Sequencing by Recognition

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DESCRIPTION (provided by applicant): Hydrogen-bond mediated electron tunneling yields a high-contrast signal of the base composition of single-stranded DNA, enough so that a small number of repeated reads can yield an error rate smaller than one part in 10,000. We seek to combine hydrogen-bond mediated molecular recognition with DNA translocation through a nanopore to present each base to a recognition reader in turn. Such a sequence reader could read genomic DNA at a speed of hundreds to thousands of bases per second, do so with high accuracy with a limited number of repeated reads and read sequence lengths of 100,000 bases (or possibly more) in one continuous read. In this proposal, we address three key issues: (1) Can we replicate the mechanical flexibility and precision of a scanning tunneling microscope (STM) on a chip, so that we can duplicate the high contrast, high accuracy chemical recognition previously achieved with an STM? (2) Can we align such a reading head with a nanopore so as to read the sequence of translocating DNA? (3) Can we design and synthesize "base-readers" that are better than the native bases at recognizing their molecular targets? We will also examine other issues, such as the role of secondary structure in translocation, and the juxtaposition of data from different reading heads. We have assembled an exemplary team with skills in nanofabrication, molecular electronics and DNA chemistry. We will: (1) Fabricate tunneling gaps on membranes that permit atomic-scale inspection, optimizing the gap fabrication and chemical functionalization for recognition of nucleoside monophosphates and DNA dimers. (2) Use a novel electrodeposition process to align gaps of optimal geometry with nanopores. (3) Study translocation of long DNA molecules through these gaps using magnetic beads both for manipulation and position read-out. (4) Design and synthesize new types of "base-reader". We will make these base-reading reagents available to the community to facilitate exploration of other types of nanoscale readout. We aim to demonstrate a prototype instrument within five years, laying the groundwork for the design and manufacture of a viable commercial instrument. PROJECT HEALTH RELEVANCE In this proposal we plan to develop an instrument based on "Sequencing by Recognition" an approach whose feasibility has now been demonstrated. The ability to read long runs of DNA rapidly is essential to lower the cost of both de novo sequencing and resequencing Facile resequencing is a pre-requisite for the widescale availability of personalized medicine with implications such as better planning of healthcare delivery, more appropriate preventative medicine and better targeting of drugs.