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 1 August 2000
  • Biology, Chemistry
  • 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… 

A New Method to Predict RNA Secondary Structure Based on RNA Folding Simulation

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.

Evolutionary solution for the RNA design problem

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.

Inverse RNA folding solution based on multi-objective genetic algorithm and Gibbs sampling method

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.

RNA Secondary Structures

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.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure

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.

Unified approach to partition functions of RNA secondary structures

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.

A complex adaptive systems approach to the kinetic folding of RNA.

Reconstruction of Natural RNA Sequences from RNA Shape, Thermodynamic Stability, Mutational Robustness, and Linguistic Complexity by Evolutionary Computation

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.

RNA in Formation : Computational Studies on RNA Structure and Evolution

Analysis of ribosomal RNA sequences and structures from a wide range of species revealed unexpected universal compositional trends that may improve the accuracy of RNA secondary structure prediction, and suggest caution in interpreting differences in the rate of change of the GC content in different parts of the molecule as evidence of differential selection.

RNA Structure as Permutation: A GA Approach Comparing Different Genetic Sequencing Operators

A comparison of several crossover operators is provided, demonstrating that CX, an operator that is marginal in the TSP domain, performs very well in the RNA folding domain and that the Keep-Best Reproduction operator has similar benefits as in theTSP domain.
...

References

SHOWING 1-10 OF 253 REFERENCES

How RNA folds.

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.

Thermodynamics of RNA Folding: When is an RNA Molecule in Equilibrium?

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.

Kinetics of Folding of Proteins and RNA

Recent advances are described in the understanding of the kinetics of in vitro folding of globular proteins in terms of the underlying energy landscape as well as the requirements for RNA folding which are analogous to those of protein folding.

Evidence for kinetic effects in the folding of large RNA molecules

A sample of large RNA molecules including 16S and 23S ribosomal RNA, and RNaseP RNA is considered, and the free energy of small domains in the phylogenetic structure of size 100 bases or less is usually much lower than the average value of the minimum freeEnergy of typical domains of corresponding size.

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 'nucleation

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.

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.

The influence of a metastable structure in plasmid primer RNA on antisense RNA binding kinetics.

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.

Comparative photocross‐linking analysis of the tertiary structures of Escherichia coli and Bacillus subtilis RNase P RNAs

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.

Applicability of urea in the thermodynamic analysis of secondary and tertiary RNA folding.

The results indicate that urea titration can be used to measure both the free energy and the magnitude of an RNA folding transition, and also indicates that the precise chemical basis of urea denaturation of RNA is uncertain.
...