Difference between revisions of "MWSU Different Riboswitches"
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Software [http://www.ibridgenetwork.org/rpi/unafold UNAFold] has been created that can predict the folding or hybridization of one or two single-stranded RNA or DNA molecules using free energy parameters. Partition function calculations predict base pair probabilities , stochastic samples of foldings or hybridization, and melting profiles as a function of increasing temperature. This software may be useful in predicting how the known riboswitches (AddA, M6, etc.) fold up when the ligand binds to the aptamer. With this knowledge we might be able to construct alternate riboswitches that function better in the melamine to ammeline system. Hopefully, we can get current riboswitches to show programmed evolution and will not need this software, but future experiments might benefit from its use. The UNAFold Academic License costs $50.00. We should use known riboswitches from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840279/ Dixon's article] (AddA, M6, M6C, M6', M6", M6C', M6C") with melamine deaminase before experimenting with new riboswitches. | Software [http://www.ibridgenetwork.org/rpi/unafold UNAFold] has been created that can predict the folding or hybridization of one or two single-stranded RNA or DNA molecules using free energy parameters. Partition function calculations predict base pair probabilities , stochastic samples of foldings or hybridization, and melting profiles as a function of increasing temperature. This software may be useful in predicting how the known riboswitches (AddA, M6, etc.) fold up when the ligand binds to the aptamer. With this knowledge we might be able to construct alternate riboswitches that function better in the melamine to ammeline system. Hopefully, we can get current riboswitches to show programmed evolution and will not need this software, but future experiments might benefit from its use. The UNAFold Academic License costs $50.00. We should use known riboswitches from [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840279/ Dixon's article] (AddA, M6, M6C, M6', M6", M6C', M6C") with melamine deaminase before experimenting with new riboswitches. | ||
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| + | == May 22, 2014 == | ||
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| + | In order to predict the folding of our current riboswitches, a program called NAVA can use base pairing probabilities to predict the secondary structure of the RNA. This [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514005/ article] discusses the math behind the base-pairing probability matrix which is used in NAVA to predict the folding we would like to observe. | ||
Revision as of 13:23, 22 May 2014
Research
May 21, 2014
Software UNAFold has been created that can predict the folding or hybridization of one or two single-stranded RNA or DNA molecules using free energy parameters. Partition function calculations predict base pair probabilities , stochastic samples of foldings or hybridization, and melting profiles as a function of increasing temperature. This software may be useful in predicting how the known riboswitches (AddA, M6, etc.) fold up when the ligand binds to the aptamer. With this knowledge we might be able to construct alternate riboswitches that function better in the melamine to ammeline system. Hopefully, we can get current riboswitches to show programmed evolution and will not need this software, but future experiments might benefit from its use. The UNAFold Academic License costs $50.00. We should use known riboswitches from Dixon's article (AddA, M6, M6C, M6', M6", M6C', M6C") with melamine deaminase before experimenting with new riboswitches.
May 22, 2014
In order to predict the folding of our current riboswitches, a program called NAVA can use base pairing probabilities to predict the secondary structure of the RNA. This article discusses the math behind the base-pairing probability matrix which is used in NAVA to predict the folding we would like to observe.
