ArticlePLoS computational biology2013
Full design automation of multi-state RNA devices to program gene expression using energy-based optimization.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed, 33 citations in OpenAlex.
- Multiplexable and Biocomputational Virus Detection by CRISPR-Cas9-Mediated Strand Displacement.Analytical chemistry · 2023Article
- Engineering a Circular Riboregulator inBiodesign research · 2020Article
- Automated Design of Diverse Stand-Alone Riboswitches.ACS synthetic biology · 2019Article
- Model-based design of RNA hybridization networks implemented in living cells.Nucleic acids research · 2017Article
- Ribo-attenuators: novel elements for reliable and modular riboswitch engineering.Scientific reports · 2017Article
- A versatile framework for microbial engineering using synthetic non-coding RNAs.Nature reviews. Microbiology · 2014Review
- Regulatory RNAs: charming gene management styles for synthetic biology applications.RNA biology · 2013Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small RNAs (sRNAs) can operate as regulatory agents to control protein expression by interaction with the 5' untranslated region of the mRNA. We have developed a physicochemical framework, relying on base pair interaction energies, to design multi-state sRNA devices by solving an optimization problem with an objective function accounting for the stability of the transition and final intermolecular states. Contrary to the analysis of the reaction kinetics of an ensemble of sRNAs, we solve the inverse problem of finding sequences satisfying targeted reactions. We show here that our objective function correlates well with measured riboregulatory activity of a set of mutants. This has enabled the application of the methodology for an extended design of RNA devices with specified behavior, assuming different molecular interaction models based on Watson-Crick interaction. We designed several YES, NOT, AND, and OR logic gates, including the design of combinatorial riboregulators. In sum, our de novo approach provides a new paradigm in synthetic biology to design molecular interaction mechanisms facilitating future high-throughput functional sRNA design.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.