This Small Business Innovation Research Phase II project aims to develop new, sensitive, accurate, and reliable detection methods for measuring genomic DNA or RNA samples isolated from living cells. The intellectual merit of this project lies in the development of new detection methods that are essential for improving high-throughput genomic microarray analyses of gene activity. Problems with current microarray and genomic analysis techniques, including hybridization perturbation, slow enzymatic labeling methods using expensive labeled nucleotides and sequence dependence, are solved using a direct labeling approach. These new systems will provide the detection tools needed to advance the promising pharmaceutical, research and diagnostic uses of genomic analysis to determine the pattern of gene expression in disease or upon therapeutic treatment. Marker Gene Technologies, Inc. has established the feasibility of these detection methods by preparing new ultrasensitive fluorescent labeling reagents and developing protocols for directly labeling DNA or RNA samples isolated from live cells. These reagents are able to efficiently and sensitively label oligonucleotides for high-throughput microarray analysis. In Phase II these systems will be validated by further analysis of the fluorescent labeling methods and characterization of their ability to monitor changes in gene expression upon application of drugs or other bioactive compounds or in response to biological changes in cell function or disease, in a cell-specific manner.
The broader impacts of this project include development and commercialization of new methods for rapid screening of genomic expression patterns in response to specific drug application in normal cells and tissues as well as in disease, bacterial or viral infections. These methods are a significant improvement over existing technologies by using a direct labeling approach that is quicker, more accurate and more cost-effective. These systems will be marketed to the pharmaceutical and diagnostics industries for high-throughput pre-clinical screening of drug efficacy by comparative cellular genomic analysis. In addition, existing collaborations with industrial and research partners assure quick commercial development of the technology. The combined techniques will improve U.S. competitiveness in the burgeoning genomic analysis field as well as in pharmaceutical therapeutic drug development and lead to further job creation based on both the products and systems developed.
Fluorescent Genes: Labeling DNA for Better Understanding of Genetic Abnormalities Our new and innovative fluorescent DNA labeling techniques allow researchers to easily light up specific regions of a chromosome. In this way, disease-associated genetic abnormalities can be identified and studied. Chromosomal abnormalities are associated with a large array of genetic diseases including cancer, Parkinson's disease, cystic fibrosis and Alzheimer’s disease. Our new fluorescent DNA labeling systems can detect the presence of a specific section of the chromosome quickly and easily. In addition, these new methods can be used to quickly and accurately identify bacterial or viral infections. We expect them to have a large impact on the study of these diseases and the search for effective treatments. DNA is the code upon which all living things are built. Our genes are carried in the DNA code and provide the blueprint that tells the machinery in our cells how to make its components. Each cell in our bodies contains a full copy of our DNA that is some 3 billion base pairs and is divided across 26 chromosomes. The structure of these chromosomes is vital to correct development. The loss of even a tiny part of a chromosome will result in abnormalities, mutations or disease; similarly the duplication of this code may also cause genetic defects. DNA acts like a zipper when it reproduces itself in the chromosome. It unzips into two complementary halves and zips back up with the new side upon replication. The teeth of the zipper are the base groups adenine, thymine, guanine and cytosine, which we’ve all seen abbreviated as A, T, G and C. The backbone of the DNA zipper contains phosphate groups. Researchers now label DNA using either chemical or enzymatic methods. While the chemical methods are often simpler to use, they are more difficult to accurately interpret, as they usually label the base groups (ATCG) and interfere with the zipper system. Our new DNA labeling reagents are directed to chemically label the phosphate backbone of the DNA which leaves the bases intact. This allows researchers to zip the DNA back up without the interference of a bulky label on the teeth (bases) of the zipper. Labeling the DNA in such a way allows easy detection of the presence or absence of regions of the chromosomes. Analyzing these regions and the changes they produce in the body is a step toward developing methods of treatment or prevention of chromosomal abnormalities or infective diseases in the future. The success of our new DNA labeling project opens up enormous commercial possibilities in the fields of functional genomic analysis, genetic screening of new proteins and drugs in cell-culture systems, discovery of new antineoplastic, antibacterial and antiviral agents and medical intervention in genetic diseases. In addition, it contributes new information and techniques for drug development by the pharmaceutical industry, and the labeling reagents and techniques produced are being marketed for both research and commercial uses. The innovation is related to basic research in the laboratories of Marker Gene Technologies, Inc. under a grant from the National Science Foundation (SBIR IIP-0923953) to prepare ultrasensitive fluorescent labeling reagents and develop protocols for directly labeling DNA or RNA samples isolated from live cells.
