SBIR-STTR Award

Building upon the complete sequence of the human genome, intense efforts are currently underway to identify the underlying genetic link to common diseases by single nucleotide polymorphism (SNP) mapping or direct association. Technology development focused on rapid, high-throughput, and low cost SNP detection would represent a major advance for the application of genetic information in applied medicine. The aim of the R41 proposal is the development of the Base Addition Sequencing Scheme (BASS) with potential application for targeted mini-sequencing from PCR-amplified from genomic DNA materials. We have demonstrated the feasibility of BASS and have identified the major challenges in development for DNA sequencing applications. Namely, they are (a) non-uniform UV deprotection of the different 2-nitrobenzyl nucleobase triphosphates and (b) poor incorporation efficiencies of 3'-(substituted-2-nitrobenzyl)-dNTPs by commercially available DNA polymerases. To overcome these obstacles, we propose the synthesis of '3-0- (substituted-2-nitrobenzyl)-dNTPs, which show uniform deprotection efficiencies for the four nucleobases and the identification of novel Taq DNA polymerase variants by random mutagenesis screens. The test of feasibility for the BASS technology will be two cycles of stepwise DNA synthesis (that is, two rounds of incorporation and deprotection) in all sixteen 2-base extension combinations. The outcome of this research will provide a more accurate estimate of the cycle efficiency, which will be an indicator of the sequence readlength. Successful implementation of these aims will result would demonstrate the BASS technology for application of de novo SNP discovery

Building upon the complete sequence of the human genome, intense efforts are currently underway to identify the underlying genetic link to common diseases by single nucleotide polymorphism (SNP) mapping or direct association. Technology development focused on rapid, high-throughput, and low cost SNP detection would represent a major advance for the application of genetic information in applied medicine. The aim of the R41 proposal is the development of the Base Addition Sequencing Scheme (BASS) with potential application for targeted mini-sequencing from PCR-amplified from genomic DNA materials. We have demonstrated the feasibility of BASS and have identified the major challenges in development for DNA sequencing applications. Namely, they are (a) non-uniform UV deprotection of the different 2-nitrobenzyl nucleobase triphosphates and (b) poor incorporation efficiencies of 3'-(substituted-2-nitrobenzyl)-dNTPs by commercially available DNA polymerases. To overcome these obstacles, we propose the synthesis of '3-0- (substituted-2-nitrobenzyl)-dNTPs, which show uniform deprotection efficiencies for the four nucleobases and the identification of novel Taq DNA polymerase variants by random mutagenesis screens. The test of feasibility for the BASS technology will be two cycles of stepwise DNA synthesis (that is, two rounds of incorporation and deprotection) in all sixteen 2-base extension combinations. The outcome of this research will provide a more accurate estimate of the cycle efficiency, which will be an indicator of the sequence readlength. Successful implementation of these aims will result would demonstrate the BASS technology for application of de novo SNP discovery.

Thesaurus Terms:
genetic screening, genome, single nucleotide polymorphism, technology /technique development DNA directed DNA polymerase, nitrobenzene, nucleic acid sequence, nucleobase X ray crystallography, high performance liquid chromatography, high throughput technology, mass spectrometry, nuclear magnetic resonance spectroscopy, polymerase chain reaction, site directed mutagenesis