Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector-Quantization

The main theme of this paper is to take inspiration from methods used in computer science and related disciplines, and to apply these to develop improved biotechnology. In particular, our proposed improvements are made by adapting various information theoretic coding techniques which originate in computational and information processing disciplines, but which we re-tailor to work in the biotechnology context. (a) We apply Error-Correcting Codes, developed to correct transmission errors in electronic media, to decrease (in certain contexts, optimally) error rates in optically-addressed DNA synthesis (e.g., of DNA chips). (b) We apply Vector-Quantization (VQ) Coding techniques (which were previously used to cluster, quantize, and compress data such as speech and images) to improve I/O rates (in certain contexts, optimally) for transformation of electronic data to and from DNA with bounded error. (c) We also apply VQ Coding techniques, some of which hierarchically cluster the data, to improve associative search in DNA databases by reducing the problem to that of exact aanity separation. These improvements in biotechnology appear to have some general applicability beyond biomolecular computing. As a motivating example, this paper improves biotechnology methods to do associative search in DNA databases. Baum B95] previously proposed the use of biotechnology aanity methods (DNA annealing) to do massively parallel associative search in large databases encoded as DNA strands, but many remaining issues were not developed. Using in part our improved biotechnology techniques based on Error-Correction and VQ Coding, we develop detailed procedures for the following tasks: (i) The database may initially be in conventional (electronic, magnetic, or optical) media, rather than the form of DNA strands. For input and output (I/O) to and from conventional media, we apply DNA chip technology improved by Error-Correction and VQ Coding methods for error-correction and compression. ? A postscript version of this paper is at URL (ii) The query may not be an exact match or even partial match with any data in the database, but since DNA annealing aanity methods work best for these cases, we apply various VQ Coding methods for reening the associative search to exact matches. (iii) We also brieey discuss how to extend associative search queries in DNA databases to more sophisticated hybrid queries that include also Boolean formula conditionals with a bounded number of Boolean variables , by combining our methods for DNA associative search with known BMC methods for solving small size SAT problems. For example, these extended queries could …