MersV1, Ncbi, Merge, bibRecord, 000457

Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.

Identifieur interne : 000457 ( Ncbi/Merge ); précédent : 000456; suivant : 000458

Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.

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

Source :

Biochemistry [ 0006-2960 ] ; 2006.

RBID : pubmed:16893182

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.

DOI: 10.1021/bi052618x
PubMed: 16893182

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pubmed:16893182

Le document en format XML

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<author><name sortKey="Duan, Shenghua" sort="Duan, Shenghua" uniqKey="Duan S" first="Shenghua" last="Duan">Shenghua Duan</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.</nlm:affiliation>
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<term>Animals</term>
<term>Base Pairing</term>
<term>Base Sequence</term>
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<front><div type="abstract" xml:lang="en">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...)

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki