BACKGROUND:  Microarrays are widely used as a high throughput analysis of gene expression. However, the ability of these tests for use in multiplex reactions remains limited, while the costs are relatively high. Solution arrays using encoded substrate particles offer a cheaper and more flexible alternative to traditional microarrays.

INNOVATION:   Researchers at UCLA have developed a novel technology for hybridization studies using shape-encoded particles (SEPs). Each SEP has a distinct shape and is a carrier of a specific chemical/biological probe species. In an experiment, the SEP attached probes will hybridize complementary molecules. A recognition-software developed by the Researchers can decode SEPs after an experiment via their distinctive shapes and identify the presence or absence of probe species.

ADVANTAGES

1. Type and amount of probes can be subselected or extended without manufacturing a new microarray.
2. Quantity of reagents and sample materials are reduced.
3. Experiments can be done in a test tube on a lab bench or scaled up to high-throughput.
4. Compared to other barcoding and microarray techniques, SEPs are easy to manufacture, of lower cost, have an unlimited combination of shapes, and non-interfering with reporter signals.
5. The decoding step is simple and efficient compared to other encoding methods since the software decodes the SEPs while scanning the expression data on each particle.

APPLICATIONS:  Broad applications in biological analysis: from gene expression to SNP genotyping to assaying proteins.

DEVELOPMENT TO DATE:  All major aspects of the invention have undergone preliminary testing. Specifically, shape encoded particles have been etched from silicon wafers. The shapes have been coupled to oligonucleotide probes and hybridized to fluorescent-labeled reaction products. Mixtures of SEPs were then deposited onto a microscope slide, imaged under white and fluorescent lighting, and decoded using the recognition software.

The Researchers have performed a preliminary Single Nucleotide Polymorphism (SNP) genotyping experiment utilizing the encoded particles and demonstrated this approach to genotyping is successful. The result of the experiment is in agreement with traditional experiments done with tag array on glass slides.

The researchers are undertaking computer simulation studies to optimize shape design, shape decoding, and the random assembly procedure. In addition, they are working toward increasing the amount of particles available by shape-encoding on all four sides of SEPs and synthesizing the DNA oligos on the particle.

Reference: UCLA Case No. 2003-075

PCT Application: PCT/US05/02872