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| 2. |
- Repsilber, Dirk, 1971-, et al.
(författare)
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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
- 1999
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Ingår i: RNA. - New York, USA : Cambridge University Press. - 1355-8382 .- 1469-9001. ; 5:4, s. 574-84
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 4. |
- Tallsjö, Annika, et al.
(författare)
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Interaction between Escherichia coli RNase P RNA and the discriminator base results in slow product release
- 1996
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Ingår i: RNA. - 1355-8382 .- 1469-9001. ; 2:4, s. 299-307
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Tidskriftsartikel (refereegranskat)abstract
- We suggested previously that a purine at the discriminator base position in a tRNA precursor interacts with the well-conserved U294 in M1 RNA, the catalytic subunit of Escherichia coli RNase P. Here we investigated this interaction and its influence on the kinetics of cleavage as well as on cleavage site selection. The discriminator base in precursors to tRNA(Tyr)Su3 and tRNA(Phe) was changed from A to C and cleavage kinetics were studied by wild-type M1 RNA and a mutant M1 RNA carrying the compensatory substitution of a U to a G at position 294 in M1 RNA. Our data suggest that the discriminator base interacts with the residue at position 294 in M1 RNA. Although product release is a rate-limiting step both in the absence and in the presence of this interaction, its presence results in a significant reduction in the rate of product release. In addition, we studied cleavage site selection on various tRNA(His) precursor derivatives. These precursors carry a C at the discriminator base position. The results showed that the mutant M1 RNA harboring a G at position 294 miscleaved a wild-type tRNA(His) precursor and a tRNA(His) precursor carrying an inosine at the cleavage site. The combined data suggest a functional interaction between the discriminator base and the well-conserved U294 in M1 RNA. This interaction is suggested to play an important role in determining the rate of product release during multiple turnover cleavage of tRNA precursors by M1 RNA as well as in cleavage site selection.
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| 8. |
- Kufel, J, et al.
(författare)
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The P15-loop of Escherichia coli RNase P RNA is an autonomous divalent metal ion binding domain
- 1998
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Ingår i: RNA-A PUBLICATION OF THE RNA SOCIETY. - : CAMBRIDGE UNIV PRESS. - 1355-8382. ; 4:7, s. 777-788
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- We have studied the structure and divalent metal ion binding of a domain of the ribozyme RNase P RNA that is involved in base pairing with its substrate. Our data suggest that the folding of this internal loop, the P15-loop, is similar irrespective of whe
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| 10. |
- Svard, SG, et al.
(författare)
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Phylogenetic comparative mutational analysis of the base-pairing between RNase P RNA and its substrate
- 1996
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Ingår i: RNA-A PUBLICATION OF THE RNA SOCIETY. - : CAMBRIDGE UNIV PRESS. - 1355-8382. ; 2:5, s. 463-472
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- We have studied the base-pairing between the 3'-terminal CCA motif of a tRNA precursor and RNase P RNA by a phylogenetic mutational comparative approach. Thus, various derivatives of the Escherichia coli tRNA(Ser)Su1 precursor harboring all possible subst
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