A first step toward the development of a method to sequence a single DNA molecule in real-time is proposed. Engineering a polymerase to act as a direct molecular sensor of DNA base identity, coupled with the synthesis of appropriately modified nucleotides, allows us to create the fastest enzymatic DNA sequencing system possible. Our motivation for developing a single-molecule sequencing approach includes eliminating the intermediate steps currently necessary for determining DNA sequence information, thereby meeting the needs of both the genomics and the medical diagnostics communities. We outline a series of milestones towards our ultimate goal of a single-molecule DNA sequencing system. However, only two of these intermediate goals are the specific aims of the proposed research. In particular, we propose to synthesize an appropriately modified nucleotide and to determine the relative efficiency at which commercially available DNA polymerases use this modified nucleotide to extend a DNA strand.
Development of a single-molecule sequencing system is generally applicable for DNA diagnostics. Furthermore, parallel processing of samples will allow a genome to be sequence in a day or less, and will be important for pathogen identification and large-scale, comprehensive genome analysis. This system eliminates sequencing reaction processing, gel or capillary loading, and electrophoresis, promising huge savings in time, labor, and cost per base. This single-molecule DNA sequencing system is expected to replace current DNA sequencing technology.
