Digital protein sequencing with one binary measurement per residue
Conventional protein sequencing methods and recently reported theoretical and experimental single molecule methods are based on analog measurements. Here a digital method for use in the bulk or with a small number of molecules is introduced. It is based on the superspecificity property of transfer RNAs (tRNAs) and requires only one binary measurement per residue/amino acid (AA). When the terminal residues of 20 copies of a protein molecule are cleaved and each brought together with a different tRNA in one of 20 different cavities, tRNA-AA binding occurs in exactly one cavity. The bound AA is chemically separated from the tRNA into a channel where its presence can be detected electrically or optically. The result is a binary high output from the cognate channel that is independent of the AA, the other 19 outputs are low, and the AA's identity is given by the position of the high bit in the 20-bit output. One way to detect the freed AA is to translocate it through a nanopore in an electrolytic cell under electrophoresis. A feasibility and accuracy analysis and related computations and simulation results are presented.