Sciences; Jung Kyoon Choi of the Department of Bio and Brain Engineering; Seokwoo Jeon, Sang Ouk Kim, and Il-Doo Kim of the Department of Materials Science and Engineering; Jang Wook Choi of the Graduate School of EEWS (Energy, Environment, Water and Sustainability); and Jeong Ho Lee of the Graduate School of Medical Science and Engineering.
The leading countries of the Academy of Science, which include Germany, Sweden, Belgium, Canada, and Japan, have established the Young Academy of Science since 2010 in order to encourage the research activities of their young scientists and to establish a global platform for collaborative research projects through their active networking at home and abroad.
President Myung-Chul Lee of KAST said, “We will spare no effort to connect these outstanding mid-career researchers for their future collaboration. Their networking will make significant impacts toward their own research activities as well as the global stature of Korea’s science and technology R&D.
(Photo caption: Members of Y-KAST pose at the inaugural ceremony of Y-KAST on February 24.)
2017.03.02 View 17525 -
2016 KAIST EEWS Workshop
The Energy, Environment, Water and Sustainability (EEWS) Graduate School of KAIST hosted a workshop entitled “Progress and Perspectives of Energy Science and Technology” on October 20, 2016. The workshop took place at the Fusion Hall of the KAIST Institute on campus.
About 400 experts in energy science and engineering participated in the event. Eight globally recognized scientists introduced the latest research trends in nanomaterials, energy theory, catalysts, and photocatalysts and led discussions on the current status and prospects of EEWS.
Professors Yi Cui of Stanford University, an expert in nanomaterials, and William A. Goddard of California Institute of Technology presented their research experiments on materials design and recent results on the direction of theory under the topics of energy and environment.
Dr. Miquel Salmeron, a former head of the Material Science Division of Lawrence Berkeley National Laboratory, and Professor Yuichi Ikuhara of Tokyo University introduced their analysis of catalysts and energy matters at an atomic scale.
Professor Sukbok Chang of the Chemistry Department at KAIST, a deputy editor of ACS Catalysis and the head of the Center for Catalytic Hydrocarbon Functionalizations at the Institute of Basic Science, and Professor Yang-Kook Sun of Energy Engineering at Hanyang University, who is also a deputy editor of ACS Energy Letters, presented their latest research results on new catalytic reaction development and energy storage.
The workshop consisted of three sections which addressed the design of energy and environment materials; analysis of energy and catalytic materials; and energy conversion and catalysts.
The EEWS Graduate School was established in 2008 with the sponsorship of the Korean government’s World Class University (WCU) project to support science education in Korea. Professor J. Fraser Stoddart, the winner of the 2016 Nobel Prize in Chemistry, was previously worked at the KAIST EEWS Graduate School as a WCU visiting professor for two years, from 2011 to 2013. Professor Ali Coskun, who was a postdoctoral researcher in the laboratory of Professor Stoddart, now teaches and conducts research as a full-time professor at the graduate school.
Dean Yousung Jung of the EEWS Graduate School said:
“This workshop has provided us with a meaningful opportunity to engage in discussions on energy science and technology with world-class scholars from all around the world. It is also a good venue for our graduate school to share with them what we have been doing in research and education.”
2016.10.20 View 12567 -
Affordable Genetic Diagnostic Technique for Target DNA Analysis Developed
Professor Hyun-Gyu Park of the Department of Chemical and Biomolecular Engineering at KAIST has developed a technique to analyze various target DNAs using an aptamer, a DNA fragment that can recognize and bind to a specific protein or enzyme. This technique will allow the development of affordable genetic diagnoses for new bacteria or virus, such as Middle Ease Respiratory Syndrome (MERS). The research findings were published in the June issue of Chemical Communications, issued by the Royal Society of Chemistry in the United Kingdom. The paper was selected as a lead article of the journal.
The existing genetic diagnosis technique, based on molecular beacon probes, requires a new beacon probe whenever a target DNA mutates. As a result, it was costly to analyze various target DNA fragments. To address this problem, Professor Park’s team designed an aptamer that binds and deactivates DNA polymerase. The technique was used in reverse, so that the aptemer did not bind to the polymerase, maintaining its activated state, only if the target DNA was present. These probes are called TagMan probes.
