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Formation of metast...
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
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- Repsilber, Dirk, 1971- (author)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
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- Wiese, S (author)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
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- 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
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- Riesner, D (author)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
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- 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.
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In: RNA. - New York, USA : Cambridge University Press. - 1355-8382 .- 1469-9001. ; 5:4, s. 574-84
- Related links:
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https://doi.org/10.1...
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https://urn.kb.se/re...
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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
Publication and Content Type
- ref (subject category)
- art (subject category)
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