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Trends in Biotechnology May 2024RNA switches respond to specific ligands to control gene expression. They are widely used in synthetic biology applications and hold potential for future RNA-based... (Review)
Review
RNA switches respond to specific ligands to control gene expression. They are widely used in synthetic biology applications and hold potential for future RNA-based therapeutic breakthroughs. However, the crux is their precise design. Here, we will discuss how inverse-RNA-folding could be utilized for the accurate design of RNA switches.
Topics: Synthetic Biology; RNA; RNA Folding
PubMed: 38040620
DOI: 10.1016/j.tibtech.2023.11.005 -
Briefings in Bioinformatics Mar 2018Computational programs for predicting RNA sequences with desired folding properties have been extensively developed and expanded in the past several years. Given a... (Review)
Review
Computational programs for predicting RNA sequences with desired folding properties have been extensively developed and expanded in the past several years. Given a secondary structure, these programs aim to predict sequences that fold into a target minimum free energy secondary structure, while considering various constraints. This procedure is called inverse RNA folding. Inverse RNA folding has been traditionally used to design optimized RNAs with favorable properties, an application that is expected to grow considerably in the future in light of advances in the expanding new fields of synthetic biology and RNA nanostructures. Moreover, it was recently demonstrated that inverse RNA folding can successfully be used as a valuable preprocessing step in computational detection of novel noncoding RNAs. This review describes the most popular freeware programs that have been developed for such purposes, starting from RNAinverse that was devised when formulating the inverse RNA folding problem. The most recently published ones that consider RNA secondary structure as input are antaRNA, RNAiFold and incaRNAfbinv, each having different features that could be beneficial to specific biological problems in practice. The various programs also use distinct approaches, ranging from ant colony optimization to constraint programming, in addition to adaptive walk, simulated annealing and Boltzmann sampling. This review compares between the various programs and provides a simple description of the various possibilities that would benefit practitioners in selecting the most suitable program. It is geared for specific tasks requiring RNA design based on input secondary structure, with an outlook toward the future of RNA design programs.
Topics: Algorithms; Animals; Computational Biology; Humans; Models, Molecular; Nucleic Acid Conformation; RNA; RNA Folding; Software
PubMed: 28049135
DOI: 10.1093/bib/bbw120 -
Quarterly Reviews of Biophysics Aug 2013Nearly two decades after Westhof and Michel first proposed that RNA tetraloops may interact with distal helices, tetraloop–receptor interactions have been recognized... (Review)
Review
Nearly two decades after Westhof and Michel first proposed that RNA tetraloops may interact with distal helices, tetraloop–receptor interactions have been recognized as ubiquitous elements of RNA tertiary structure. The unique architecture of GNRA tetraloops (N=any nucleotide, R=purine) enables interaction with a variety of receptors, e.g., helical minor grooves and asymmetric internal loops. The most common example of the latter is the GAAA tetraloop–11 nt tetraloop receptor motif. Biophysical characterization of this motif provided evidence for the modularity of RNA structure, with applications spanning improved crystallization methods to RNA tectonics. In this review, we identify and compare types of GNRA tetraloop–receptor interactions. Then we explore the abundance of structural, kinetic, and thermodynamic information on the frequently occurring and most widely studied GAAA tetraloop–11 nt receptor motif. Studies of this interaction have revealed powerful paradigms for structural assembly of RNA, as well as providing new insights into the roles of cations, transition states and protein chaperones in RNA folding pathways. However, further research will clearly be necessary to characterize other tetraloop–receptor and long-range tertiary binding interactions in detail – an important milestone in the quantitative prediction of free energy landscapes for RNA folding.
Topics: Base Sequence; Kinetics; Nucleic Acid Conformation; Nucleotide Motifs; RNA; RNA Folding; Thermodynamics
PubMed: 23915736
DOI: 10.1017/S0033583513000048 -
Chembiochem : a European Journal of... Oct 2022To discover the cytomimetic that accounts for cytoplasmic crowding and sticking on RNA stability, we conducted a two-dimensional scan of mixtures of artificial crowding...
