20.109(S11):Module 1 - Revision history

AgiStachowiak at 18:48, 31 January 2011

2011-01-31T18:48:05Z

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	[[20.109(S11):Purify RNA and run affinity column (Day4)\| Module 1 Day 4: Purify RNA and run affinity column]]<br>		[[20.109(S11):Purify RNA and run affinity column (Day4)\| Module 1 Day 4: Purify RNA and run affinity column]]<br>
	[[20.109(S11):RNA to DNA by RT-PCR (Day5)\| Module 1 Day 5: RNA to DNA by RT-PCR]]<br>		[[20.109(S11):RNA to DNA by RT-PCR (Day5)\| Module 1 Day 5: RNA to DNA by RT-PCR]]<br>
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		+	Note: 1 week between day 5 and day 6.
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	[[20.109(S11):Post-selection IVT and journal club (Day6)\| Module 1 Day 6: Post-selection IVT and journal club]]<br>		[[20.109(S11):Post-selection IVT and journal club (Day6)\| Module 1 Day 6: Post-selection IVT and journal club]]<br>
	[[20.109(S11):Aptamer binding assay (Day7)\| Module 1 Day 7: Aptamer binding assay]]<br>		[[20.109(S11):Aptamer binding assay (Day7)\| Module 1 Day 7: Aptamer binding assay]]<br>

Carrie M Thompson at 21:54, 17 January 2011

2011-01-17T21:54:17Z

←Older revision		Revision as of 21:54, 17 January 2011
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	'''Instructors:''' [http://web.mit.edu/be/people/niles.htm Jacquin Niles] and [[User:AgiStachowiak\| Agi Stachowiak]]		'''Instructors:''' [http://web.mit.edu/be/people/niles.htm Jacquin Niles] and [[User:AgiStachowiak\| Agi Stachowiak]]

-	'''TA:''' Carrie Thompson	+	'''TA:''' [[User:Carrie M Thompson\| Carrie Thompson]]

	In this module you will investigate RNA aptamer selection. You may already be familiar with biological entities that bind to specific molecules, such as antibody proteins or their peptide derivatives. Short fragments of RNA can also have high-order structures that allow them to bind a target molecule with good affinity and specificity; successful binders are called aptamers. Normally, RNA aptamers that bind particular targets are found by screening many candidates at random in a process called SELEX, or systematic evolution of ligands by exponential enrichment. (Predictive computational tools can also be used to design rather than select aptamers.) In the coming weeks, you will essentially perform one round of SELEX. Because SELEX typically takes several rounds to isolate target-binding aptamers, you will start with a known RNA mixture rather than than a completely random library. Your goal will be to explore what experimental parameters affect the enrichment of a heme-binding RNA aptamer from a mixture of heme-binding and non-binding RNAs.		In this module you will investigate RNA aptamer selection. You may already be familiar with biological entities that bind to specific molecules, such as antibody proteins or their peptide derivatives. Short fragments of RNA can also have high-order structures that allow them to bind a target molecule with good affinity and specificity; successful binders are called aptamers. Normally, RNA aptamers that bind particular targets are found by screening many candidates at random in a process called SELEX, or systematic evolution of ligands by exponential enrichment. (Predictive computational tools can also be used to design rather than select aptamers.) In the coming weeks, you will essentially perform one round of SELEX. Because SELEX typically takes several rounds to isolate target-binding aptamers, you will start with a known RNA mixture rather than than a completely random library. Your goal will be to explore what experimental parameters affect the enrichment of a heme-binding RNA aptamer from a mixture of heme-binding and non-binding RNAs.

AgiStachowiak: New page: {{Template:20.109(S11)}}
==Module 1== '''Instructors:''' [http://web.mit.edu/be/people/niles.htm Jacquin Niles] an...

2010-11-23T18:44:29Z

New page: {{Template:20.109(S11)}} <div style="padding: 10px; width: 640px; border: 5px solid #3399FF;"> ==Module 1== '''Instructors:''' [http://web.mit.edu/be/people/niles.htm Jacquin Niles] an...

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==Module 1==

'''Instructors:''' [http://web.mit.edu/be/people/niles.htm Jacquin Niles] and [[User:AgiStachowiak| Agi Stachowiak]]

'''TA:''' Carrie Thompson

In this module you will investigate RNA aptamer selection. You may already be familiar with biological entities that bind to specific molecules, such as antibody proteins or their peptide derivatives. Short fragments of RNA can also have high-order structures that allow them to bind a target molecule with good affinity and specificity; successful binders are called aptamers. Normally, RNA aptamers that bind particular targets are found by screening many candidates at random in a process called SELEX, or systematic evolution of ligands by exponential enrichment. (Predictive computational tools can also be used to design rather than select aptamers.) In the coming weeks, you will essentially perform one round of SELEX. Because SELEX typically takes several rounds to isolate target-binding aptamers, you will start with a known RNA mixture rather than than a completely random library. Your goal will be to explore what experimental parameters affect the enrichment of a heme-binding RNA aptamer from a mixture of heme-binding and non-binding RNAs.

We thank 20.109 instructor [[Natalie Kuldell]] for helpful discussions and for acquiring funding for module development.

[[Image:20109_6-5_crop.png|thumb|center|400px|'''Structure of a putative aptamer''' Image was prepared using ''RNA folding'' at http://mfold.bioinfo.rpi.edu/]]

[[20.109(S11):Amplify aptamer-encoding DNA (Day1)| Module 1 Day 1: Amplify aptamer-encoding DNA]]<br>
[[20.109(S11):Purify aptamer-encoding DNA (Day2)| Module 1 Day 2: Purify aptamer-encoding DNA]]<br>
[[20.109(S11):Prepare RNA by IVT (Day3)| Module 1 Day 3: Prepare RNA by IVT]]<br>
[[20.109(S11):Purify RNA and run affinity column (Day4)| Module 1 Day 4: Purify RNA and run affinity column]]<br>
[[20.109(S11):RNA to DNA by RT-PCR (Day5)| Module 1 Day 5: RNA to DNA by RT-PCR]]<br>
[[20.109(S11):Post-selection IVT and journal club (Day6)| Module 1 Day 6: Post-selection IVT and journal club]]<br>
[[20.109(S11):Aptamer binding assay (Day7)| Module 1 Day 7: Aptamer binding assay]]<br>
[[20.109(S11):Journal club (Day8)| Module 1 Day 8: Journal club]]<br>

[[20.109(S11): RNA engineering report | Laboratory Report]]<br>
[[20.109(S11): RNA computational analysis | Computational analysis]]

[[20.109(S11): TA notes for module 1| TA notes, mod 1]]

20.109(S11):Module 1 - Revision history

AgiStachowiak at 18:48, 31 January 2011

Carrie M Thompson at 21:54, 17 January 2011

AgiStachowiak: New page: {{Template:20.109(S11)}} ==Module 1== '''Instructors:''' [http://web.mit.edu/be/people/niles.htm Jacquin Niles] an...

AgiStachowiak: New page: {{Template:20.109(S11)}}
==Module 1== '''Instructors:''' [http://web.mit.edu/be/people/niles.htm Jacquin Niles] an...