Difference between revisions of "Part:BBa K1614016"

Revision as of 13:36, 20 September 2015

Hammerhead Ribozyme and Malchite Green Aptamer in BBF RFC 110 transcription cassette

Hammerhead Ribozyme (HHR) and Malchite Green (MG) Aptamer in BBF RFC 110 transcription cassette for live tracking of in vitro transcription.

Usage and Biology

Establishing a read out system that would give the information that the DNA was fully transcribed into RNA was provided by the Malachite Green Aptamer. Therefore we provide a new biobrick which contains a hammerhead ribozyme fused to the Malachite Green Aptamer (BBa_K1614016). This aptamer can bind malachite green dye which lead to a fluorescence at 652 nm if excited at 630 nm. This part was used for the detection of fully extended RNA during in vitro transcription in presence of malachite green dye. The ligand dependent aptamer folds correctly during the transcription thereby emitting light that was measured in a 384 well plate format. Experiments have shown that the Malachite Green Aptamer can be used as a universal read out system by adding a Hammerhead Ribozyme that cleaves at the 3’ end of the RNA of Interest. This setup allows the cleavage of an RNA of Interest (ROI) from the Hammerhead Ribozyme-Malachite Green Aptamer (Fig. 1). Experiments with the Substrate of the RNA cleaving DNAzyme have shown that the Hammerhead Ribozyme-Malachite Green Aptamer cleaves from the substrate. Hence, the substrate and the Hammerhead Ribozyme-Malachite Green Aptamer could be purified on a denaturing polyacrylamide gel electrophoresis (Fig. 2).

Fig.1. Real time monitoring of the RNA synthesis using a Malachite Green Aptamer.(A) To analyze RNA synthesis in real time we applied a DNA template encoding for the RNA of interest (ROI) and a hammerhead ribozyme (HHR). Both fragments are inserted between the promotor (T7) and the Malachite Green Aptamer (MGA). Inducing the hammerhead ribozyme allows cleavage during the in vitrotranscription. Hereby two RNA fragments emerge, the ROI and the hammerhead ribozyme fused to Malachite Green Aptamer (HHR-MGA). Using such setup, the emitted fluorescence of the HHR-MGA will be independent on the applied ROI. Thus the fluorescence is induced by the Malachite Green Aptamer that can be applied to compare efficiencies of different RNAs at the same time. (B) As a proof of principle we performed transcriptions and monitored the malachite green fluorescence signal in real time. (C)To confirm the results of the fluorescence measurements as well as the transcription efficiency is not hampered by the malachite green dye, all in vitrotranscription reactions were analyzed using denaturing acrylamide gels.

Fig.2. Monitoring of the ATP consumption and RNA synthesis of difficult transcription templates. (A) Using our fluorescent tool box we can demonstrate again that substrate of RNA-cleaving DNAzyme causes problems during transcription. We can identify a slight decrease of Spinach fluorescence and increase in the Malachite Green signal. (B) We were applying a DNA template containing a HHR in front of the Malachite Green Aptamer, we analyzed cleavage by denaturing acrylamide gel electrophoresis. We could identify the cleaved HHR-MGA RNA by high sensitive Sybr Gold staining.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BamHI site found at 85
Illegal BamHI site found at 117
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 124
Illegal NgoMIV site found at 153
1000
COMPATIBLE WITH RFC[1000]

