SHF:Medium:Collaborative Research: From Molecules to Complex Shapes: Programming Pattern Formation with DNA

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Development in humans and other higher organisms creates complex,precisely defined multicellular structures and patterns. Thesestructures are the result of molecular programs that are stored in thesequences and concentrations of biomolecules and are executed whenmolecules interact and change state through chemical reactions. Thegoal of this proposal is to understand how biochemical systems can bereliably programmed to form asymmetric patterns with multiple layersof organization. This proposal is part of a general goal to understandhow to program global behavior and structure based on local rules,which a key intellectual challenge in many areas of computer science. The PIs propose that complex, hierarchical chemical patterns can be formedby systems in which the molecules collectively execute a molecularprogram for pattern formation. The PIs will develop achemical programming language in which information from simple inputpatterns is integrated by logical operations to form new patternregions. These logical operations are then systematically integratedinto larger programs, allowing the generation of patterns withcomplex, multiscale structure similar to that seen inbiology. Designed synthetic DNA molecules that together act as circuitelements will be used to implement this language. DNA molecules areideal substrates for a molecular programming approach because theyhave complex sequences with predictable behaviors and interactions.This research is tightly integrated with an outreach program that will develop an educational program dedicated to teaching theinterdisciplinary skills that are necessary to be successful inmolecular programming.