To discover the cytomimetic that accounts for cytoplasmic crowding and sticking on RNA stability, we conducted a two-dimensional scan of mixtures of artificial crowding and sticking agents, PEG10k and M-PER . As our model RNA, we investigate the fourU RNA thermometer motif of Salmonella, a hairpin-structured RNA that regulates translation by unfolding and exposing its ribosome binding site (RBS) in response to temperature perturbations. We found that the addition of artificial crowding and sticking agents leads to a stabilization and destabilization of RNA folding, respectively, through the excluded volume effect and surface interactions. FRET-labels were added to the fourU RNA and Fast Relaxation Imaging (FReI), fluorescence microscopy coupled to temperature-jump spectroscopy, probed differences between folding stability of RNA inside single living cells and in vitro. Our results suggest that the cytoplasmic environment affecting RNA folding is comparable to a combination of 20 % v/v M-PER and 150 g/L PEG10k.
Topics: RNA Folding; Fluorescence Resonance Energy Transfer; RNA; Microscopy, Fluorescence; Temperature; Protein Folding; Kinetics
PubMed: 35999178
DOI: 10.1002/cbic.202200406 -
Cell Nov 2019Ribosome assembly is an efficient but complex and heterogeneous process during which ribosomal proteins assemble on the nascent rRNA during transcription. Understanding...
Ribosome assembly is an efficient but complex and heterogeneous process during which ribosomal proteins assemble on the nascent rRNA during transcription. Understanding how the interplay between nascent RNA folding and protein binding determines the fate of transcripts remains a major challenge. Here, using single-molecule fluorescence microscopy, we follow assembly of the entire 3' domain of the bacterial small ribosomal subunit in real time. We find that co-transcriptional rRNA folding is complicated by the formation of long-range RNA interactions and that r-proteins self-chaperone the rRNA folding process prior to stable incorporation into a ribonucleoprotein (RNP) complex. Assembly is initiated by transient rather than stable protein binding, and the protein-RNA binding dynamics gradually decrease during assembly. This work questions the paradigm of strictly sequential and cooperative ribosome assembly and suggests that transient binding of RNA binding proteins to cellular RNAs could provide a general mechanism to shape nascent RNA folding during RNP assembly.
Topics: Models, Biological; Nucleic Acid Conformation; Protein Binding; RNA Folding; RNA Stability; RNA, Ribosomal; RNA-Binding Proteins; Transcription, Genetic
PubMed: 31761533
DOI: 10.1016/j.cell.2019.10.035 -
RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias.Biophysical Journal Aug 2023Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic...
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. As a step forward in tackling these issues, we extend to RNA an enhanced path-sampling method previously successfully applied to proteins. In this scheme, the information about the RNA's native structure is harnessed by a soft history-dependent biasing force promoting the generation of productive folding trajectories in an all-atom force field with explicit solvent. A rigorous variational principle is then applied to minimize the effect of the bias. Here, we report on an application of this method to RNA molecules from 20 to 47 nucleotides long and increasing topological complexity. By comparison with analog simulations performed on small proteins with similar size and architecture, we show that the RNA folding landscape is significantly more frustrated, even for relatively small chains with a simple topology. The predicted RNA folding mechanisms are found to be consistent with the available experiments and some of the existing coarse-grained models. Due to its computational performance, this scheme provides a promising platform to efficiently gather atomistic RNA folding trajectories, thus retain the information about the chemical composition of the sequence.
Topics: Protein Folding; RNA Folding; Proteins; Molecular Conformation; RNA; Molecular Dynamics Simulation; Thermodynamics
PubMed: 37355771
DOI: 10.1016/j.bpj.2023.06.012 -
Journal of Chemical Theory and... Mar 2022RNA molecules fold as they are transcribed. Cotranscriptional folding of RNA plays a critical role in RNA functions . Present computational strategies focus on...
