... understanding life in molecular detail

Dr Jung-uk Shim

Microfluidics, Single molecule analysis, Immunoassay, Directed evolution


I am interested in studying biological systems ranging from cells to molecules using microfluidics that facilitate the quantitative study of biological systems. We are developing a platform able to identify the presence of diseases significantly more sensitively than the standard ELISA using microfluidic approach by quantification of a very low abundance biomarker. In addition, I am also interested in analysis of molecular structure of protein at single molecule level for directed evolution.

Current major projects include:
  • Microfluidic biodiagnostics
  • Single protein molecule biophysics
  • High throughput biochemical analysis
  • Microfluidic droplets for synthetic biology

The objective of my research is the development of methods using microfluidics primarily for highly sensitive immunoassay and directed evolution at single molecule level.

 

Microfluidics

Microfluidics is the science and technology of systems that control a small amount (10-9 to 10-15 liters) of liquids in channels with dimensions of between 1 and 100 micrometers. One of its advantages is obviously miniaturizing components and scaling-down processes, therefore leading to reduced-reagent consumption, in addition to expanding a few possible trials into a much larger number of high throughput screenings. Microfluidics has many advantages, particularly its ability to handle and detect small sample volumes, fast system response and processing of biological materials such as DNA, proteins and cells.

Despite the relatively short history of microfluidic systems, they are considered as one of the most promising experimental or manufacturing tools in various natural and life sciences as well as biotechnology applications. There have been significant attempts to apply microfluidic technology in biology and biochemistry, and there are also many applications realized in the physical sciences. As microelectronics initiated the integrated circuit revolution, which caused a fundamental alteration to everyday life, microfluidic-based products could also generate a significant impact on human society with precise manipulation of fluids on the microscopic scale while discovering and exploiting new phenomena.

 

 

Development of highly sensitive immunoassay

Protein biomarkers are used for biodiagnosis to identify the state of patient’s disease by sensitively measuring concentrations of target molecules. The diagnostic technology widely used in clinics is ELISA(Enzyme-linked immunosorbent assay), which can detect biomarkers at concentrations above picomolar. However, the major biomarker’s concentrations of important diseases such as neurogenerative diseases and cancers in complex human fluids are ranged from pico- to attomolar.

The aim of this research is the creation of a platform to measure the concentration of target protein biomarkers down to attomolar concentration for accurate, rapid and quantitative diagnosis of the early state of diseases. This platform is based on a microfluidic device that has a capability to measure the chemical reaction of single molecules of enzyme encapsulated in femtoliters microfluidic droplets.(Shim, J.-u. ACS Nano, 2013. 7(7), p. 5955-5964)

 

 

Directed evolution to discover an enzyme with new functions

The development of novel biocatalysts involves a long and iterative process to optimise the high dimensional matrix of reagents and conditions. The screening techniques have led to rapid developments in directed evolution. In vitro compartmentalization was found to be one of the recent developments in directed evolution and has proven as a powerful method in terms of miniaturization and high throughput screening. However, these high throughput screening technologies are normally based on the assay of large sized molecular ensembles, which observables would be measured as an average value in experimental systems.

The aim of this research is to create a microfluidic technology platform that can be applied to the discovery of enzyme proteins at single molecule level that catalyse novel chemical reactions. This will enable the discovery of very rarely populated mutant enzymes that would be buried and averaged out in ensemble measurements.

Detailed research programme                  Close ▲
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Lecturer (Leeds) 2013-present

PhD student (Brandeis) 2001-2007
Visiting Researcher (Harvard) 2003-2005
Research Fellow (Cambridge) 2007-2012
Postdoc (Glasgow) 2012-2013

EC Stoner 8.40
School of Physics
01133 433903
j.shim@leeds.ac.uk

http://www.physics.leeds.ac.uk/index.php?id=263&uid=1319

Selected Publications

  1. J.U.Shim, R.Ranasinghe, C.Smith, S.Ibrahim, F.Hollfelder, W.T.S.Huck, D.Klenerman, C.Abell, "Ultra-rapid generation of femtoliter microfluidic droplets for single-molecule counting immunoassays” ACS Nano, 7(7), 5955-5964, 2013

  2. M.H.Horrocks*, H.Li*, J.U.Shim*, R.Ranasinghe, R.Clarke, W.T.S.Huck , C.Abell, D.Klenerman. "Single molecule fluorescence under conditions of fast flow" Anal. Chem., 84 (1), 179 – 185. 2012

  3. J.U.Shim, L.Olguin, G.Whyte, D.Scott, A.Babtie, F.Hollfelder, C.Abell, W.Huck "Simultaneous determination of gene expression and enzymatic activity in individual bacterial cells in microdroplet compartments" J. Am. Chem. Soc., 131 (42), 15251-15256, 2009

  4. J.U.Shim, G.Cristobal, D.Link, T.Thorsen, Y.Jia, K.Piattelli, S.Fraden, "Control and Measurement of the Phase Behavior of Aqueous Solutions Using Microfluidics" J. Am. Chem. Soc., 129 (28), 8825, 2007