The controlled activation and deactivation of DNA polymerase enables nucleic acid to elongate or dwindle, making it possible to measure fluorescence signals coming from TaqMan probes. This same probe can be used to detect various target DNAs, leading to the development of a new and sensitive genetic diagnostic technique.
Unlike the existing molecular beacon probe technique which requires a new probe for every target DNA, this new technique uses the same fluorescent TaqMan probe, which is cheaper and easier to detect a number of different target nucleic acid fragments. The application of this technique will make the process of identifying and detecting foreign DNAs from pathogens such as virus and bacteria more affordable and simple.
Professor Park said, “This technique will enable us to develop simpler diagnostic kits for new pathogens, such as MERS, allowing a faster response to various diseases. Our technology can also be applied widely in the field of genetic diagnostics.”
Picture: A schematic image of target nucleic acid extracted through the activation and deactivation of DNA polymerase
2015.07.31 View 10294 -
Mystery in Membrane Traffic How NSF Disassembles Single SNAR Complex Solved
KAIST researchers discovered that the protein N-ethylmaleimide-sensitive factor (NSF) unravels a single SNARE complex using one round ATP turnover by tearing the complex with a single burst, contradicting a previous theory that it unwinds in a processive manner.
In 2013, James E. Rothman, Randy W. Schekman, and Thomas C. Südhof won the Nobel Prize in Physiology or Medicine for their discoveries of molecular machineries for vesicle trafficking, a major transport system in cells for maintaining cellular processes. Vesicle traffic acts as a kind of “home-delivery service” in cells. Vesicles package and deliver materials such as proteins and hormones from one cell organelle to another. Then it releases its contents by fusing with the target organelle’s membrane. One example of vesicle traffic is in neuronal communications, where neurotransmitters are released from a neuron. Some of the key proteins for vesicle traffic discovered by the Nobel Prize winners were N-ethylmaleimide-sensitive factor (NSF), alpha-soluble NSF attachment protein (α-SNAP), and soluble SNAP receptors (SNAREs).
SNARE proteins are known as the minimal machinery for membrane fusion. To induce membrane fusion, the proteins combine to form a SNARE complex in a four helical bundle, and NSF and α-SNAP disassemble the SNARE complex for reuse. In particular, NSF can bind an energy source molecule, adenosine triphosphate (ATP), and the ATP-bound NSF develops internal tension via cleavage of ATP. This process is used to exert great force on SNARE complexes, eventually pulling them apart. However, although about 30 years have passed since the Nobel Prize winners’ discovery, how NSF/α-SNAP disassembled the SNARE complex remained a mystery to scientists due to a lack in methodology.
In a recent issue of Science, published on March 27, 2015, a research team, led by Tae-Young Yoon of the Department of Physics at the Korea Advanced Institute of Science and Technology (KAIST) and Reinhard Jahn of the Department of Neurobiology of the Max-Planck-Institute for Biophysical Chemistry, reports that NSF/α-SNAP disassemble a single SNARE complex using various single-molecule biophysical methods that allow them to monitor and manipulate individual protein complexes.
“We have learned that NSF releases energy in a burst within 20 milliseconds to “tear” the SNARE complex apart in a one-step global unfolding reaction, which is immediately followed by the release of SNARE proteins,” said Yoon.
Previously, it was believed that NSF disassembled a SNARE complex by unwinding it in a processive manner. Also, largely unexplained was how many cycles of ATP hydrolysis were required and how these cycles were connected to the disassembly of the SNARE complex.
Yoon added, “From our research, we found that NSF requires hydrolysis of ATPs that were already bound before it attached to the SNAREs—which means that only one round of an ATP turnover is sufficient for SNARE complex disassembly. Moreover, this is possible because NSF pulls a SNARE complex apart by building up the energy from individual ATPs and releasing it at once, yielding a “spring-loaded” mechanism.”
NSF is a member of the ATPases associated with various cellular activities family (AAA+ ATPase), which is essential for many cellular functions such as DNA replication and protein degradation, membrane fusion, microtubule severing, peroxisome biogenesis, signal transduction, and the regulation of gene expression. This research has added valuable new insights and hints for studying AAA+ ATPase proteins, which are crucial for various living beings.
