ArticleRNA (New York, N.Y.)2001
Design of multistable RNA molecules.
Article in RNA (New York, N.Y.), 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- Designing molecular RNA switches with Restricted Boltzmann machines.Nature communications · 2025Article
- Tiny but multi-stable: four distinct conformational states govern the ligand-free state of the preQ1 riboswitch from a thermophilic bacterium.Nucleic acids research · 2025Article
- Sequence Design for RNA-RNA Interactions.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Classified Dynamic Programming in RNA Structure Analysis.Methods in molecular biology (Clifton, N.J.) · 2024Article
- AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures.Bioinformatics (Oxford, England) · 2023Article
- DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model.Bioinformatics (Oxford, England) · 2023Article
- Modelling ribosome kinetics and translational control on dynamic mRNA.PLoS computational biology · 2023Article
- The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements.Nucleic acids research · 2021Article
- A Mathematical Analysis of HDV Genotypes: From Molecules to Cells.Mathematics (Basel, Switzerland) · 2021Article
- The energy-spectrum of bicompatible sequences.Algorithms for molecular biology : AMB · 2021Article
- Simulation of Folding Kinetics for Aligned RNAs.Genes · 2021Article
- Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model.Bioinformatics (Oxford, England) · 2020Article
- Automated Design of Diverse Stand-Alone Riboswitches.ACS synthetic biology · 2019Article
- Pairwise visual comparison of small RNA secondary structures with base pair probabilities.BMC bioinformatics · 2019Article
- Fixed-parameter tractable sampling for RNA design with multiple target structures.BMC bioinformatics · 2019Article
- Effects of Preferential Counterion Interactions on the Specificity of RNA Folding.The journal of physical chemistry letters · 2018Article
- RNAblueprint: flexible multiple target nucleic acid sequence design.Bioinformatics (Oxford, England) · 2017Article
- Design of Artificial Riboswitches as Biosensors.Sensors (Basel, Switzerland) · 2017Review
- Efficient approximations of RNA kinetics landscape using non-redundant sampling.Bioinformatics (Oxford, England) · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We show that the problem of designing RNA sequences that can fold into multiple stable secondary structures can be transformed into a combinatorial optimization problem that can be solved by means of simple heuristics. Hence it is feasible to design RNA switches with prescribed structural alternatives. We discuss the theoretical background and present an efficient tool that allows the design of various types of switches. We argue that both the general properties of the sequence structure map of RNA secondary structures and the ease with which our design tool finds bistable RNAs strongly indicates that RNA switches are easily accessible in evolution. Thus conformational switches are yet another function for which RNA can be employed.
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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.