Talk:CH391L/S13/In vitro Selection of FNAs

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Current revision (17:07, 18 February 2013) (view source)
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==FNAs Talk==
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==Noncoding RNAs==
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*'''[[User:Kevin Baldridge|Kevin Baldridge]] 17:24, 11 February 2013 (EST)''':The first thing I see is that small non-coding RNAs are not represented in this group. Maybe it would be a good idea to add a section about prokaryotic small RNAs or eukaryotic micro- or piwi-interacting RNAs that are involved in pre-translational regulation.
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**'''[[User:Alvaro E. Rodriguez M.|Alvaro E. Rodriguez M.]] 21:16, 11 February 2013 (EST)''':Hello Kevin he reason why none of the small non-coding RNAs are mentioned is that they do no perform any type of catalysis/ligand binding on their own.
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*'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 12:12, 17 February 2013 (EST)''':It probably would have been better to call this topic ''in vitro selection''. Functional nucleic acids just covers too much! We could have a completely separate topic about riboregulators and include small RNAs and the fun things people are doing with RNAi, etc.
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== Deoxyribozymes / Unnatural Bases ==
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*'''[[User:Benjamin Gilman|Benjamin Gilman]] 17:59, 11 February 2013 (EST)''': There's been been some work done on evolving deoxyribozymes (with or without unnatural bases) that catalyze a range of organic and inorganic synthesis reactions.  Checking out some papers from [http://chem.colorado.edu/index.php?option=com_content&view=article&id=249:bruce-eaton&catid=41:faculty&Itemid=93 Bruce Eaton] might be a good place to start.
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==First Ribozyme Discovered==
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**'''[[User:Alvaro E. Rodriguez M.|Alvaro E. Rodriguez M.]] 21:16, 11 February 2013 (EST)''': Hey, Ben do you happen to have a copy of the RNA world article were you mention RNase P as being discovered much earlier. I also appreciate the link to the Bruce Eaton page as it would be helpful to include his work in this wiki page.
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***'''[[User:Benjamin Gilman|Benjamin Gilman]] 12:30, 14 February 2013 (EST)''': I said that I thought RNase P was discovered before the tetrahymena group I intron, but I think it took a little while to figure out that the RNA portion of it was responsible for catalysis.  The best place to look wouldn't be the RNA world, it would be Sidney Altman's original papers about it, or any of the many reviews he's written since.  I'd bet that Jeff owns a copy of the RNA world though if you want to check it out.  The life science library also has it.
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***'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 12:12, 17 February 2013 (EST)''': Yes, I do own the newest version that they renamed "RNA Worlds", but I think I lost my earlier edition. Strangely, RNase P occurs nowhere in the current book. Older chapters, including ones that focused on self-splicing introns seem to have been replaced by newer topics.
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== General Content and Formatting ==
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*'''[[User:Gabriel Wu|Gabriel Wu]] 02:10, 14 February 2013 (EST)''': You have a note to self about including a discussion on RNA world. Include or move to talk section.
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*'''[[User:Gabriel Wu|Gabriel Wu]] 02:10, 14 February 2013 (EST)''': Ribozyme section is numbered twice.
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*'''[[User:Gabriel Wu|Gabriel Wu]] 02:10, 14 February 2013 (EST)''': Could you add a conclusion and/or a future directions section to put the topic in context?
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**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 12:12, 17 February 2013 (EST)''': Yeah. Come on. These are supposed to look complete at the time you present them. At least not with confusing misformatting and notes to yourself.
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*'''[[User:Max E. Rubinson|Max E. Rubinson]] 11:03, 14 February 2013 (EST)''': Can you update this page to include a more detailed discussion of ''in vitro'' selection methods and maybe discuss some potential applications of functional nucleic acids?
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*'''[[User:Evan J WeaverIEvan Weaver]] 17:52, 14 February 2013 (CST)''':  Could you put more links for ease of reading?  I find that if makes life much easier when there are good sources in a wiki page.  Also, could you better explain the different ribozymes in the classification?  A useful link or short explanation would be nice.  I also added a comma.
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**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 12:12, 17 February 2013 (EST)''': I'm not sure I see the usefulness of the classification. It's just a list -- and doesn't seem to really help with understanding the topic.
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== Greater catalytic potential of RNA ==
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*'''[[User:Aurko Dasgupta|Aurko Dasgupta]] 21:38, 14 February 2013 (EST)''':Is the 2'OH the key to RNA's greater catalytic tendencies? Does it play a role in RNA's significantly lower stability compared to DNA?
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**'''[[User:Evan J WeaverIEvan Weaver]] 21:52, 15 February 2013 (CST)''':  The 2' hydroxyl group can react with the phosphate group in the RNA backbone to cleave the RNA.  Not sure about RNA catalysis though.
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**'''[[User:Jeffrey E. Barrick|Jeffrey E. Barrick]] 12:12, 17 February 2013 (EST)''':Yes. That 2'OH gives RNA more structural and catalytic possibilities. It's good for positioning metal ions and can also participate in general acid-base catalysis (which is what happens when RNA cleaves itself). Still, there are good reasons for wanting to use modified bases with other functional groups to improve in vitro selection.