The title of the research paper is “Spring-loaded unraveling of a single SNARE complex by NSF in one round of ATP turnover.” (DOI: 10.1126/science.aaa5267)
Youtube Link: https://www.youtube.com/watch?v=FqTSYHtyHWE&feature=youtu.be
Picture 1. Working model of how NSF/α-SNAP disassemble a single SNARE complex
Picture 2. After neurotransmitter release, NSF disassembles a single SNARE complex using a single round of ATP turnover in a single burst reaction.
2015.03.28 View 10829 -
Professor YongKeun Park Produces Undergraduate Students with International Achievements
Three undergraduate students under the supervision of Professor YongKeun Park from the Department of Physics, KAIST, have published papers in globally renowned academic journals.
The most recent publication was made by YoungJu Jo, a senior in physics. Jo’s paper entitled “Angle-resolved light scattering of individual rod-shaped bacteria based on Fourier transform light scattering” was published in the May 28th edition of Scientific Reports.
Analyzing bacteria is a very important task in the field of health and food hygiene, but using the conventional biochemical methods of analysis takes days. However, observation with Jo’s newly developed method using light scattering analyzes bacteria within a matter of seconds.
SangYeon Cho from the Department of Chemistry also published papers in Cell (2012) and Nature (2013), respectively, under the guidance of Professor Park. SangYeon Cho’s outstanding research achievements were recognized by Harvard and MIT. He was accepted with a full scholarship to Harvard-MIT Health Sciences and Technology Graduate School. He will begin his graduate studies at Harvard-MIT this September.
Last March, SeoEun Lee from the Department of Biology was the recipient of the Best Paper Award by the Optical Society of Korea. She plans to pursue a doctoral degree at the College of Physicians and Surgeons, Columbia University in New York.
Professor Park said, “Undergraduate students, who are learning a variety of subjects concurrently, are at the most creative time of their lives. KAIST has offered many opportunities to undergraduate students to partake in various research programs.”
- Picture (a) and (b): Rod-shaped bacteria’s phase image and light-scattering patterns
- Picture (c): Quantitative analysis to illustrate the extraction of information from bacteria
2014.06.03 View 13054 -
Rechargeable Lithium Sulfur Battery for Greater Battery Capacity
Professor Do Kyung Kim from the Department of Material Science and Engineering and Professor Jang Wook Choi from the Graduate School of EEWS have been featured in the lead story of the renowned nanoscience journal Advanced Materials for their research on the lithium sulfur battery. This new type of battery developed by Professor Kim is expected to have a longer life battery life and [higher] energy density than currently commercial batteries.
With ample energy density up to 2100Wh/kg—almost 5.4 times that of lithium ion batteries—lithium sulfur batteries can withstand the sharp decrease in energy capacity resulting from charging and discharging—which has been considered the inherent limitation of the conventional batteries.
Professor Kim and his research team used one-dimensional, vertical alignment of 75nm tick, 15μm long sulfur nanowires to maximize electric conductivity. Then, to prevent loss of battery life, they carbon-coated each nanowire and prohibited direct contact between the sulfur and electrolyte.
The result was one of the most powerful batteries in terms of both energy performance and density. Compared to conventional batteries which suffer from continuous decrease in energy capacity after being discharged, the lithium sulfur battery maintained 99.2% of its initial capacity after being charged and discharged 300 times and up to 70% even after 1000 times.
Professor Kim claims that his new battery is an important step forward towards a high-performance rechargeable battery which is a vital technology for unmanned vehicles, electric automobiles and energy storage. He hopes that his research can solve the problems of battery-capacity loss and contribute to South Korea’s leading position in battery technology. Professor Kim’s research team has filed applications for one domestic and international patent for their research.
2013.12.11 View 12540 -
KAIST to establish Ombudsperson system
KAIST has recently undergone a massive reorganization to achieve a streamlined system and highly efficient administration; and it will now implement the new “Ombudsperson” system to hear the opinions of the members of the university.
On September 9th, President Sungmo Kang held a ceremony to appoint Professors Sang-Young Shin and Hong-Gu Shim as the new “Ombudspersons”.
