Innovative Approaches to DNA Sequencing
Thursday, November 8, 2007
Organizers: Thomas Leyh, Albert Einstein College of Medicine and Ruben Gonzalez, Columbia University
Speakers: Linda Reha-Krantz, University of Alberta; Jingyue Ju, Columbia University; Ido Braslavsky, Ohio University; Patrice Milos, Helicos Biosciences Corporation
Recent years have seen an increasing level of dialogue between chemists and biologists, the lines of communication consolidated by the availability of recombinant biotechnology tools for manipulating the chemical structure of genes and the proteins they encode. This has led to an explosion of interdisciplinary activity at the chemistry-biology interface, now coined chemical biology. The goal of the Chemical Biology Discussion Group is to bring together chemists and biologists working in the New York area who are interested in hearing about the latest ideas in this rapidly growing field. This group will provide a forum for lively discussion and for establishing connections, and perhaps collaborations, between chemists armed with novel technologies and biologists receptive to using these approaches to solve their chosen biological problem.
Abstracts
Engineering DNA Polymerases for DNA Sequencing
Linda J. Reha-Krantz
University of Alberta
The ability to efficiently determine DNA sequences in the past, now and in the future depends on DNA polymerases, which are enzymes that have the ability to make accurate copies of the genetic information held in DNA molecules. "Natural" DNA polymerases, however, have activities that can interfere with obtaining reliable DNA sequence information and they are limited to a small repertoire of substrates. We have used experimental methods from the fields of genetics, biochemistry and chemistry to identify mutant DNA polymerases and substrates that have advantageous properties for the development of new DNA sequencing methods.
Toward the $1,000 Genome: Molecular Engineering Approaches for DNA Sequencing by Synthesis
Jingyue Ju
Columbia University
DNA sequencing by synthesis (SBS) on a solid surface during polymerase reaction offers a new paradigm to decipher DNA sequences. We have developed such a novel DNA sequencing system using molecular engineering approaches. In this approach, four nucleotides (A, C, G, T) are modified as reversible terminators by attaching a cleavable fluorophore to the base and capping the 3'-OH group with a small reversible moiety so that they are still recognized by DNA polymerase as substrates. DNA templates consisting of homopolymer regions were accurately sequenced by using these new molecules on a DNA chip and a 4-color fluorescent scanner. This general strategy to rationally design cleavable fluorescent nucleotide reversible terminators for DNA sequencing by synthesis has the potential to achieve the $1000 genome paradigm for personalized medicine.
Single Molecule DNA Sequencing by Cyclic Synthesis
Ido Braslavsky
Ohio University
In recent years, single molecule DNA sequencing by cyclic synthesis has been developed from the demonstration stage to a working system with high throughput sequencing capacity. Using this system, fluorescence microscopy is applied to individually monitor tens of millions of immobilized DNA molecules for incorporation of labeled nucleotides. This process yields read length with sufficient sequence information to allow reliable and unique alignment of most tested fragments to a reference sequence, supporting amplification free, fast and chip resequencing method. In this presentation, different aspects of single molecule DNA sequencing by cyclic synthesis will be discussed.