Structural Features of Target RNA Molecules Greatly Modulate the Cleavage Efficiency of trans-Acting Delta Ribozymes†
Identifieur interne : 002B87 ( Main/Exploration ); précédent : 002B86; suivant : 002B88Structural Features of Target RNA Molecules Greatly Modulate the Cleavage Efficiency of trans-Acting Delta Ribozymes†
Auteurs : Agata Wia Tkowska [Pologne] ; Mariola Dutkiewicz [Pologne] ; Jerzy Ciesiołka [Pologne]Source :
- Biochemistry [ 0006-2960 ] ; 2007.
Abstract
The aim of this work was to shed some more light on factors influencing the effectiveness of delta ribozyme cleavage of structured RNA molecules. An oligoribonucleotide that corresponds to the 3‘-terminal region X of HCV RNA and yeast tRNAPhe were used as representative RNA targets. Only a few sites susceptible to ribozyme cleavage were identified in these targets using a combinatorial library of ribozyme variants, in which the region responsible for ribozyme−target interaction was randomized. On the other hand, the targets were fairly accessible for binding of complementary oligonucleotides, as was shown by 6-mer DNA libraries and RNase H approach. Moreover, the specifically acting ribozymes cleaved the targets precisely but with unexpectedly modest efficacy. To explain these observations, six model RNA molecules were designed, in which the same seven nucleotide long sequence recognized by the delta ribozyme was always single stranded but was embedded into different RNA structural context. These molecules were cleaved with differentiated rates, and the corresponding k2 values were in the range of 0.91−0.021 min-1; thus they differed almost 50-fold. This clearly shows that cleavage of structured RNAs might be much slower than cleavage of a short unstructured oligoribonucleotide, despite full accessibility of the targeted regions for hybridization. Restricted possibilities of conformational transitions, which are necessary to occur on the cleavage reaction trajectory, seem to be responsible for these differences. Their magnitude, which was evaluated in this work, should be taken into account while considering the use of delta ribozymes for practical applications.
Url:
DOI: 10.1021/bi6024287
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 001277
- to stream Istex, to step Curation: 001277
- to stream Istex, to step Checkpoint: 000840
- to stream Main, to step Merge: 002C13
- to stream Main, to step Curation: 002B87
Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title>Structural Features of Target RNA Molecules Greatly Modulate the Cleavage Efficiency of trans-Acting Delta Ribozymes†</title><author><name sortKey=" Wia Tkowska, Agata" sort=" Wia Tkowska, Agata" uniqKey=" Wia Tkowska A" first="Agata" last=" Wia Tkowska">Agata Wia Tkowska</name></author><author><name sortKey="Dutkiewicz, Mariola" sort="Dutkiewicz, Mariola" uniqKey="Dutkiewicz M" first="Mariola" last="Dutkiewicz">Mariola Dutkiewicz</name></author><author><name sortKey="Ciesiolka, Jerzy" sort="Ciesiolka, Jerzy" uniqKey="Ciesiolka J" first="Jerzy" last="Ciesiołka">Jerzy Ciesiołka</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:8349829BF69C1D4FF68C4D9986A545ABA52473B6</idno><date when="2007" year="2007">2007</date><idno type="doi">10.1021/bi6024287</idno><idno type="url">https://api.istex.fr/ark:/67375/TPS-6FPSCRFV-B/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">001277</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001277</idno><idno type="wicri:Area/Istex/Curation">001277</idno><idno type="wicri:Area/Istex/Checkpoint">000840</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000840</idno><idno type="wicri:doubleKey">0006-2960:2007: Wia Tkowska A:structural:features:of</idno><idno type="wicri:Area/Main/Merge">002C13</idno><idno type="wicri:Area/Main/Curation">002B87</idno><idno type="wicri:Area/Main/Exploration">002B87</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main">Structural Features of Target RNA Molecules Greatly Modulate the Cleavage
