LIGHT-UP PNA ARRAYS

Microarrays offer the potential to profile the molecular alterations in cancer in a highly multiplexed format, but have suffered from sub- optimal sensitivity, specificity and ease-of-use. Array technologies with improved performance characteristics will therefore be of commercial value in cancer analysis by making microarray use easier and more widespread. We propose to develop a novel "light-up" technology that consists of arrayed peptide nucleic acid (PNA) probes that will only fluoresce if bound by complementary target, thereby obviating sample labeling. In contrast to other detection methods, the propose Light-Up probes contain structural motifs that are easily introduced into arrays using our existing manufacturing platform for making PNA arrays. We hypothesize that proposed Light-Up probes will exhibit improved sensitivity, specificity and quantitative capability. We will test the feasibility of two Light-Up strategies, wherein PNA probes will be conformationally constrained by an intramolecular chelate. Upon binding to target the probe will undergo a fluorogenic conformational change resulting in either intercalation of a conjugated cyanine dye, or disruption of a fluorophore-quencher pair. Demonstrating the feasibility will set the stage to move into an intensive Phase II program involving development and testing of a prototype cancer analysis array for detecting K-ras mutations. Phase III will result in innovative Light-Up arrays for cancer analysis in basic, clinical, and epidemiological research markets that will meet the needs of end-users better than competing products both in terms of their performance and use of use.