RNA secondary structure: physical and computational aspects

@article{Higgs2000RNASS,
  title={RNA secondary structure: physical and computational aspects},
  author={Paul G. Higgs},
  journal={Quarterly Reviews of Biophysics},
  year={2000},
  volume={33},
  pages={199 - 253}
}
  • P. Higgs
  • Published 2000
  • Chemistry, Medicine
  • Quarterly Reviews of Biophysics
1. Background to RNA structure 200 1.1 Types of RNA 200 1.1.1 Transfer RNA (tRNA) 200 1.1.2 Messenger RNA (mRNA) 201 1.1.3 Ribosomal RNA (rRNA) 201 1.1.4 Other ribonucleoprotein particles 202 1.1.5 Viruses and viroids 202 1.1.6 Ribozymes 202 1.2 Elements of RNA secondary structure 203 1.3 Secondary structure versus tertiary structure 205 2. Theoretical and computational methods for RNA secondary structure determination 208 2.1 Dynamic programming algorithms 208 2.2 Kinetic folding algorithms… Expand
A New Method to Predict RNA Secondary Structure Based on RNA Folding Simulation
TLDR
This paper presents a novel method for predicting RNA secondary structure based on an RNA folding simulation model and proposes the First Large Free Energy Difference (FLED) in order to find the helical regions most urgently needed for optimal final state formation among all the possible helicals regions. Expand
Evolutionary solution for the RNA design problem
TLDR
A new evolutionary algorithm is introduced for the RNA inverse folding problem, in which an RNA secondary structure is given as a target structure and the goal is to design an RNA sequence that folds into the target structure. Expand
Inverse RNA folding solution based on multi-objective genetic algorithm and Gibbs sampling method
TLDR
A new algorithm called GGI-Fold is introduced based on multi-objective genetic algorithm and Gibbs sampling method for the inverse RNA folding problem, which generates a sequence where its structure is the same or very similar to the given target structure. Expand
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure
TLDR
A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper, and RNACompress is developed, as a useful tool for academic users. Expand
RNA Secondary Structures
TLDR
This work states that RNAsecondary structures are a convenient representation because efficient exact algorithms are known to enumerate the structures that can be formed by a given sequence, to solve the folding problem, and to compute the partition function from a well-measured set of empirical energy parameters. Expand
Base-pair Ambiguity and the Kinetics of RNA Folding: a Hypothesis-Driven Statistical Analysis
TLDR
It is argued that more emphasis should be placed on the folding process when trying to develop computational methods for RNA structure prediction, and some statistical analyses using the primary and secondary data of RNA molecules are presented, based on the concept of “local ambiguity”. Expand
Unified approach to partition functions of RNA secondary structures
  • R. Bundschuh
  • Physics, Medicine
  • Journal of mathematical biology
  • 2014
TLDR
This work proves a generic theorem for the calculation of RNA folding partition functions and shows that this approach can be applied to the study of the molten-native transition, denaturation of RNA molecules, as well as to studies of the glass phase of random RNA sequences. Expand
A complex adaptive systems approach to the kinetic folding of RNA.
TLDR
The model is shown to reproduce characteristic (nonlinear) RNA folding dynamics such as the attainment by RNAs of alternative stable states and possible applications of the model to the analysis of properties of fitness landscapes, and of the RNA sequence-to-structure mapping are discussed. Expand
Reconstruction of Natural RNA Sequences from RNA Shape, Thermodynamic Stability, Mutational Robustness, and Linguistic Complexity by Evolutionary Computation
TLDR
This work uses evolutionary computation for the new reconstruction problem of reconstructingRNAs from secondary structure into reconstructing RNAs from shapes, and incorporates physical quantities as constraints to allow for the design of novel RNA sequences by inverse folding while considering various physical quantities of interest such as thermodynamic stability, mutational robustness, and linguistic complexity. Expand
Self-similarity of rRNA secondary structures: A clue to RNA folding
In this paper, we analyze helices in the secondary structures of the 16S and 23S rRNAs from the statistical physics perspective. The results of the analysis lead to propose a possible mechanism ofExpand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 265 REFERENCES
Thermodynamics of RNA Folding: When is an RNA Molecule in Equilibrium?
TLDR
The equilibrium thermodynamic properties of the complete set of transfer RNA sequences in the tRNA database are analysed and suggest that evolution has selected for sequences with thermodynamics properties substantially different from those of typical random sequences. Expand
How RNA folds.
TLDR
A folding algorithm to predict the structure of an RNA from its sequence is suggested, but to solve the RNA folding problem one needs thermodynamic data on tertiary structure interactions, and identification and characterization of metal-ion binding sites. Expand
Kinetics of Folding of Proteins and RNA
The assembly of biological molecules, most notably globular proteins1 and RNA,2,3 into unique threedimensional structures with well-defined topology is a complex and fascinating phenomenon inExpand
Evidence for kinetic effects in the folding of large RNA molecules
When RNA secondary structures predicted by free energy minimization programs are compared with the structures obtained by phylogenetic comparison it is found that there are often substantialExpand
Prediction of RNA secondary structure, including pseudoknotting, by computer simulation.
A computer program is presented which determines the secondary structure of linear RNA molecules by simulating a hypothetical process of folding. This process implies the concept of 'nucleationExpand
Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme
TLDR
The secondary structure of the bacterial RNase P RNA has now been determined, models for its three-dimensional structure have been proposed, and numerous correlations between catalytic function and structure are being discovered. Expand
Thermodynamic prediction of conserved secondary structure: application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein.
TLDR
The algorithm combines the advantages of thermodynamic structure prediction by energy minimization with the information obtained from phylogenetic alignment of sequences to give a consensus probability matrix emphasizing the conserved secondary structure elements of the RNA set. Expand
The influence of a metastable structure in plasmid primer RNA on antisense RNA binding kinetics.
TLDR
The effect of copy number mutations can be interpreted as a compression of the time window of effective inhibition due to an increased time spent by the RNA II in the metastable state, resulting in a delay of the formation of the stable RNA II structure. Expand
Comparative photocross‐linking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNase P RNAs
TLDR
Bacterial ribonuclease P contains a catalytic RNA subunit that cleaves precursor sequences from the 5′ ends of pre‐tRNAs, consistent with the homology of the RNAs and indicating that these RNAs contain a common, core tertiary structure. Expand
An analysis of large rRNA sequences folded by a thermodynamic method.
TLDR
This work folded 72 23S rRNA sequences with the Zuker-Turner method and scored the resulting secondary structure predictions against the comparative model, finding three semiquantitative predictors of score thatcorrelate with the score. Expand
...
1
2
3
4
5
...