Towards DNA Sequencing Chips

DNA sequencing is an important technology for the determination of the sequences of nucleotides that make up a given DNA fragment. In view of the limitations of current sequencing technology, it would be advantageous to have a DNA sequencing method that provides the sequences of long DNA fragments and is amenable to automation. Sequencing by Hybridization (SBH) is a challenging alternative to the classical sequencing methods. The basic approach is to build an array (Sequencing Chip) of short DNA fragments of lenght I and to use biochemical methods for finding all substrings of lenght l of an unknown DNA fragment. Combinatorial algorithms are then used to reconstruct the sequence of the fragment from the l-tuple composition. In this article we review biochemical, mathematical, and technological aspects of SBH and present a new sequencing chip design which might allow significant chip miniaturization without loss of the resolution of the method. 1 I n t r o d u c t i o n DNA sequencing is an important technology for the determination of the sequences of nucleotides (referred to as A, C, G, T) that make up a given DNA fragment. Using current sequencing technologies the most proficient laboratories can today sequence 25,000-125,000 nucleotides per person per year at a cost of several dollars per nucleotide. One of the goals set out by the Human Genome Project is to increase the sequencing rate by an order of magnitude and reduce the cost by an order of magnitude. Significant strides have been made in improving existing technologies using automation and incremental improvements to the instruments, however a tenfold increase in throughput will probably require an entirely new technology. Sequencing by Hybridization (SBH) is a new approach to DNA sequencing proposed simultaneously and independently by Drmanac and Crkvenjakov,1987 [5], Bains and Smith,1988 [2], Lysov et a1,1988 [16], Southern,1988 [24] and Macevicz,1989 [17]. Sequencing by hybridization relies on the following biochemical phenomenon. Given a short (8-30 nucleotides) piece of DNA, called an oligonucleotide or a probe, and a single-stranded target DNA fragment; the probe will bind (hybridize) * The research was supported in part by the National Science Foundation under the grant CCR-9308567 and by the National Institutes of Health under the grant 1R01 HG00987-01 ** The research was supported in part by the National Institutes of Health under the grant HG-00813 and by the Department of Energy under the grant DE-FG03-92-ER81275