ArticleNature protocols2013
Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli.
Article in Nature protocols, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- Hfq-dependent artificial regulatory small RNAs for targeted gene expression control in the nitrogen-fixingSynthetic and systems biotechnology · 2026Article
- SUPER: Upcycling Genetic Parts for Precise Gene Expression Control, Leakage Minimization, and Genetic Circuit Stability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Tuning Ultrasensitivity in Genetic Logic Gates Using Antisense RNA Feedback.ACS synthetic biology · 2025Article
- Article
- Golden Gate Cloning of Expression Plasmids for Synthetic Small RNAs in Bacteria.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Small RNA MicF Represses ObgE and SeqA inMicroorganisms · 2024Article
- Article
- Beyond membrane permeability: A role for the small RNA MicF in regulation of chromosome replication and partitioning.bioRxiv : the preprint server for biology · 2024Article
- Model-guided metabolic rewiring to bypass pyruvate oxidation for pyruvate derivative synthesis by minimizing carbon loss.mSystems · 2024Article
- A coarse-grained bacterial cell model for resource-aware analysis and design of synthetic gene circuits.Nature communications · 2024Article
- Advances and applications of CRISPR/Cas-mediated interference inEngineering microbiology · 2024Review
- CRISPR-dCas13a system for programmable small RNAs and polycistronic mRNA repression in bacteria.Nucleic acids research · 2024Article
- Gene knockdown by structure defined single-stem loop small non-coding RNAs with programmable regulatory activities.Synthetic and systems biotechnology · 2023Article
- Design of artificial small regulatorySynthetic and systems biotechnology · 2023Article
- Systems metabolic engineering of Escherichia coli for hyper-production of 5‑aminolevulinic acid.Biotechnology for biofuels and bioproducts · 2023Article
- An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria.ACS synthetic biology · 2022Article
- A programmable encapsulation system improves delivery of therapeutic bacteria in mice.Nature biotechnology · 2022Article
- Post-transcriptional control of bacterial nitrogen metabolism by regulatory noncoding RNAs.World journal of microbiology & biotechnology · 2022Review
- Synthetic fused sRNA for the simultaneous repression of multiple genes.Applied microbiology and biotechnology · 2022Article
- Harnessing plasmid replication mechanism to enable dynamic control of gene copy in bacteria.Metabolic engineering · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene knockout experiments are often essential in functional genomics and metabolic engineering studies. However, repeated multiple gene knockout experiments are laborious, time consuming and sometimes impossible to perform for those genes that are essential for cell function. Small regulatory RNAs (sRNAs) are short noncoding RNAs in prokaryotes that can finely control the expression of target genes in trans at the post-transcriptional level. Here we describe the protocol for synthetic sRNA-based gene expression control, including sRNA design principles. Customized synthetic sRNAs consist of a scaffold and a target-binding sequence, and they can be created by simply replacing an existing target-binding sequence with one that is complementary to the target mRNA to be repressed, while retaining the scaffold. Our plasmid-based synthetic sRNA system does not require chromosomal modifications, and it enables one to perform high-throughput studies on the effects of knockdowns on host cell physiology, and it further allows the simultaneous screening of target genes in different Escherichia coli strains for applications in metabolic engineering and synthetic biology. Once an sRNA scaffold-harboring plasmid is constructed, customized synthetic sRNAs can be made within 3-4 d; after this time, the synthetic sRNAs can be applied to the desired experiments.
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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.