DEVELOPMENT OF SOFTWARE FOR HIGH-THROUGHPUT PCR DESIGN

The mission of DNA Software Inc. is to enable the field of genomics by writing enterprise grade simulation software that incorporates state-of- the-art knowledge of the thermodynamics and kinetics of nucleic acid folding and hybridization. To accomplish this goal, we are developing core software called the Oligonucleotide Modeling Platform (OMP). OMP uses a standardized architecture, which allows it to accept different input and output data structures and to combine modules in a deployable fashion. OMP will reduce the development time and improve the reliability of any process involving oligonucleotide hybridization such as multiplex PCR, DNA sequencing, SNP detection assays, mRNA expression profiling, and a variety of chip array and microfluidics applications. This proposal focuses on the customization of OMP for automated high-throughput design of primers and in sillico optimization of reaction conditions for PCR in a variety of formats. The PCR OMP software will utilize a completely new approach for stimulating the product distribution after each step of PCR using both equilibrium and kinetic models of hybridization, target unfolding, and polymerase extension. The availability of the PCR OMP software is essential for the development of robust methods for low-cost high-throughput genotyping to enable disease association studies and personalized medicine.