  Biomolecular computation has emerged as an important area of computer science
research due to its high information density, immense parallelism opportunity
along with potential applications in cryptography, genetic engineering and
bioinformatics. Computational frameworks using DNA molecules have been proposed
in the literature to accomplish varied tasks such as simulating logical
operations, performing matrix multiplication, and encoding instances of NP-hard
problems. In one of the key applications, several studies have proposed
construction of finite automata using DNA hybridisation and ligation. The state
and symbol encoding of these finite automata are done manually. In this
manuscript, we study the codeword construction problem for this approach. We
derive exact theoretical bounds on the number of symbols and states in the
finite automata and also obtain the complete set of symbols in a specific case.
For automatic encoding, two different solutions, based on a heuristic and on
Integer Linear Programming (ILP), are proposed. Furthermore, we propose an
early simulation-based validation of laboratory experiments. Our proposed flow
accepts a finite automaton, automatically encodes the symbols for the actual
experiments and executes the simulation step-by-step.
