Difference between revisions of "Team:Heidelberg/Software"

Revision as of 03:39, 19 September 2015

Software

Nowadays detection of new aptamers is dependent on systematic evolution of ligands by exponential enrichment (SELEX)ellington1990tuerk1990bartel1993. This process involves numerous cycles to select potential candidates from a random pool. These selected sequences have to be further mutated over and over again in order to generate an aptamer with a high affinity. To substitute this very time consuming and expensive SELEX we developed a new software with different featuressoftware Making Apatmers Without SELEX (MAWS), which enables us to efficiently generate new aptamers within less than a day compared. Thus we were able to predict many aptamers by MAWS and validated them in different assay during the summer. If we had been restricted to use the existing methods this would not have been possible. Every aptamer bears the potential to be used as module in order to generate switchable aptazymes.Soukup In order to obtain the best possible fusion of an aptamer with a ribozyme or DNAzyme another SELEX with several cycles would have been needed. In order to bypass this second time-cosuming SELEX we developed Joining Apatmers Without SELEX (JAWS). We are able to optimize the transition element to create a bistable system where either one conformation is favored in presence of the ligand while the other one is in absence of the ligand. MAWS enables the scientific community the possibility to generate aptamers for any ligand in silico. The JAWS generated modules can be fused to a ribozyme or DNAzyme to create ligand-dependent tools. JAWS thus bypasses the requirement for SELEX and, in conjunction with MAWS, enables rapid design-prototype-test cycles, drastically improving the stardardization and modularization of nucleic acid-based devices. Read more about MAWS Read more about JAWS

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-Until now aptamers could only be created through a laborious in vitro procedure made of successive rounds of selection (SELEX). We read an inspirational paper, in which the authors proposed in their discussion the possibility to create aptamers via an in silico approach (note that they did not implement the software but simply wrote down some suggestions as how it could be done) Tseng2011. We therefore got excited at the idea of implementing such software. We created the software (open source) and called it MAWS. We could experimentally prove that the software can design functional aptamers. Moreover, we created a second software (JAWS) to in silico ligate in the most optimal way an aptamer with a ribozyme or DNAzyme. Also the results coming from this software were amply validated with experiments.
+Nowadays detection of new aptamers is dependent on systematic evolution of ligands by exponential enrichment (SELEX)<x-ref>ellington1990</x-ref><x-ref>tuerk1990</x-ref><x-ref>bartel1993</x-ref>. This process involves numerous cycles to select potential candidates from a random pool. These selected sequences have to be further mutated over and over again in order to generate an aptamer with a high affinity.
+To substitute this very time consuming and expensive SELEX we developed a new software with different featuressoftware <b>M</b>aking <b>A</b>patmers <b>W</b>ithout <b>S</b>ELEX (MAWS), which enables us to efficiently generate new aptamers within less than a day compared. Thus we were able to predict many aptamers by MAWS and validated them in different assay during the summer. If we had been restricted to use the existing methods this would not have been possible.
+Every aptamer bears the potential to be used as module in order to generate switchable aptazymes.<x-ref>Soukup</x-ref> In order to obtain the best possible fusion of an aptamer with a ribozyme or DNAzyme another SELEX with several cycles would have been needed. In order to bypass this second time-cosuming SELEX we developed <b>J</b>oining <b>A</b>patmers <b>W</b>ithout <b>S</b>ELEX (JAWS). We are able to optimize the transition element to create a bistable system where either one conformation is favored in presence of the ligand while the other one is in absence of the ligand.
+MAWS enables the scientific community the possibility to generate aptamers for any ligand <i>in silico</i>. The JAWS generated modules can be fused to a ribozyme or DNAzyme to create ligand-dependent tools. JAWS thus bypasses the requirement for SELEX and, in conjunction with MAWS, enables rapid design-prototype-test cycles, drastically improving the stardardization and modularization of nucleic acid-based devices.