RNA molecules fold as they are transcribed. Cotranscriptional folding of RNA plays a critical role in RNA functions . Present computational strategies focus on simulations where large structural changes may not be completely sampled. Here, we describe an alternative approach to predicting cotranscriptional RNA folding by zooming in and out of the RNA folding energy landscape. By classifying the RNA structural ensemble into "partitions" based on long, stable helices, we zoom out of the landscape and predict the overall slow folding kinetics from the interpartition kinetic network, and for each interpartition transition, we zoom in on the landscape to simulate the kinetics. Applications of the model to the 117-nucleotide SRP RNA and the 59-nucleotide HIV-1 TAR RNA show agreements with the experimental data and new structural and kinetic insights into biologically significant conformational switches and pathways for these important systems. This approach, by zooming in/out of an RNA folding landscape at different resolutions, might allow us to treat large RNAs with transcriptional pause, transcription speed, and other effects.
Topics: Escherichia coli; Kinetics; Nucleic Acid Conformation; RNA; RNA Folding; Thermodynamics; Transcription, Genetic
PubMed: 35133833
DOI: 10.1021/acs.jctc.1c01233 -
Methods in Molecular Biology (Clifton,... 2014The stability of RNA secondary structure can be predicted using a set of nearest neighbor parameters. These parameters are widely used by algorithms that predict... (Review)
Review
The stability of RNA secondary structure can be predicted using a set of nearest neighbor parameters. These parameters are widely used by algorithms that predict secondary structure. This contribution introduces the UV optical melting experiments that are used to determine the folding stability of short RNA strands. It explains how the nearest neighbor parameters are chosen and how the values are fit to the data. A sample nearest neighbor calculation is provided. The contribution concludes with new methods that use the database of sequences with known structures to determine parameter values.
Topics: Algorithms; Computational Biology; Nucleic Acid Conformation; RNA; RNA Folding; Thermodynamics
PubMed: 24639154
DOI: 10.1007/978-1-62703-709-9_3 -
Journal of Molecular Biology Sep 2022Recent advances in interrogating RNA folding dynamics have shown the classical model of RNA folding to be incomplete. Here, we pose three prominent questions for the... (Review)
Review
Recent advances in interrogating RNA folding dynamics have shown the classical model of RNA folding to be incomplete. Here, we pose three prominent questions for the field that are at the forefront of our understanding of the importance of RNA folding dynamics for RNA function. The first centers on the most appropriate biophysical framework to describe changes to the RNA folding energy landscape that a growing RNA chain encounters during transcriptional elongation. The second focuses on the potential ubiquity of strand displacement - a process by which RNA can rapidly change conformations - and how this process may be generally present in broad classes of seemingly different RNAs. The third raises questions about the potential importance and roles of cellular protein factors in RNA conformational switching. Answers to these questions will greatly improve our fundamental knowledge of RNA folding and function, drive biotechnological advances that utilize engineered RNAs, and potentially point to new areas of biology yet to be discovered.
Topics: Kinetics; RNA; RNA Folding
PubMed: 35659535
DOI: 10.1016/j.jmb.2022.167665 -
Nature Chemistry Jun 2021RNA origami is a framework for the modular design of nanoscaffolds that can be folded from a single strand of RNA and used to organize molecular components with...
RNA origami is a framework for the modular design of nanoscaffolds that can be folded from a single strand of RNA and used to organize molecular components with nanoscale precision. The design of genetically expressible RNA origami, which must fold cotranscriptionally, requires modelling and design tools that simultaneously consider thermodynamics, the folding pathway, sequence constraints and pseudoknot optimization. Here, we describe RNA Origami Automated Design software (ROAD), which builds origami models from a library of structural modules, identifies potential folding barriers and designs optimized sequences. Using ROAD, we extend the scale and functional diversity of RNA scaffolds, creating 32 designs of up to 2,360 nucleotides, five that scaffold two proteins, and seven that scaffold two small molecules at precise distances. Micrographic and chromatographic comparisons of optimized and non-optimized structures validate that our principles for strand routing and sequence design substantially improve yield. By providing efficient design of RNA origami, ROAD may simplify the construction of custom RNA scaffolds for nanomedicine and synthetic biology.
Topics: Base Sequence; Microscopy, Electron, Transmission; Nanostructures; Nanotechnology; Protein Biosynthesis; RNA; RNA Folding; Small Molecule Libraries; Software; Synthetic Biology
PubMed: 33972754
DOI: 10.1038/s41557-021-00679-1