Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, Montpellier, France.
Department of Biology, University of Washington, Seattle, WA, USA.
Methods Mol Biol. 2021;2189:31-43. doi: 10.1007/978-1-0716-0822-7_3.
Synthetic biology aims at engineering new biological systems and functions that can be used to provide new technological solutions to worldwide challenges. Detection and processing of multiple signals are crucial for many synthetic biology applications. A variety of logic circuits operating in living cells have been implemented. One particular class of logic circuits uses site-specific recombinases mediating specific DNA inversion or excision. Recombinase logic offers many interesting features, including single-layer architectures, memory, low metabolic footprint, and portability in many species. Here, we present two automated design strategies for recombinase-based logic circuits, one based on the distribution of computation within a multicellular consortia and the other one being a single-cell design. The two design strategies are complementary and are both adapted for none expert as a design web-interface exits for each strategy, the CALIN and RECOMBINATOR web-interface for respectively the multicellular and single-cell design strategy. In this book chapter, we are guiding the reader step by step through recombinase-logic circuit design from selecting the design strategy fitting to his/her final system of interest to obtaining the final design using one of our design web-interface.
合成生物学旨在设计新的生物系统和功能，这些系统和功能可用于为全球挑战提供新的技术解决方案。 多种信号的检测和处理对于许多合成生物学应用至关重要。 已经实现了在活细胞中运行的各种逻辑电路。 一类特殊的逻辑电路使用介导特定 DNA 反转或切除的位点特异性重组酶。 重组酶逻辑具有许多有趣的特征，包括单层架构、记忆、低代谢足迹和在许多物种中的可移植性。 在这里，我们提出了两种基于重组酶的逻辑电路的自动化设计策略，一种基于多细胞联合体中的计算分布，另一种是单细胞设计。 这两种设计策略是互补的，都适合非专家作为设计网页界面，两种策略都有各自的设计网页界面，CALIN 和 RECOMBINATOR 网页界面分别用于多细胞和单细胞设计策略。 在这一章中，我们将引导读者逐步完成从选择适合其感兴趣的最终系统的设计策略到使用我们的设计网页界面之一获得最终设计的重组酶逻辑电路设计。
