John Oliver
Assistant Professor (Research):
Chemistry
Phone: 401 863 2844
john_oliver@brown.edu
A recent effort in our lab is a collaboration with colleagues in the Chemistry Department (Kathlyn Parker and William J. Suggs) and in the Computer Science Department (Eli Upfal and Franco Preparata). We are investigating the behavior of synthetic and natural nucleosides in DNA hybridization experiments. Our goal is to find a ""universal"" base with particular characteristics that will allow us to use gapped or patterned probes for Sequencing By Hybridization (SBH). When used for SBH, gapped probes will increase the information content of oligonucleotide based microarrays by at least 100-fold and will lower the cost of DNA sequencing.
Interests
A recent effort in our lab is a collaboration with colleagues in the Computer Science Department (Eli Upfal and Franco Preparata). We are investigating the behavior of synthetic and natural nucleosides in DNA hybridization experiments. Our goal is to find a "universal" base with particular characteristics that will allow us to use gapped or patterned probes for Sequencing By Hybridization (SBH). When used for SBH, gapped probes will increase the information content of oligonucleotide based microarrays by at least 100-fold and will lower the cost of DNA sequencing. Our investigation of nucleoside analogs capable of acting as universal bases has resulted in the development of probes containing 8 natural bases and 5 universal bases. When placed in arrays, the probes are capable of selectively hybridizing to perfect complements in the presence of single mismatches. The results indicate that patterned probes will be able to increase the efficiency of SBH.
Awards
N/A
Affiliations
N/A
Funded Research
National Institutes of Health - National Human Genome Research Institute; "Enhanced DNA Microarray Performance with Patterned Probes"; $792,270; 5/1/04 - 4/30/06
National Science Foundation: "NIRT: DNA Sequencing and Translocation Studies using Electrically-Addressable Nanopore Arrays"; $1,550,000; 8/1/04 - 7/31/08
National Institutes of Health - National Human Genome Research Institute; "A Shape Sensitive Mass Spectrometer for Protein Analysis"; $167,581; 9/26/05 - 8/31/06
