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A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than...

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Detalles Bibliográficos
Autores principales: Lu, Zhi John, Turner, Douglas H., Mathews, David H.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635246/
https://www.ncbi.nlm.nih.gov/pubmed/16982646
http://dx.doi.org/10.1093/nar/gkl472
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author Lu, Zhi John
Turner, Douglas H.
Mathews, David H.
author_facet Lu, Zhi John
Turner, Douglas H.
Mathews, David H.
author_sort Lu, Zhi John
collection PubMed
description A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37°C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60°C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures.
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spelling pubmed-16352462006-11-29 A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation Lu, Zhi John Turner, Douglas H. Mathews, David H. Nucleic Acids Res RNA A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37°C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60°C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures. Oxford University Press 2006-10 2006-08-18 /pmc/articles/PMC1635246/ /pubmed/16982646 http://dx.doi.org/10.1093/nar/gkl472 Text en © 2006 The Author(s)
spellingShingle RNA
Lu, Zhi John
Turner, Douglas H.
Mathews, David H.
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
title A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
title_full A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
title_fullStr A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
title_full_unstemmed A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
title_short A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
title_sort set of nearest neighbor parameters for predicting the enthalpy change of rna secondary structure formation
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635246/
https://www.ncbi.nlm.nih.gov/pubmed/16982646
http://dx.doi.org/10.1093/nar/gkl472
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