Current revision

Contents

Noncoding RNAs

  • Kevin Baldridge 17:24, 11 February 2013 (EST):The first thing I see is that small non-coding RNAs are not represented in this group. Maybe it would be a good idea to add a section about prokaryotic small RNAs or eukaryotic micro- or piwi-interacting RNAs that are involved in pre-translational regulation.
    • Alvaro E. Rodriguez M. 21:16, 11 February 2013 (EST):Hello Kevin he reason why none of the small non-coding RNAs are mentioned is that they do no perform any type of catalysis/ligand binding on their own.
  • Jeffrey E. Barrick 12:12, 17 February 2013 (EST):It probably would have been better to call this topic in vitro selection. Functional nucleic acids just covers too much! We could have a completely separate topic about riboregulators and include small RNAs and the fun things people are doing with RNAi, etc.

Deoxyribozymes / Unnatural Bases

  • Benjamin Gilman 17:59, 11 February 2013 (EST): There's been been some work done on evolving deoxyribozymes (with or without unnatural bases) that catalyze a range of organic and inorganic synthesis reactions. Checking out some papers from Bruce Eaton might be a good place to start.

First Ribozyme Discovered

    • Alvaro E. Rodriguez M. 21:16, 11 February 2013 (EST): Hey, Ben do you happen to have a copy of the RNA world article were you mention RNase P as being discovered much earlier. I also appreciate the link to the Bruce Eaton page as it would be helpful to include his work in this wiki page.
      • Benjamin Gilman 12:30, 14 February 2013 (EST): I said that I thought RNase P was discovered before the tetrahymena group I intron, but I think it took a little while to figure out that the RNA portion of it was responsible for catalysis. The best place to look wouldn't be the RNA world, it would be Sidney Altman's original papers about it, or any of the many reviews he's written since. I'd bet that Jeff owns a copy of the RNA world though if you want to check it out. The life science library also has it.
      • Jeffrey E. Barrick 12:12, 17 February 2013 (EST): Yes, I do own the newest version that they renamed "RNA Worlds", but I think I lost my earlier edition. Strangely, RNase P occurs nowhere in the current book. Older chapters, including ones that focused on self-splicing introns seem to have been replaced by newer topics.

General Content and Formatting

  • Gabriel Wu 02:10, 14 February 2013 (EST): You have a note to self about including a discussion on RNA world. Include or move to talk section.
  • Gabriel Wu 02:10, 14 February 2013 (EST): Ribozyme section is numbered twice.
  • Gabriel Wu 02:10, 14 February 2013 (EST): Could you add a conclusion and/or a future directions section to put the topic in context?
    • Jeffrey E. Barrick 12:12, 17 February 2013 (EST): Yeah. Come on. These are supposed to look complete at the time you present them. At least not with confusing misformatting and notes to yourself.
  • Max E. Rubinson 11:03, 14 February 2013 (EST): Can you update this page to include a more detailed discussion of in vitro selection methods and maybe discuss some potential applications of functional nucleic acids?
  • User:Evan J WeaverIEvan Weaver 17:52, 14 February 2013 (CST): Could you put more links for ease of reading? I find that if makes life much easier when there are good sources in a wiki page. Also, could you better explain the different ribozymes in the classification? A useful link or short explanation would be nice. I also added a comma.
    • Jeffrey E. Barrick 12:12, 17 February 2013 (EST): I'm not sure I see the usefulness of the classification. It's just a list -- and doesn't seem to really help with understanding the topic.

Greater catalytic potential of RNA

  • Aurko Dasgupta 21:38, 14 February 2013 (EST):Is the 2'OH the key to RNA's greater catalytic tendencies? Does it play a role in RNA's significantly lower stability compared to DNA?
    • User:Evan J WeaverIEvan Weaver 21:52, 15 February 2013 (CST): The 2' hydroxyl group can react with the phosphate group in the RNA backbone to cleave the RNA. Not sure about RNA catalysis though.
    • Jeffrey E. Barrick 12:12, 17 February 2013 (EST):Yes. That 2'OH gives RNA more structural and catalytic possibilities. It's good for positioning metal ions and can also participate in general acid-base catalysis (which is what happens when RNA cleaves itself). Still, there are good reasons for wanting to use modified bases with other functional groups to improve in vitro selection.
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