Science and Software Combined to Solve Real-World Genomic Problems

Why Probe and Primer Design Software is Necessary

Ideally, a probe could be designed simply as the Watson-Crick complement of the target sequences - A<>T, C<>G. However, DNA hybridization does not strictly follow these pairing rules. Instead, depending on the sequences of bases involved and certain external conditions, such as temperature and salt concentration, a variety of error-causing artifacts often occur:

• Oligonucleotides pair with alternate, non-targeted sites on the genome with perhaps only one or a few mismatches,
  
  
• Target sites of single-stranded DNA or mRNA fold into stable structures that must be unfolded to allow an oligonucleotide to bind or, sometimes the target folding is so stable that the probe does not bind at all,
  
  
• Other artifacts occur including probe folding and probe-to-probe binding (homodimer formation).
  

These artifacts lead to false positives and false negatives in diagnostic uses and may disrupt the effectiveness or efficiency of the assay.

Nucleic acid hybridization is at the heart of today's genomic research. PCR, performed by a majority of biotech researchers, relies on hybridization, as do most methods currently being developed for high-throughput genotyping. If the probes and primers used in these assays always followed the Watson-Crick base pairing rules, then developing these assays would be simple. Unfortunately, this is not the case. Single-stranded DNA is unstable compared to the double-stranded form and the thermodynamic and kinetic forces at work produce many non-confroming results (see the sidebar "Why We Need Probe and Pimer Design Software").

Most solutions to this problem lack the rigor and precision needed for today's demanding, high-throughput assays....until now. DNA Software has determined the most comprehensive database of nucleic acid thermodyamic parameters and structural motifs available. We've also developed a proprietary numerical analysis of multi-state coupled equilibria that predicts concentrations of all DNA species in the assay. These models are combined in our Oligonucleotide Modeling Platform (OMP), state-of-the-art modeling and simulation software that forms the foundation for all our application development. Using OMP, we are able to quickly develop applications focused on our customers' unique needs.