DNA represents one of the most capable and powerful biomolecular structures: functional as genetic material, hybridizing to complementary strands, being functional as aptamers, and active in transcription and translation as well as being capable of inducing organization and enabling the formation of designed nanostructures. DNA performs numerous natural biological functions as well as being used in drug development, biodetection, gene knockout, and genomics assays as well as many others. Despite these capabilities, DNA remains prohibitively expensive and/or difficult to implement for use in any but the most valuable applications, particularly in the materials realm. The overall hypothesis of the proposed research is that the synergistic combination of thiol-ene-based click chemistry with oligonucleotide synthesis will lead to the formation of an entirely new and highly capable class of oligonucleotide structures, i.e., thio-ether nucleic acids (TNAs), that are capable of interacting with sequence specificity with DNA in vivo, in vitro and in biofunctional applications such as biodetection and as aptamer mimics. The synergistic combination of thiol-ene click chemistry with synthetic oligonucleotide production will yield functional oligonucleotides that have enhanced DNA-binding capability, are easier to produce at scale, and have distinct chemical advantages over DNA and PNA structures. Broadly, the overall aim of this project is to develop and perform preliminary characterization of an entirely new class of oligonucleotide molecules that would have significant advantages over both biological oligonucleotides (DNA and RNA) as well as the synthetic PNAs for DNA hybridization, for biodetection, and for other biofunctional applications.
The specific aims of this work are to (i) synthesize base-functionalized TNA monomers, (ii) form controlled sequence oligomers from these monomers and evaluate their capacity for strong, selective hybridization with DNA, and (iii) demonstrate the utility of these TNA sequences in SNP detection of the KRAS oncogene.

Public Health Relevance

DNA and its accompanying sequence specific molecular interactions are among the most critical attributes and functions of biological systems. This behavior gives rise to essentially all genetic information and has also found value in disease diagnosis, aptamers, and in biological mechanism determination, and in disease treatment. Unfortunately, DNA remains largely untapped for many potential applications because of its cost and difficulty to synthesize. Here, we propose to develop a novel polymeric material, a thio-ether-based oligonucleotide that is a synthetic material which combines the benefits of DNA and its sequence-specific interactions with the broader capability, stability and control afforded by synthetic materials. Here, we specifically explore the ability of this material class to be used in diagnosing genetic mutations associated with cancer that are critical in proper identification and ultimate treatment and outcomes.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Exploratory/Developmental Grants (R21)
Project #
1R21CA174479-01
Application #
8440227
Study Section
Gene and Drug Delivery Systems Study Section (GDD)
Program Officer
Li, Jerry
Project Start
2013-01-01
Project End
2014-12-31
Budget Start
2013-01-01
Budget End
2013-12-31
Support Year
1
Fiscal Year
2013
Total Cost
$179,234
Indirect Cost
$42,353
Name
University of Colorado at Boulder
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
007431505
City
Boulder
State
CO
Country
United States
Zip Code
80309