Difference between revisions of "Team:Heidelberg/project/hlpd"

Revision as of 02:46, 19 September 2015

Abstract

Results

We computationally designed a communication module for an HRP-F8 fusion DNAzyme using our software JAWS. Aptamers for ampicillin and ketamine were joined to the stem of the fused F8 DNAzyme to regulate its cleavage activity. The ketamine-binding aptamer was previously designed by our software MAWS to specifically target the anesthetic, while the ampicillin-specific aptamer was previously published <x-ref>Song2012</x-ref>. The fusion DNAzymes were tested against their respective ligand in solution, where 1 µM DNAzyme hemine solution was incubated together with the ligand, hydrogen peroxide, and TMB. Reactions were stopped using 1 mM hydrochloric acid. Catalytic activity of the ampicillin-responsive DNAzyme drastically increased upon exposure to its ligand (Fig. iA), indicated by the solution turning deep blue, while the negative control lacking ampicillin was only faintly coloured. To test this detection system in a more realistic setting, the DNAzyme was incubated in energy drink spiked with ampicillin. Here, a fainter change in color, presumably due to suboptimal buffer conditions was observed, with the ampicillin-spiked beverage still showing significant discoloration compared to the pure drink (Fig. iB). From the two DNAzymes designed for ketamine one switched on in the presence of ketamine, while the other switched off. Both produced similar colors after the reaction was stopped (Fig i+1). Thus, our software suite proved successfull in designing a detection system for a drug within less than a day of computation.

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-We computationally designed a communication module for an HRP-F8 fusion DNAzyme using our software JAWS. Aptamers for ampicillin and ketamine were joined to the stem of the fused F8 DNAzyme to regulate its cleavage activity. The ketamine-binding aptamer was previously designed by our software MAWS to specifically target the anesthetic, while the ampicillin-specific aptamer was previously published. The fusion DNAzymes were tested against their respective ligand in solution, where 1 µM DNAzyme hemine solution was incubated together with the ligand, hydrogen peroxide, and TMB. Reactions were stopped using 1 mM hydrochloric acid. Catalytic activity of the ampicillin-responsive DNAzyme drastically increased upon exposure to its ligand (Fig. iA), indicated by the solution turning deep blue, while the negative control lacking ampicillin was only faintly coloured. To test this detection system in a more realistic setting, the DNAzyme was incubated in energy drink spiked with ampicillin. Here, a fainter change in color, presumably due to suboptimal buffer conditions was observed, with the ampicillin-spiked beverage still showing significant discoloration compared to the pure drink (Fig. iB). From the two DNAzymes designed for ketamine one switched on in the presence of ketamine, while the other switched off. Both produced similar colors after the reaction was stopped (Fig i+1). Thus, our software suite proved successfull in designing a detection system for a drug within less than a day of computation.
+We computationally designed a communication module for an HRP-F8 fusion DNAzyme using our software JAWS. Aptamers for ampicillin and ketamine were joined to the stem of the fused F8 DNAzyme to regulate its cleavage activity. The ketamine-binding aptamer was previously designed by our software MAWS to specifically target the anesthetic, while the ampicillin-specific aptamer was previously published <x-ref>Song2012</x-ref>. The fusion DNAzymes were tested against their respective ligand in solution, where 1 µM DNAzyme hemine solution was incubated together with the ligand, hydrogen peroxide, and TMB. Reactions were stopped using 1 mM hydrochloric acid. Catalytic activity of the ampicillin-responsive DNAzyme drastically increased upon exposure to its ligand (Fig. iA), indicated by the solution turning deep blue, while the negative control lacking ampicillin was only faintly coloured. To test this detection system in a more realistic setting, the DNAzyme was incubated in energy drink spiked with ampicillin. Here, a fainter change in color, presumably due to suboptimal buffer conditions was observed, with the ampicillin-spiked beverage still showing significant discoloration compared to the pure drink (Fig. iB). From the two DNAzymes designed for ketamine one switched on in the presence of ketamine, while the other switched off. Both produced similar colors after the reaction was stopped (Fig i+1). Thus, our software suite proved successfull in designing a detection system for a drug within less than a day of computation.
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