This paper discusses how multi-step Polymerase Chain Reaction (PCR) along with the DNA molecule can be used to construct a practical non-deterministic finite state automaton. It explores the problems that are encountered when constructing a nanotechnology computer based on molecular biology and develops a methodology for computing symbols giving full consideration to the melting temperature of oligonucleotides. This research expands the power of PCR that until now has been limited to detecting simple sequences and could not recognize a regular expression and therefore could not approximate the function of mRNA when coding a protein from a gene sequence. This result has tremendous potential for impacting the fields of computational biology, bioinformatics and genomics by potentially allowing computing and genetic sequence recognition to be done in vitro without need for conventional genetic sequencing or computer resources. This powerful technique may lead to new methods for drug development, disease diagnosis and treatment.
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