The previous Shinmungo system raised complaints and recommendations for improvements by members of the university, but this is the first time that KAIST has assigned a direct department for handling such matters.
The newly appointed Ombudspersons will review for the possibility of any unjust, irrational systems, violations of research ethics and such. It is their role to take a neutral stance and advise on the correction and improvement.
The merit of the Ombudsperson system is that diverse opinions can be reflected on the policy. The Ombudsperson guarantees the security of the contents of discussion so that anyone can share his or her opinion without fear of being recorded in documents.
It is expected that the Ombudsperson system will protect the interests of the individuals and thus contribute to making a “happy campus”.
President [Sungmo] Kang has said that the reason establishing the office of the Ombudsperson is “In order for KAIST to take a new leap toward the world, it is crucial to bring the minds of the members together…. Even the smallest voices must be heard to present solutions to make the university where everyone’s happy.”
In 1809, the Swedish Parliament appointed the first “Ombudsperson” to investigate and resolve civil complaints. Now, it is widely used in public institutions, corporations and universities to improve the communication and work efficiency of the members.
The new Ombudsmen: Prof. Sang-Young Shin (left) and Prof. Hong-Gu Shim (right)
2013.09.27 View 11315 -
Chemistry World: Interview with Professor Cafer Yavuz of EEWS Graduate School
Professor Cafer Yavuz of the Graduate School of EEWS (energy, environment, water, and sustainability) at KAIST had an interview with the Chemistry World, the print and online magazine issued by the Royal Society of Chemistry, the largest organization in Europe for advancing the chemical sciences. The link below is the article published by the magazine:
http://www.rsc.org/chemistryworld/2013/08/interview-cafer-yavuz-carbon-dioxide-capture
2013.08.07 View 8112 -
Review of organophosphonate nerve agent remediation and sensing chemistry
Professor David Churchill, Dept. of Chemistry, KAIST
Scientists in Daejeon, South Korea and Lexington, Kentucky (USA) have recently published a review on the subject of nerve agent remediation and probing chemistry (Chemical Reviews, DOI:10.1021/cr100193y). This article endeavored to pursue organophosphonate nerve agent chemistry deeply and comprehensively and to reflect that decontamination / sensing and nerve agents / pesticides are quite inextricable: when one tries to degrade nerve agents one also needs to detect what components are still present “downstream,” etc. Nerve agents and many pesticides also share a common generalized organophosphate / -phosphonate structure.
Also, the use of simulant molecules (mimics) and a consideration of the closely related organophosphonate pesticides were also treated comprehensively in the Review. The authors reached back into the literature when developing some sections to make important connections to the contemporary topics of interest. The review also includes industrial insights.
Kibong Kim, Olga G. Tsay and David G. Churchill of the Department of Chemistry at KAIST and David A. Atwood of the Department of Chemistry of the University of Kentucky endeavored to "make a variety of connections in research strategies and (sub-) fields to present what is still possible, fruitful, practical, and necessary and to facilitate a current comprehensive molecular level understanding of organophosphonate degradation and sensing," Churchill says.
The authors feel that for the time being, researchers in varying research areas “can use this manuscript effectively when considering future research directions.”
2011.09.19 View 9173 -
New Diagnosis System for Cardiovascular Disease Developed
Professor Park Hyun Kyu of the department of Biological-Chemical Engineering developed a new diagnosis system for diagnosing cardiovascular diseases using E.coli to test the homocysteine concentration in the blood.
The research team used the genetic recombination process to produce two different biologically illuminant nutrition cultures and compared the growth rate of the homocysteine between the two cultures by comparing the degree of luminescence.
The technology can allow the simultaneous analysis of blood samples en masse and is also economical and thus is being regarded as a major step forward in the field of homocysteine concentration analysis which is a rapidly growing field.
The conventional method used high performance liquid chromatography which took a long time to complete and was costly to run.
The advantage of the newly developed system is that it gets rid of costly steps as it only needs to grow E.coli and measure the luminescence of the naturally occurring illuminant.
The research was published as the cover paper of the April edition of ‘Analytical Chemistry’.
2011.05.11 View 8815