Rapid identification and tracing the origin of pathogenic bacteria are imperative in response to a bioterrorist attack or an infectious disease outbreak. Pulsed-Field Gel Electrophoresis (PFGE) fingerprinting is frequently used for these tasks, particularly for tracing bacterium origins. However, the short fragment bands are lost in PFGE when extended separation times are used to resolve the long DNA molecules, thus reduce the detection specificity, because the lengths of the short fragments provide additional genotype information that could be critical to discriminate two similar genomes. Another drawback of PFGE is that the electrophoresis is too slow. In a rapid (24-hour) PFGE method the electrophoresis takes 14-18 hours. Additionally, the intra- and inter-laboratory reproducibility of PFGE also needs to be improved. Although diverse approaches such as entropic traps and DNA prisms have been explored for DNA separations, none have thus far been practically utilized. We have recently discovered a new and efficient technique to resolve broad size ranges of DNA molecules. In this application we propose to construct a novel instrument to demonstrate the proof-of-principle of this new technique for high-speed and accurate microbial identification.

Public Health Relevance

We have recently discovered a new and efficient technique to resolve broad size ranges of DNA molecules. On the basis of this discovery and as a first step toward our ultimate goal of developing a system for fast microbial identification, we plan to construct a novel instrument to demonstrate the proof-of-principle of this new technique for high-speed and accurate microbial identification.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21GM104526-02
Application #
8515478
Study Section
Special Emphasis Panel (ZRR1-BT-7 (01))
Program Officer
Friedman, Fred K
Project Start
2012-08-01
Project End
2015-07-31
Budget Start
2013-08-01
Budget End
2014-07-31
Support Year
2
Fiscal Year
2013
Total Cost
$179,030
Indirect Cost
$58,405
Name
University of Oklahoma Norman
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
848348348
City
Norman
State
OK
Country
United States
Zip Code
73019
Yu, Haiqing; Lu, Joann J; Rao, Wei et al. (2016) Capitalizing Resolving Power of Density Gradient Ultracentrifugation by Freezing and Precisely Slicing Centrifuged Solution: Enabling Identification of Complex Proteins from Mitochondria by Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass S J Anal Methods Chem 2016:8183656
Chen, Huang; Zhu, Zaifang; Yu, Haiqing et al. (2016) Simple Means for Fractionating Protein Based on Isoelectric Point without Ampholyte. Anal Chem 88:9293-9
Chen, Huang; Zhu, Zaifang; Lu, Joann Juan et al. (2015) Charging YOYO-1 on capillary wall for online DNA intercalation and integrating this approach with multiplex PCR and bare narrow capillary-hydrodynamic chromatography for online DNA analysis. Anal Chem 87:1518-22
Wang, Wei; Gu, Congying; Lynch, Kyle B et al. (2014) High-pressure open-channel on-chip electroosmotic pump for nanoflow high performance liquid chromatography. Anal Chem 86:1958-64
Zhu, Zaifang; Chen, Huang; Chen, Apeng et al. (2014) Simultaneously sizing and quantitating zeptomole-level DNA at high throughput in free solution. Chemistry 20:13945-50
Zhu, Xiaocui; Xu, Lei; Wu, Tongbo et al. (2014) Continuous monitoring of bisulfide variation in microdialysis effluents by on-line droplet-based microfluidic fluorescent sensor. Biosens Bioelectron 55:438-45
Zhu, Zaifang; Chen, Huang; Wang, Wei et al. (2013) Integrated bare narrow capillary-hydrodynamic chromatographic system for free-solution DNA separation at the single-molecule level. Angew Chem Int Ed Engl 52:5612-6
Zhu, Zaifang; Liu, Lei; Wang, Wei et al. (2013) Resolving DNA at efficiencies of more than a million plates per meter using bare narrow open capillaries without sieving matrices. Chem Commun (Camb) 49:2897-9
Wang, Wei; Lu, Joann J; Gu, Congying et al. (2013) Performing isoelectric focusing and simultaneous fractionation of proteins on a rotary valve followed by sodium dodecyl-polyacrylamide gel electrophoresis. Anal Chem 85:6603-7