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  Is the in situ accessibility of the 16S rRNA of Escherichia coli for Cy3-labeled oligonucleotide probes predicted by a three-dimensional structure model of the 30S ribosomal subunit?

Behrens, S., Fuchs, B. M., Mueller, F., & Amann, R. (2003). Is the in situ accessibility of the 16S rRNA of Escherichia coli for Cy3-labeled oligonucleotide probes predicted by a three-dimensional structure model of the 30S ribosomal subunit? Applied and Environmental Microbiology, 69(8), 4935-4941. doi:10.1128/AEM.69.8.4935-4941.2003.

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アイテムのパーマリンク: https://hdl.handle.net/11858/00-001M-0000-0010-89E2-B 版のパーマリンク: https://hdl.handle.net/11858/00-001M-0000-0010-89E3-9
資料種別: 学術論文
その他のタイトル : Appl. Environ. Microbiol.

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 作成者:
Behrens, Sebastian1, 著者
Fuchs, Bernhard M.1, 著者
Mueller, Florian1, 著者
Amann, Rudolf1, 著者
所属:
1Max Planck Society, ou_persistent13              

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キーワード: -
 要旨: Systematic studies on the hybridization of fluorescently labeled, rRNA-targeted oligonucleotides have shown strong variations in in situ accessibility. Reliable predictions of target site accessibility would contribute to more-rational design of probes for the identification of individual microbial cells in their natural environments. During the past 3 years, numerous studies of the higher-order structure of the ribosome have advanced our understanding of its spatial conformation. These studies range from the identification of rRNA-rRNA interactions based on covariation analyses to physical imaging of the ribosome for the identification of protein-rRNA interactions. Here we reevaluate our Escherichia coli 16S rRNA in situ accessibility data with regard to a tertiary-structure model of the small subunit of the ribosome. We localized target sequences of 176 oligonucleotides on a 3.0-Å-resolution three-dimensional (3D) model of the 30S ribosomal subunit. Little correlation was found between probe hybridization efficiency and the proximity of the probe target region to the surface of the 30S ribosomal subunit model. We attribute this to the fact that fluorescence in situ hybridization is performed on fixed cells containing denatured ribosomes, whereas 3D models of the ribosome are based on its native conformation. The effects of different fixation and hybridization protocols on the fluorescence signals conferred by a set of 10 representative probes were tested. The presence or absence of the strongly denaturing detergent sodium dodecyl sulfate had a much more pronounced effect than a change of fixative from paraformaldehyde to ethanol.

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言語: eng - English
 日付: 2003-08
 出版の状態: 出版
 ページ: -
 出版情報: -
 目次: -
 査読: -
 識別子（DOI, ISBNなど）: eDoc: 194819
ISI: 000184672500076
DOI: 10.1128/AEM.69.8.4935-4941.2003
 学位: -

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出版物 1

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出版物名: Applied and Environmental Microbiology
  出版物の別名 : Appl. Environ. Microbiol.
種別: 学術雑誌
 著者・編者:
所属:
出版社, 出版地: -
ページ: - 巻号: 69 (8) 通巻号: - 開始・終了ページ: 4935 - 4941 識別子（ISBN, ISSN, DOIなど）: ISSN: 0099-2240