ReviewInternational journal of molecular sciences2017
Computational Methods for Modeling Aptamers and Designing Riboswitches.
Review in International journal of molecular sciences, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- RNA structure: implications in viral infections and neurodegenerative diseases.Advanced biotechnology · 2024Review
- T7 phage-assisted evolution of riboswitches using error-prone replication and dual selection.Scientific reports · 2024Article
- Advances in Synthetic-Biology-Based Whole-Cell Biosensors: Principles, Genetic Modules, and Applications in Food Safety.International journal of molecular sciences · 2023Review
- The assessment of molecular dynamics results of three-dimensional RNA aptamer structure prediction.PloS one · 2023Article
- Successes and Failures of Static Aptamer-Target 3D Docking Models.International journal of molecular sciences · 2022Review
- Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation.Nucleic acids research · 2022Article
- Transcription complexes as RNA chaperones.Transcription · 2021Article
- Recent trends in biocatalysis.Chemical Society reviews · 2021Review
- Using sliding mode observers to estimateIET systems biology · 2020Article
- Methods and Applications of In Silico Aptamer Design and Modeling.International journal of molecular sciences · 2020Review
- Aptamers: a novel targeted theranostic platform for pancreatic ductal adenocarcinoma.Radiation oncology (London, England) · 2020Review
- Modeling a synthetic aptamer-based riboswitch biosensor sensitive to low hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) concentrations.PloS one · 2020Article
- Fluorometric determination of okadaic acid using a truncated aptamer.Mikrochimica acta · 2019Article
- Prediction of the secondary structure of short DNA aptamers.Biophysics and physicobiology · 2019Article
- Molecular Modeling Applied to Nucleic Acid-Based Molecule Development.Biomolecules · 2018Review
- Review
- Potential Inherent Stimulation of the Innate Immune System by Nucleic Acid Aptamers and Possible Corrective Approaches.Pharmaceuticals (Basel, Switzerland) · 2018Review
- Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA.Frontiers in microbiology · 2018Article
- Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools.Frontiers in genetics · 2017Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches, which are located within certain noncoding RNA region perform functions as genetic "switches", regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers. As structural changes in aptamers must be achieved within the certain time window for effective regulation, kinetics is another key point for understanding aptamer function in riboswitch-mediated gene regulation. The coarse-grained self-organized polymer (SOP) model using Langevin dynamics simulation has been successfully developed to investigate folding kinetics of aptamers, while their co-transcriptional folding kinetics can be modeled by the helix-based computational method and BarMap approach. Based on the known aptamers, the web server Riboswitch Calculator and other theoretical methods provide a new tool to design synthetic riboswitches. This review will represent an overview of these computational methods for modeling structure and kinetics of riboswitch aptamers and for designing riboswitches.
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