Encoding and processing information in DNA-, RNA- and other biomolecule-based devices is an important requirement for DNA-based computing with potentially important applications. Recent experimental and theoretical advances have produced and tested new methods to obtain large code sets of oligonucleotides to support virtually any kind of application. We report results of a tour de force to conduct an exhaustive search to produce code sets that are arguably of sizes comparable to that of maximal sets while guaranteeing high quality, as measured by the minimum Gibbs energy between any pair of code words and other criteria. The method is constructive and directly produces the actual composition of the sets, unlike their counterpart in vitro . The sequences allow a quantitative characterization of their composition. We also present a new technique to generate code sets with desirable more stringent constraints on their possible interaction under a variety of conditions, as measured by Gibbs energies of duplex formation. The results predict close agreement with known results in vitro for 20–mers. Consequences of these results are bounds on the capacity of DNA for information storage and processing in wet tubes for a given oligo length, as well as many other applications where specific and complex self-directed assembly of large number of components may be required. Keywords: Word design, encoding data on DNA, Gibbs energy, fault-tolerant DNA computing, maximal code sets, complex DNA self-assembly, shuffle codes.
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