Molecular Codebreaking and Double Encoding

We have evaluated the practical feasibility of implementing part of a molecular codebreaker, a DNA computer that uses a known-plaintext attack to recover an encryption key. Molecular biology techniques such as ligation, gel electrophoresis, polymerase chain reaction (PCR), and graduated PCR were found to be feasible but currently have some limitations such as error accumulation. A so-called “error resistance technique” of double encoding, where bits are encoded twice in a DNA strand, was also designed and attempted. Although the double encoding implementation was not completely successful, several important issues associated with using ligation for double encoding were identified, such as encoding adaptation problems, strand generation penalties, strand length increases, and the possibility that double encoding may not reduce the number of false