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

人类和其他高等生物的发育创造了复杂的、精确定义的多细胞结构和模式。这些结构是存储在生物分子序列和浓度中的分子程序的结果，并在分子相互作用和通过化学反应改变状态时执行。本提案的目标是了解生化系统如何能够可靠地编程形成具有多层组织的不对称模式。该建议是理解如何基于局部规则编程全局行为和结构的总体目标的一部分，这是计算机科学许多领域的关键智力挑战。PI提出，复杂的、分层的化学模式可以由分子共同执行模式形成的分子程序的系统形成。PI将开发化学编程语言，其中来自简单输入模式的信息通过逻辑运算集成，形成新的模式区域。然后，这些逻辑操作被系统地整合到更大的程序中，从而产生类似于生物学中所见的复杂、多尺度结构的模式。设计的合成DNA分子一起充当电路元件，将用于实现这种语言。DNA分子是分子编程方法的理想底物，因为它们具有可预测的行为和相互作用的复杂序列。这项研究与一个拓展项目紧密结合，该项目将开发一个教育项目，致力于教授成功进行分子编程所必需的跨学科技能。

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 PI's propose that complex, hierarchical chemical patterns can be formedby systems in which the molecules collectively execute a molecularprogram for pattern formation. The PI's 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.,