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Design of Ribocomputing Devices for Complex Cellular Logic.
Methods Mol Biol
June 2022
Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute, and the School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
The ability to control cell function is a critical goal for synthetic biology and motivates the development of ever-improving methods for precise regulation of gene expression. RNA-based systems represent powerful tools for this purpose since they can take full advantage of the predictable and programmable base pairing properties of RNA to control gene expression. This chapter is focused on the computational design of RNA-only biological circuits that can execute complex Boolean logic expressions in living cells.
View Article and Find Full Text PDFCellular Computational Logic Using Toehold Switches.
Int J Mol Sci
April 2022
Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-ro, Pohang 37673, Gyeongbuk, Korea.
The development of computational logic that carries programmable and predictable features is one of the key requirements for next-generation synthetic biological devices. Despite considerable progress, the construction of synthetic biological arithmetic logic units presents numerous challenges. In this paper, utilizing the unique advantages of RNA molecules in building complex logic circuits in the cellular environment, we demonstrate the RNA-only bitwise logical operation of XOR gates and basic arithmetic operations, including a half adder, a half subtractor, and a Feynman gate, in .
View Article and Find Full Text PDFProbing the operability regime of an engineered ribocomputing unit in terms of dynamic range maintenance with extracellular changes and time.
J Biol Eng
March 2020
1Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980 Paterna, Valencia Spain.
Synthetic biology aims at engineering gene regulatory circuits to end with cells (re)programmed on purpose to implement novel functions or discover natural behaviors. However, one overlooked question is whether the resulting circuits perform as intended in variety of environments or with time. Here, we considered a recently engineered genetic system that allows programming the cell to work as a minimal computer (arithmetic logic unit) in order to analyze its operability regime.
View Article and Find Full Text PDFRibocomputing: Cellular Logic Computation Using RNA Devices.
Biochemistry
February 2018
Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States.
Complex cellular logic computation using ribocomputing devices.
Nature
August 2017
Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.
Synthetic biology aims to develop engineering-driven approaches to the programming of cellular functions that could yield transformative technologies. Synthetic gene circuits that combine DNA, protein, and RNA components have demonstrated a range of functions such as bistability, oscillation, feedback, and logic capabilities. However, it remains challenging to scale up these circuits owing to the limited number of designable, orthogonal, high-performance parts, the empirical and often tedious composition rules, and the requirements for substantial resources for encoding and operation.
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