Foundational Aspects of Biomolecular Information and Computation

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In the same way we use the letters of the alphabet to write text, and the bits 0 and 1 to write computer machine code, the four basic DNA units (Adenine, Guanine, Cytosine, Thymine) are used by Nature to write genetic information as DNA strands. The possibility of encoding symbolic information on DNA, and the fact that biochemical processes such as cut-and-paste of DNA strands have been proved to be able to perform arithmetic and logic operations, led to the development of the field of DNA computing. The primary goal of my research is to analyze this new way of storing and manipulating data on DNA strands, as bioinformation and biocomputation are fundamentally different from their electronic counterparts in several aspects. Most importantly, DNA-encoded information is not associated with a memory location but consists of infinitesimal free-floating DNA strands that interact with each other due to their Watson-Crick complementarity. This proposal aims to develop the foundations for a "theory of bioinformation and biocomputation", by defining and investigating formal-language-theoretic models of DNA-based information and bio-operations, that take into account the intrinsic characteristics of their biological substrates. Besides expanding the traditional notions of information and computation to account for computation taking place in nature, the results of this research could provide insights into the computational properties of biomolecular information and consequently have potential implications for their practical applications in, e.g., multi-input RNA-based logic circuits for medical diagnosis, or building DNA nanostructures for nanoelectronic and nano-optical devices. Another aspect of the proposed research is an exploration of the paradigm of nanocomputation by self-assembly by investigating the power and limitations of models of computational self-assembly systems with DNA tiles. The results of this research could have potential implications for the design, evaluation, and analysis of DNA architectures for bionanotechnology.