Talk:CH391L/S13/Riboswitches: Difference between revisions
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*'''[[User:Catherine I. Mortensen|Catherine I. Mortensen]] 13:45, 25 February 2013 (EST)''': How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein? | *'''[[User:Catherine I. Mortensen|Catherine I. Mortensen]] 13:45, 25 February 2013 (EST)''': How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein? | ||
**'''[[User:Benjamin Gilman|Benjamin Gilman]] 18:15, 28 February 2013 (EST)''': For that application it's not useful at all, but in a previous paper they used a fluorescently tagged version of the same aptamer to detect TNT ''in vitro'' in a purpose-built instrument [http://link.springer.com/article/10.1007%2Fs00216-008-2150-5 Biosensor-based on-site explosives detection using aptamers as recognition elements]. The aptamer was generated to bind TNT, but DNT was used in the later paper because it's easier to obtain and still binds well. The E.coli system may be more sensitive for detecting small amounts of DNT or TNT in things like groundwater, where they're using it to detect contamination and the speed of the test doesn't matter as much. | |||
*'''[[User:Kevin Baldridge|Kevin Baldridge]] 17:08, 25 February 2013 (EST)''':Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system. | *'''[[User:Kevin Baldridge|Kevin Baldridge]] 17:08, 25 February 2013 (EST)''':Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system. | ||
**'''[[User:Catherine I. Mortensen|Catherine I. Mortensen]] 08:59, 26 February 2013 (EST)''':What would be the advantage of IRES as opposed to a Shine Dalgarno? | **'''[[User:Catherine I. Mortensen|Catherine I. Mortensen]] 08:59, 26 February 2013 (EST)''':What would be the advantage of IRES as opposed to a Shine Dalgarno? | ||
Revision as of 16:15, 28 February 2013
- Catherine I. Mortensen 13:45, 25 February 2013 (EST): How practical is DNT detecting E. Coli in airports and other public areas considering the time it takes for E. Coli to start producing fluorescent protein?
- Benjamin Gilman 18:15, 28 February 2013 (EST): For that application it's not useful at all, but in a previous paper they used a fluorescently tagged version of the same aptamer to detect TNT in vitro in a purpose-built instrument Biosensor-based on-site explosives detection using aptamers as recognition elements. The aptamer was generated to bind TNT, but DNT was used in the later paper because it's easier to obtain and still binds well. The E.coli system may be more sensitive for detecting small amounts of DNT or TNT in things like groundwater, where they're using it to detect contamination and the speed of the test doesn't matter as much.
- Kevin Baldridge 17:08, 25 February 2013 (EST):Are there any known examples of a riboswitch with an IRES (Internal Ribosome Entry Site, an alternate way to initiate translation that doesn't use the Shine Dalgarno sequence) expression platform? If not, that might be something we could look into for iGEM, directed evolution or SELEX to design such a system.
- Catherine I. Mortensen 08:59, 26 February 2013 (EST):What would be the advantage of IRES as opposed to a Shine Dalgarno?
- Gabriel Wu 17:17, 25 February 2013 (EST): Connecting with Max's topic, directed evolution strategies are very relevant in developing riboswitches, especially for aptamer design. Might be nice to discuss the connection between the two topics.
- Kevin Baldridge 17:18, 25 February 2013 (EST):Here is a nice example of taking advantage of riboswitch concepts for synthetic biology Isaacs 2004, our group is working on developing a probe for in vivo analysis of RNA tertiary structure
- Kevin Baldridge 17:26, 25 February 2013 (EST):it looks like your biblio section might have a few of the entries merged together at the end?
- Catherine I. Mortensen 08:59, 26 February 2013 (EST): Thank you! Fixed.
