Simulations of DNA Computing with In Vitro Selection

An attractive feature of DNA-based computers is the large number of possible sequences (4n) of a given length n with which to represent information. The problem, however, is that any given sequence is not necessarily independent of the other sequences, and thus, reactions among them can interfere with the reliability and efficiency of the computation. Independent sequences might be manufactured in the test tube using evolutionary methods. To this end, an in vitro selection has been developed that selects maximally mismatched DNA sequences. In order to understand the behavior of the protocol, a computer simulation of the protocol was done, results of which showed that Watson-Crick pairs of independent oligonucleotides were preferentially selected. In addition, to explore the computational capability of the selection protocol, a design is presented that generates the Fibonacci sequence of numbers.