Organism specific microarrays are
perhaps the best available technology to study gene expression.
However, the costs of designing and fabricating full genome microarrays
limit their use to the most popular model organisms. We have developed
a new multiple use primer design technology for significantly reducing
the cost of making spotted microarrays. A substantial percentage
of the expense in constructing full genome spotted microarrays comes
from synthesizing PCR primcrs to amplify the desired DNA. Historically,
PCR primers are designed so that each primer occurs uniquely in
the genome. This condition is unnecessarily strong for selective
amplification, since only the primer pair associated with each amplification
need be unique. Thus by careful design in a genome level amplification
project we can reuse literally thousands of primers in multiple
roles. To demonstrate our methodology, we will perform a genome
level primer design for Borrelia burgdorferi, and construct a spotted
microarray for this organism. We will also produce a full genome
primer design software supporting both single gene and multiple
use primer techologies for license and commercial development. |
