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Formation of metastable RNA structures by sequential folding during transcription : time-resolved structural analysis of potato spindle tuber viroid (-)-stranded RNA by temperature-gradient gel electrophoresis

Repsilber, Dirk, 1971- (author)
Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
Wiese, S (author)
Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
Rachen, M (author)
Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
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Schröder, A W (author)
Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
Riesner, D (author)
Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
Steger, G (author)
Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
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 (creator_code:org_t)
New York, USA : Cambridge University Press, 1999
1999
English.
In: RNA. - New York, USA : Cambridge University Press. - 1355-8382 .- 1469-9001. ; 5:4, s. 574-84
  • Journal article (peer-reviewed)
Abstract Subject headings
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  • A model of functional elements critical for replication and infectivity of the potato spindle tuber viroid (PSTVd) was proposed earlier: a thermodynamically metastable structure containing a specific hairpin (HP II) in the (-)-strand replication intermediate is essential for template activity during (+)-strand synthesis. We present here a detailed kinetic analysis on how PSTVd (-)-strands fold during synthesis by sequential folding into a variety of metastable structures that rearrange only slowly into the structure distribution of the thermodynamic equilibrium. Synthesis of PSTVd (-)-strands was performed by T7-RNA-polymerase; the rate of synthesis was varied by altering the concentration of nucleoside triphosphates to mimic the in vivo synthesis rate of DNA-dependent RNA polymerase II. With dependence on rate and duration of the synthesis, the structure distributions were analyzed by temperature-gradient gel electrophoresis (TGGE). Metastable structures are generated preferentially at low transcription rates--similar to in vivo rates--or at short transcription times at higher rates. Higher transcription rates or longer transcription times lead to metastable structures in low or undetectable amounts. Instead different structures do gradually appear having a more rod-like shape and higher thermodynamic stability, and the thermodynamically optimal rod-like structure dominates finally. It is concluded that viroids are able to use metastable as well as stable structures for their biological functions.

Subject headings

NATURVETENSKAP  -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)

Keyword

Kinetics; rate of transcription; RNA secondary structure; structure formation

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Repsilber, Dirk, ...
Wiese, S
Rachen, M
Schröder, A W
Riesner, D
Steger, G
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NATURAL SCIENCES
NATURAL SCIENCES
and Biological Scien ...
and Biochemistry and ...
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RNA
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Örebro University

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