MersV1, Main, Exploration, bibRecord, 002D72

Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of Bombyx mori R2 RNA†

Identifieur interne : 002D72 ( Main/Exploration ); précédent : 002D71; suivant : 002D73

Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of Bombyx mori R2 RNA†

Auteurs : Shenghua Duan ; David H. Mathews ; Douglas H. Turner [États-Unis]

Source :

Biochemistry [ 0006-2960 ] ; 2006.

RBID : ISTEX:961BE605853C8968681415ECE22FAFABE448C8CB

Descripteurs français

English descriptors

KwdEn :
- 3' Untranslated Regions (chemistry), 3' Untranslated Regions (genetics), Algorithms, Animals, Base Pairing, Base Sequence, Bombyx (chemistry), Escherichia coli (chemistry), Hydrogen-Ion Concentration, Magnesium Chloride (pharmacology), Molecular Sequence Data, Nucleic Acid Conformation, Oligonucleotide Array Sequence Analysis, RNA Probes (drug effects), RNA, Ribosomal, 5S (chemistry), Retroelements (genetics), Ribonuclease H (metabolism), Sodium Chloride (pharmacology), Thermodynamics.
MESH :
- chemical , chemistry : 3' Untranslated Regions, RNA, Ribosomal, 5S.
- chemical , drug effects : RNA Probes.
- chemical , genetics : 3' Untranslated Regions, Retroelements.
- chemistry : Bombyx, Escherichia coli.
- chemical , metabolism : Ribonuclease H.
- chemical , pharmacology : Magnesium Chloride, Sodium Chloride.
- Algorithms, Animals, Base Pairing, Base Sequence, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Conformation, Oligonucleotide Array Sequence Analysis, Thermodynamics.

Abstract

A method to deduce RNA secondary structure on the basis of data from microarrays of 2‘-O-methyl RNA 9-mers immobilized in agarose film on glass slides is tested with a 249 nucleotide RNA from the 3‘ end of the R2 retrotransposon from Bombyx mori. Various algorithms incorporating binding data and free-energy minimization calculations were compared for interpreting the data to provide possible secondary structures. Two different methods give structures with 100 and 87% of the base pairs determined by sequence comparison. In contrast, structures predicted by free-energy minimization alone by Mfold and RNAstructure contain 52 and 72% of the known base pairs, respectively. This combination of high throughput microarray techniques with algorithms using free-energy calculations has potential to allow for fast determination of RNA secondary structure. It should also facilitate the design of antisense and siRNA oligonucleotides.

Url:

https://api.istex.fr/ark:/67375/TPS-CR0P76RD-4/fulltext.pdf

DOI: 10.1021/bi052618x

Affiliations:

États-Unis

Le document en format XML

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<front><div type="abstract">A method to deduce RNA secondary structure on the basis of data from microarrays of 2‘-O-methyl RNA 9-mers immobilized in agarose film on glass slides is tested with a 249 nucleotide RNA from the 3‘ end of the R2 retrotransposon from Bombyx mori. Various algorithms incorporating binding data and free-energy minimization calculations were compared for interpreting the data to provide possible secondary structures. Two different methods give structures with 100 and 87% of the base pairs determined by sequence comparison. In contrast, structures predicted by free-energy minimization alone by Mfold and RNAstructure contain 52 and 72% of the known base pairs, respectively. This combination of high throughput microarray techniques with algorithms using free-energy calculations has potential to allow for fast determination of RNA secondary structure. It should also facilitate the design of antisense and siRNA oligonucleotides.</div>
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Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of Bombyx mori R2 RNA†

Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of Bombyx mori R2 RNA†

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

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