We will develop optimized methods for the enzymatic production of modified oligonucleotides which have strong advantages as therapeutic agents and biosensors. We will first implement a Sequential Injection Analysis (SIA) platform with continuous data collection to optimize biochemical protocols with large parameter spaces. We will use this platform to optimize conditions for in vitro transcription of 2'-O-methyl and 2'-fluoro RNA. We will also implement a continuous, continuous- or semi-continuous-flow bioreactor for in vitro production of modified RNA for use in ongoing projects including microfluidic cancer cell capture and in vivo evaluations of aptamer therapeutics. Microreactors of the type we will build have been demonstrated for controlled, efficient, scalable, synthetic organic chemistry. These same advantages make the strategy attractive for biochemical reactions.

Public Health Relevance

Chemically modified DNA and RNA are more resistant to being destroyed by the environment in blood, and so they are preferred as tools to develop drugs or instruments used for clinical testing. Current methods for generating these valuable substances are very expensive and produce very little of the product, which limits their use. This project will develop an improved method to generate modified DNA and RNA which will allow wider use of these important chemical tools.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Postdoctoral Individual National Research Service Award (F32)
Project #
5F32GM095280-02
Application #
8195405
Study Section
Special Emphasis Panel (ZRG1-F14-C (20))
Program Officer
Fabian, Miles
Project Start
2010-09-01
Project End
2012-08-31
Budget Start
2011-09-01
Budget End
2012-08-31
Support Year
2
Fiscal Year
2011
Total Cost
$51,326
Indirect Cost
Name
University of Texas Austin
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
170230239
City
Austin
State
TX
Country
United States
Zip Code
78712
Allen, Peter B; Chen, Xi; Simpson, Zack B et al. (2014) Modeling Scalable Pattern Generation in DNA Reaction Networks. Nat Comput 13:583-595
Chirieleison, Steven M; Allen, Peter B; Simpson, Zack B et al. (2013) Pattern transformation with DNA circuits. Nat Chem 5:1000-5
Wan, Yuan; Tamuly, Deepika; Allen, Peter B et al. (2013) Proliferation and migration of tumor cells in tapered channels. Biomed Microdevices 15:635-643
Allen, Peter B; Chen, Xi; Ellington, Andrew D (2012) Spatial control of DNA reaction networks by DNA sequence. Molecules 17:13390-402
Ilyas, Azhar; Asghar, Waseem; Allen, Peter B et al. (2012) Electrical detection of cancer biomarker using aptamers with nanogap break-junctions. Nanotechnology 23:275502
Wan, Yuan; Liu, Yaling; Allen, Peter B et al. (2012) Capture, isolation and release of cancer cells with aptamer-functionalized glass bead array. Lab Chip 12:4693-701
Allen, Peter B; Arshad, Seyed A; Li, Bingling et al. (2012) DNA circuits as amplifiers for the detection of nucleic acids on a paperfluidic platform. Lab Chip 12:2951-8
Allen, Peter B; Ellington, Andrew D (2011) Sequential injection analysis for optimization of molecular biology reactions. Anal Chem 83:2194-200