Research Funding:

Applying Universal Bases to Achieving the Full Potential of Sequencing-By-Hybridization (SBH)

Support provided by National Science Foundation

Description

The goal of this interdisciplinary project is to establish the feasability of a more powerful and robust experimental system for the sequencing of DNA by hybridization. A conceptually novel approach is based on a new probe design and a new algorithm for sequence reconstruction which have been demonstrated by computational modeling to provide optimum information extraction in sequencing by hybridization. The probe pattern is based on a recent combinatorial result showing that the use of probes composed of natural bases and universal bases in a well defined periodic pattern is crucial for utilizing the full power of DNA hybridization chips. The successful implementation of this new method depends on the suitable performance of universal bases (wild cards), i.e., of natural or artificial bases with the capability of "hybridizing" with any of the standard nucleic acid bases, on chips. This method will be tested in chemical systems in order to discover optimum patterns in the context of non-ideal behavior of oligonucleotide probes. Specific activities for the proposed grant period are: 1. A program of experiments with oligomers incorporating universal bases. 2. Research on the synthesis of a new best suited universal base. 3. Matching of sequence reconstruction procedures to developed models.

Principal Investigator

Franco P. Preparata

Co-PIs

Eli Upfal
John Suggs
Kathlyn Parker

Projects Supported

Details

Amount:$866,920
Dates:2000-2003
Status:Complete