Sequencing by Recognition

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We will explore a new approach to DNA "sequencing by recognition" in nanopores. It is based on a recent report of chemical recognition of the DNA bases via enhanced electron-tunneling when Watson-Crick hydrogen bonded base pairs form between a base-functionalized probe and a base on the DNA to be read. This mechanism is confirmed by preliminary experiments reported in this application. When combined with a nanopore-DNA translocation system that presents each base sequentially to the electronic sensor, it appears that at least 108 bases per day could be read with continuous sequence runs of at least 80,000 bases. The single molecule base-calling accuracy might approach 99%, in which case an array of 10,000 nanopores would yield the required 99.99% accuracy. In order to establish the plausibility of this approach, two key issues need to be resolved. (a) Can flexible `molecular wires' bridge the gap between sensing electrodes and the target attachment sites on the DNA to be sequenced? These wires must reach from one electrode to a phosphate, and from another electrode to a base, be flexible enough to form bonds at the same time as being highly conductive. (b) Is the conductance of the whole assembly (metal-linker-phosphate-sugar-base-base-linker- metal) large enough to produce an acceptable single-molecule base calling accuracy? We propose to design and synthesize a number of `molecular wires' as candidate linkers and measure their single-molecule conductance, comparing our data to the results of first-principles simulations. Once suitable linkers are found, we propose to measure the conductance of the entire system, and the statistical distribution of these conductances. We will also develop a multi-scale simulation of the entire system, to help us optimize the design of a real instrument. We will collaborate with the Timp Laboratory (University of Illinois, Urbana- Champaign) in order to tie our designs to the materials constraints of the solid state nanopores being developed there.