A systematic and extensible approach to DNA primer design for whole gene synthesis

Abstract

The future of synthetic biology research hinges upon the development of accurate and inexpensive whole gene synthesis technologies. Recent advances in the purification of solid-phase manufactured oligonucleotides make it possible to manufacture whole genes by polymerase chain reaction methods. Yet, despite the improvement in laboratory methods, whole gene synthesis is not rapidly progressing because most gene design software takes an excessively naive approach to the complex problem of designing component oligonucleotides for whole gene synthesis. The synthetic biology community needs a flexible, robust and optimal primer design tool. We present the software design for a tool which designs oligonucleotides that are compatible with a wide variety of oligo purification and whole gene assembly protocols. Our design strategy uses physical sequence feature identification, optimal artificial intelligence search techniques, and sequence optimisation via intelligent codon substitution to produce near-optimal oligonucleotide arrays. We address all aspects of the oligonucleotide design problem, from physical constraints to the computational overhead involved in searching for an optimal solution, and provide an extensive set of data structures and algorithms.