Difference between revisions of "Template:Heidelberg/pages/overview/dnazymes"

 
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SELEX revealed a variety of DNA aptamers and catalytic DNA known as DNAzymes (or Deoxribozymes). Breaker and Joyce selected the first DNAzyme, a RNA-cleaving DNA.<x-ref>breaker1994</x-ref> In 1997 Santoro and Joyce describe the 7-18 and 10-23 DNAzyme<x-ref>santoro1997</x-ref> (Fig. 8) which since then have been of special interested in DNAzyme research. Both recognize their substrate RNA by Watson-Crick base pairing and catalyze the attack of a 2’ hydroxyl group that leads to the formation of a 2’,3’-cyclic phosphate and leaves a 5’ hydroxyl RNA terminus.<x-ref>santoro1998</x-ref> Their activity has also been engineered to be dependent on the presence of a small molecule by the addition of an aptamer to its substrate recognition site.<x-ref>Wanga2002</x-ref><x-ref>Wangb2002</x-ref>
 
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To verify the prediction of the software MAWS we fused the calculated aptamers to a DNAzyme with JAWS and thus created a ligand dependent activity. For this we used the HRP-mimicking DNAzyme (Fig. 9) which was described in 1998.<x-ref>Travascio1998</x-ref> It folds into a G-quadruplex that forms a complex with hemin and is then able to mimic the activity of a horse raddish peroxidase. Hence it is capable to produce reactive oxygen species (ROS) by the reduction of hydrogen peroxide to water. These ROS then leads to an activation of for example luminol which results in a chemiluminescent signal. In several of our subprojects we exploit this function as an easy readout such as for the AptaBody.
 
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RNA-cleaving DNAzymes
 
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PARAGRAPH 2
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Secondary structure of 7-18 and 10-23 RNA-cleaving DNAzyme with substrate RNA. Cleavage site is indiacted with an arrow.
 
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SELEX revealed a variety of DNA aptamers and catalytic DNA known as DNAzymes (or Deoxribozymes). Breaker and Joyce selected the first DNAzyme, a RNA-cleaving DNA.<x-ref>Breaker1994</x-ref> In 1997 Santoro and Joyce describe the 7-18 and 10-23 DNAzyme<x-ref>Santoro1997</x-ref> (Fig. 8) which since then have been of special interested in DNAzyme research. Both recognize their substrate RNA by Watson-Crick base pairing and catalyze the attack of a 2’ hydroxyl group that leads to the formation of a 2’,3’-cyclic phosphate and leaves a 5’ hydroxyl RNA terminus.<x-ref>Santoro1998</x-ref> Their activity has also been engineered to be dependent on the presence of a small molecule by the addition of an aptamer to its substrate recognition site.<x-ref>Wanga2002</x-ref><x-ref>Wangb2002</x-ref>
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To verify the prediction of the software MAWS we fused the calculated aptamers to a DNAzyme with JAWS and thus created a ligand dependent activity. For this we used the HRP-mimicking DNAzyme (Fig. 9) which was described in 1998.<x-ref>Travascio1998</x-ref> It folds into a G-quadruplex that forms a complex with hemin and is then able to mimic the activity of a horse raddish peroxidase. Hence it is capable to produce reactive oxygen species (ROS) by the reduction of hydrogen peroxide to water. These ROS then leads to an activation of for example luminol which results in a chemiluminescent signal. In several of our subprojects we exploit this function as an easy readout such as for the AptaBody.
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Latest revision as of 03:31, 19 September 2015

Catalytic DNA – DNAzymes

RNA-cleaving DNAzymes

Secondary structure of 7-18 and 10-23 RNA-cleaving DNAzyme with substrate RNA. Cleavage site is indiacted with an arrow.

SELEX revealed a variety of DNA aptamers and catalytic DNA known as DNAzymes (or Deoxribozymes). Breaker and Joyce selected the first DNAzyme, a RNA-cleaving DNA.Breaker1994 In 1997 Santoro and Joyce describe the 7-18 and 10-23 DNAzymeSantoro1997 (Fig. 8) which since then have been of special interested in DNAzyme research. Both recognize their substrate RNA by Watson-Crick base pairing and catalyze the attack of a 2’ hydroxyl group that leads to the formation of a 2’,3’-cyclic phosphate and leaves a 5’ hydroxyl RNA terminus.Santoro1998 Their activity has also been engineered to be dependent on the presence of a small molecule by the addition of an aptamer to its substrate recognition site.Wanga2002Wangb2002

To verify the prediction of the software MAWS we fused the calculated aptamers to a DNAzyme with JAWS and thus created a ligand dependent activity. For this we used the HRP-mimicking DNAzyme (Fig. 9) which was described in 1998.Travascio1998 It folds into a G-quadruplex that forms a complex with hemin and is then able to mimic the activity of a horse raddish peroxidase. Hence it is capable to produce reactive oxygen species (ROS) by the reduction of hydrogen peroxide to water. These ROS then leads to an activation of for example luminol which results in a chemiluminescent signal. In several of our subprojects we exploit this function as an easy readout such as for the AptaBody.