Efficiency of <hi rend="italic">trans</hi>-Acting Delta Ribozymes<ref type="bib" target="#bi6024287AF2">†</ref></title><author><name sortKey=" Wia Tkowska, Agata" sort=" Wia Tkowska, Agata" uniqKey=" Wia Tkowska A" first="Agata" last=" Wia Tkowska">Agata Wia Tkowska</name><affiliation wicri:level="1"><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań 61-704</wicri:regionArea><wicri:noRegion>Poznań 61-704</wicri:noRegion></affiliation></author><author><name sortKey="Dutkiewicz, Mariola" sort="Dutkiewicz, Mariola" uniqKey="Dutkiewicz M" first="Mariola" last="Dutkiewicz">Mariola Dutkiewicz</name><affiliation wicri:level="1"><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań 61-704</wicri:regionArea><wicri:noRegion>Poznań 61-704</wicri:noRegion></affiliation></author><author><name sortKey="Ciesiolka, Jerzy" sort="Ciesiolka, Jerzy" uniqKey="Ciesiolka J" first="Jerzy" last="Ciesiołka">Jerzy Ciesiołka</name><affiliation wicri:level="1"><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań 61-704</wicri:regionArea><wicri:noRegion>Poznań 61-704</wicri:noRegion></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Pologne</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Biochemistry</title><title level="j" type="abbrev">Biochemistry</title><idno type="ISSN">0006-2960</idno><idno type="eISSN">1520-4995</idno><imprint><publisher>American Chemical Society</publisher><date type="e-published">2007</date><date type="published">2007</date><biblScope unit="vol">46</biblScope><biblScope unit="issue">18</biblScope><biblScope unit="page" from="5523">5523</biblScope><biblScope unit="page" to="5533">5533</biblScope></imprint><idno type="ISSN">0006-2960</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0006-2960</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract">The aim of this work was to shed some more light on factors influencing the effectiveness of delta ribozyme cleavage of structured RNA molecules. An oligoribonucleotide that corresponds to the 3‘-terminal region X of HCV RNA and yeast tRNAPhe were used as representative RNA targets. Only a few sites susceptible to ribozyme cleavage were identified in these targets using a combinatorial library of ribozyme variants, in which the region responsible for ribozyme−target interaction was randomized. On the other hand, the targets were fairly accessible for binding of complementary oligonucleotides, as was shown by 6-mer DNA libraries and RNase H approach. Moreover, the specifically acting ribozymes cleaved the targets precisely but with unexpectedly modest efficacy. To explain these observations, six model RNA molecules were designed, in which the same seven nucleotide long sequence recognized by the delta ribozyme was always single stranded but was embedded into different RNA structural context. These molecules were cleaved with differentiated rates, and the corresponding k2 values were in the range of 0.91−0.021 min-1; thus they differed almost 50-fold. This clearly shows that cleavage of structured RNAs might be much slower than cleavage of a short unstructured oligoribonucleotide, despite full accessibility of the targeted regions for hybridization. Restricted possibilities of conformational transitions, which are necessary to occur on the cleavage reaction trajectory, seem to be responsible for these differences. Their magnitude, which was evaluated in this work, should be taken into account while considering the use of delta ribozymes for practical applications.</div></front></TEI><affiliations><list><country><li>Pologne</li></country></list><tree><country name="Pologne"><noRegion><name sortKey=" Wia Tkowska, Agata" sort=" Wia Tkowska, Agata" uniqKey=" Wia Tkowska A" first="Agata" last=" Wia Tkowska">Agata Wia Tkowska</name></noRegion><name sortKey="Ciesiolka, Jerzy" sort="Ciesiolka, Jerzy" uniqKey="Ciesiolka J" first="Jerzy" last="Ciesiołka">Jerzy Ciesiołka</name><name sortKey="Ciesiolka, Jerzy" sort="Ciesiolka, Jerzy" uniqKey="Ciesiolka J" first="Jerzy" last="Ciesiołka">Jerzy Ciesiołka</name><name sortKey="Dutkiewicz, Mariola" sort="Dutkiewicz, Mariola" uniqKey="Dutkiewicz M" first="Mariola" last="Dutkiewicz">Mariola Dutkiewicz</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002B87 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002B87 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= ISTEX:8349829BF69C1D4FF68C4D9986A545ABA52473B6
|texte= Structural Features of Target RNA Molecules Greatly Modulate the Cleavage Efficiency of trans-Acting Delta Ribozymes†
}}
| This area was generated with Dilib version V0.6.33. |  |