Thermodynamics of RNA/DNA hybridization ...
Type de document :
Article dans une revue scientifique
Titre :
Thermodynamics of RNA/DNA hybridization in high density oligonucleotide microarrays
Auteur(s) :
Titre de la revue :
Physica A: Statistical Mechanics and its Applications
Pagination :
433
Éditeur :
Elsevier
Date de publication :
2006-05-04
ISSN :
0378-4371
Discipline(s) HAL :
Physique [physics]/Matière Condensée [cond-mat]/Mécanique statistique [cond-mat.stat-mech]
Physique [physics]/Physique [physics]/Chimie-Physique [physics.chem-ph]
Physique [physics]/Physique [physics]/Chimie-Physique [physics.chem-ph]
Résumé en anglais : [en]
We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the ...
Lire la suite >We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity versus the hybridization free energy of RNA/DNA duplexes in solution, for perfect matching and mismatching probes. Both values tend to align on a single master curve in good agreement with Langmuir adsorption theory, provided one takes into account the decrease of the effective target concentration due to target-target hybridization in solution. We give an example of a deviation from the expected thermodynamical behavior for the probe set 1091\_at due to annotation problems, i.e. the surface-bound probe is not the exact complement of the target RNA sequence, because of errors present in public databases at the time when the array was designed. We show that the parametrization of the experimental data with RNA/DNA free energy improves the quality of the fits and enhances the stability of the fitting parameters compared to previous studies.Lire moins >
Lire la suite >We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity versus the hybridization free energy of RNA/DNA duplexes in solution, for perfect matching and mismatching probes. Both values tend to align on a single master curve in good agreement with Langmuir adsorption theory, provided one takes into account the decrease of the effective target concentration due to target-target hybridization in solution. We give an example of a deviation from the expected thermodynamical behavior for the probe set 1091\_at due to annotation problems, i.e. the surface-bound probe is not the exact complement of the target RNA sequence, because of errors present in public databases at the time when the array was designed. We show that the parametrization of the experimental data with RNA/DNA free energy improves the quality of the fits and enhances the stability of the fitting parameters compared to previous studies.Lire moins >
Langue :
Anglais
Comité de lecture :
Oui
Audience :
Non spécifiée
Vulgarisation :
Non
Commentaire :
11 pages, 16 figures - final version as published
Source :
Fichiers
- http://arxiv.org/pdf/q-bio.BM/0411011
- Accès libre
- Accéder au document
- https://hal.archives-ouvertes.fr/hal-00128511/document
- Accès libre
- Accéder au document