Showing papers by "Ron Weiss published in 2002"

Directed evolution of a genetic circuit

Abstract: The construction of artificial networks of transcriptional control elements in living cells represents a new frontier for biological engineering. However, biological circuit engineers will have to confront their inability to predict the precise behavior of even the most simple synthetic networks, a serious shortcoming and challenge for the design and construction of more sophisticated genetic circuitry in the future. We propose a combined rational and evolutionary design strategy for constructing genetic regulatory circuits, an approach that allows the engineer to fine-tune the biochemical parameters of the networks experimentally in vivo. By applying directed evolution to genes comprising a simple genetic circuit, we demonstrate that a nonfunctional circuit containing improperly matched components can evolve rapidly into a functional one. In the process, we generated a library of genetic devices with a range of behaviors that can be used to construct more complex circuits.

Toward in vivo Digital Circuits

Abstract: We propose a mapping from digital logic circuits into genetic regulatory networks with the following property: the chemical activity of such a genetic network in vivo implements the computation specified by the corresponding digital circuit. Logic signals are represented by the synthesis rates of cytoplasmic DNA binding proteins. Gates consist of structural genes for output proteins, fused to promoter/operator regions that are regulated by input proteins. The modular approach for building gates allows a free choice of signal proteins and thus enables the construction of complex circuits. This paper presents simulation results that demonstrate the feasibility of this approach. Furthermore, a technique for measuring gate input/output characteristics is introduced. We will use this technique to evaluate gates constructed in our laboratory. Finally, this paper outlines automated logic design and presents BioSpice, a prototype system for the design and verification of genetic digital circuits.

Engineering Signal Processing in Cells: Towards Molecular Concentration Band Detection

Abstract: We seek to couple protein-ligand interactions with synthetic gene networks in order to equip cells with the ability to process internal and environmental information in novel ways. In this paper, we propose and analyze a new genetic signal processing circuit that can be configured to detect various chemical concentration ranges of ligand molecules. These molecules freely diffuse from the environment into the cell. The circuit detects acyl-homoserine lactone ligand molecules, determines if the molecular concentration falls within two prespecified thresholds, and reports the outcome with a fluorescent protein. In the analysis of the circuit and the description of preliminary experimental results, we demonstrate how to adjust the concentration band thresholds by altering the kinetic properties of specific genetic elements, such as ribosome binding site efficiencies or dna-binding protein affinities to their operators.