ITR: Information Technology for Self-Assembling Synthetic Genes

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It is often desirable to produce a synthetic gene that encodes a protein of interest and is optimized for desirable sequence properties, such as good translation kinetics for folding and expression in a target organism. However, most genes are far longer than the limits of accurate DNA synthesis. Thus, the rapid creation of tailored genes has not been convenient. As preliminary results we have developed a method for the computational optimization of DNA sequences that encode their own correct self-assembly. Scores of short overlapping synthetic oligonucleotides are designed to hybridize correctly with great efficiency at a high temperature, while all competing nonproductive hybridization events are identified and disfavored. Sequence properties are optimized using a formal heuristic search. Based on these preliminary results this project is developing novel methods in information technology and biotechnology for the self-assembly of long strings of mixed coding, regulatory, and intergenic regions. The DNA constructs that result may be hybridized into any plasmid expression vector and transformed into cells, or used directly as DNA templates to produce proteins in coupled in vitro transcription-translation systems. The new methods will be accurate, enzyme-free, in solution, single step, scalable, and high-throughput. They will have relevance to large-scale, high-throughput crystallization and proteomics efforts and enable the facile creation of synthetic genomes.