A programmable NOR-based device for transcription profile analysis

Abstract

An autonomous synthetic programmable device that can diagnose a cell's state according to predefined markers and produce a corresponding therapeutic output may be the basis of future programmable drugs. Motivated to increase diagnosis precision, devices that integrate multiple disease markers have been implemented based on various molecular tools. As simplicity is key to future in-vivo applications, we sought a molecular device that a) integrates multiple inputs without requiring pairwise interactions, and b) harnesses only mechanisms that cells natively use. Here we show a synthetic NOR-based programmable device, operating via a biochemical obstructing approach rather than on a constructive approach, capable of differentiating between prokaryotic cell strains based on their unique expression profile. To demonstrate our system's strengths we further implemented the NOT, OR and AND gates. The device's programmability allows context-dependent selection of the inputs being sensed, and of the expressed output, thus, holding great promise in future biomedical applications.

Synthetic Biology Platform for Sensing and Integrating Endogenous Transcriptional Inputs in Mammalian Cells

“…The amplified sensors were able to trigger efficient multipronged biological actuation in the form of RNAi, transactivation, and site-specific recombination. These sensing and transduction capabilities fill the missing link between endogenous transcriptional activities and previously established strategies to implement transcriptional logic ( Hansen et al., 2014 , Khalil et al., 2012 , Leisner et al., 2010 , Ran et al., 2012 ), and they will facilitate construction of logic circuits of increasing complexity. Logic gates between arbitrary TFs could enable specific cell targeting based on complex transcriptional profiles, further contributing to the ongoing effort toward improving tissue- and lineage-specific transgene expression in mammalian cells, with applications in basic research ( Halpern et al., 2008 ) and gene therapy ( Busskamp et al., 2010 ).…”

Role of Density Functional Theory in “Ribocomputing Devices”

“…RNAs use the concentrations of specific chemical species as signals to implement the functions of logic to build up the network of multiple layers Boolean networks. Then these molecular computers were able to operate and communicate directly in a biological environment [45,46] or work inside a living cell [47]. A plasmid with a specifically encoded DNA was inserted and external program was used to control the computation inside the host cell.…”

“…The logical output is the release of ssDNA with modulation of gene expression, defined by the two states "positive and negative" [12]. An RNAi logical evaluator has also been used to perform Boolean operations for human kidney cells [47] and intracellular device in single mammalian cell.…”

The Biological Microprocessor, or How to Build a Computer With Biological Parts

“…DNA based logic gates: One strategy for engineering a logic gate in vivo is to build a core machinery, based on gene expression regulation [ 123 ] [ 124 ] [ 125 ] [ 126 ] [ 127 ] [ 128 ] [ 129 ]. One such system had two inputs such as beta-D-thiogalactopyranoside and anhydrotetracycline (aTC) and a fluorescent protein as output [ 73 ].…”