Novel Cleavable Nucleotides for DNA Sequencing by Synthesis

DESCRIPTION (provided by applicant): Intelligent Bio-Systems is developing a high-speed, low-cost DNA sequencing-by-synthesis (SBS) system which is based on the use of cleavable fluorescent nucleotides with reversible terminator technology. The cleavable l inkers utilized in these nucleotides enable efficient removal of fluorescent signals and the reversible terminator technology enables reliable sequencing of repeats. In order to extend the performance of the sequencing system, we believe it is important to minimize the effect of residual linker on the nucleotide bases left behind after cleavage. These residual linkers may disturb the DNA duplex structure and interfere with a polymerase's ability to incorporate subsequent nucleotides. The goal of this Phase I project is to synthesize and evaluate several novel cleavable nucleotides which generate minimal residues after cleavage. We anticipate that the use of such nucleotides should result in much higher cumulative cycle efficiency in the SBS and enable longer sequencing reads. During Phase I of this project we will synthesize, characterize and extensively evaluate two novel designs of nucleotides which will generate smaller residues after fluorescent signal removal. The performance of novel nucleotides will be compared with the performance of our standard design cleavable nucleotides in solution and on solid surfaces. During Phase II we will synthesize and characterize 4 nucleotides based on the best performing analogs and perform synthesis optimization and scale-up. Phase II will also involve evaluation of all 4 nucleotides in our sequencing instrument. Ultimately, the ability to produce very inexpensive detailed DNA sequence information for complex organisms' genomes will both lead to accelerated disco veries throughout biology and provide the basis for Pharmacogenomics, a new paradigm in therapeutics wherein medicines are prescribed based on individual genotypes rather than just observed symptoms.