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 <!-- Add more about the biology of this part here -->
 ===Usage and Biology===
-Establishing a read out system that would give the information that the DNA was fully transcribed into RNA was provided by the Malachite Green Aptamer. Therefore we provide a new biobrick which contains a hammerhead ribozyme fused to the Malachite Green Aptamer (BBa_K1614016). This aptamer can bind malachite green dye which lead to a fluorescence at 652 nm if excited at 630 nm. This part was used for the detection of fully extended RNA during <i> in vitro </i> transcription in presence of malachite green dye. The ligand dependent aptamer folds correctly during the transcription thereby emitting light that was measured in a 384 well plate format. Experiments have shown that the Malachite Green Aptamer can be used as a universal read out system by adding a Hammerhead Ribozyme that cleaves at the 3’ end of the RNA of Interest. This setup allows the cleavage of an RNA of Interest (ROI) from the Hammerhead Ribozyme-Malachite Green Aptamer.
+Establishing a read out system that would give the information that the DNA was fully transcribed into RNA was provided by the Malachite Green Aptamer. Therefore we provide a new biobrick which contains a hammerhead ribozyme fused to the Malachite Green Aptamer (BBa_K1614016). This aptamer can bind malachite green dye which lead to a fluorescence at 652 nm if excited at 630 nm. This part was used for the detection of fully extended RNA during in vitro transcription in presence of malachite green dye. The ligand dependent aptamer folds correctly during the transcription thereby emitting light that was measured in a 384 well plate format. Experiments have shown that the Malachite Green Aptamer can be used as a universal read out system by adding a Hammerhead Ribozyme that cleaves at the 3’ end of the RNA of Interest. This setup allows the cleavage of an RNA of Interest (ROI) from the Hammerhead Ribozyme-Malachite Green Aptamer (Fig. 1).
-Experiments with the Substrate of the RNA cleaving DNAzyme have shown that the Hammerhead Ribozyme-Malachite Green Aptamer cleaves from the substrate. Hence, the substrate and the Hammerhead Ribozyme-Malachite Green Aptamer could be purified on a denaturing polyacrylamide gel electrophoresis (Fig. 1).
+Experiments with the Substrate of the RNA cleaving DNAzyme have shown that the Hammerhead Ribozyme-Malachite Green Aptamer cleaves from the substrate. Hence, the substrate and the Hammerhead Ribozyme-Malachite Green Aptamer could be purified on a denaturing polyacrylamide gel electrophoresis (Fig. 2).
-[[File:Figure_6_final.png|300 px|right|Fig.1. Real time monitoring of the RNA synthesis using a Malachite Green Aptamer.(A) To analyze RNA synthesis in real time we applied a DNA template encoding for the RNA of interest (ROI) and a hammerhead ribozyme (HHR). Both fragments are inserted between the promotor (T7) and the Malachite Green Aptamer (MGA). Inducing the hammerhead ribozyme allows cleavage during the in vitrotranscription. Hereby two RNA fragments emerge, the ROI and the hammerhead ribozyme fused to Malachite Green Aptamer (HHR-MGA). Using such setup, the emitted fluorescence of the HHR-MGA will be independent on the applied ROI. Thus the fluorescence is induced by the Malachite Green Aptamer that can be applied to compare efficiencies of different RNAs at the same time. (B) As a proof of principle we performed transcriptions and monitored the malachite green fluorescence signal in real time. (C)To confirm the results of the fluorescence measurements as well as the transcription efficiency is not hampered by the malachite green dye, all in vitrotranscription reactions were analyzed using denaturing acrylamide gels.]]
+[[File:Figure_6_final.png|400 px|left|Fig.1. Real time monitoring of the RNA synthesis using a Malachite Green Aptamer.(A) To analyze RNA synthesis in real time we applied a DNA template encoding for the RNA of interest (ROI) and a hammerhead ribozyme (HHR). Both fragments are inserted between the promotor (T7) and the Malachite Green Aptamer (MGA). Inducing the hammerhead ribozyme allows cleavage during the in vitrotranscription. Hereby two RNA fragments emerge, the ROI and the hammerhead ribozyme fused to Malachite Green Aptamer (HHR-MGA). Using such setup, the emitted fluorescence of the HHR-MGA will be independent on the applied ROI. Thus the fluorescence is induced by the Malachite Green Aptamer that can be applied to compare efficiencies of different RNAs at the same time. (B) As a proof of principle we performed transcriptions and monitored the malachite green fluorescence signal in real time. (C)To confirm the results of the fluorescence measurements as well as the transcription efficiency is not hampered by the malachite green dye, all in vitrotranscription reactions were analyzed using denaturing acrylamide gels.]]
+[[File:Figure_11.png|400 px|right|Fig.2. Monitoring of the ATP consumption and RNA synthesis of difficult transcription templates. (A) Using our fluorescent tool box we can demonstrate again that substrate of RNA-cleaving DNAzyme causes problems during transcription. We can identify a slight decrease of Spinach fluorescence and increase in the Malachite Green signal. (B) We were applying a DNA template containing a HHR in front of the Malachite Green Aptamer, we analyzed cleavage by denaturing acrylamide gel electrophoresis. We could identify the cleaved HHR-MGA RNA by high sensitive Sybr Gold staining.]]
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 <span class='h3bb'>Sequence and Features</span>