IGEM:Peking/2007/Count-Conjugation-Procedure: Difference between revisions
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=Make more independent riboregulators= | ==Conjugation Test== | ||
* We choose to use <bbpart> | * We want to do a conjugation efficiency test with wild type F to verify the protocol. | ||
* crRNA is synthesized as two partially overlap ~ | * And then test the conjugation efficiency with all the plasmids at hand. | ||
* crRNA should be cut by | * This is '''the exact experimental''' [[IGEM:Peking/2007/Count-Procedure-Conjugation | '''procedure''']] | ||
==Helper plasmids construction== | |||
* To construct helper plasmids, we need to knock out the oriT. | |||
* To put conjugation under control, we need to knock out the relaxase. | |||
* The Knockout method: '''(Anting please explain your method here) | |||
''' | |||
==Make more independent riboregulators(Lock & Key section)== | |||
* We choose to use <bbpart>pSB1A2</bbpart> and <bbpart>BBa_R0010</bbpart>(Plac) to express the taRNA(<bbpart>J23066</bbpart>), and <bbpart>pSB3K3</bbpart> and <bbpart>BBa_R0040</bbpart> to express <bbpart>BBa_E0040</bbpart>, whose translation is under the control of crRNA. | |||
* crRNA is synthesized as two partially overlap ~70bp long primers, and 5 cycles PCR can make it to a dsDNA with some BioBrick cloning sites flanked. ('''"2 primer strategy"'''--sunnyboy 05:26, 31 August 2007 (EDT)) | |||
* crRNA should be cut by XbaI at 5' and PstI at 3' and cloned into BBa_R0040 to get the full length BioBrick prefix and suffix.--[[User:YangYifan|YangYifan]] 04:19, 9 July 2007 (EDT) | |||
* First, we will try out the UC Berkley riboregulators <bbpart>BBa_J23078</bbpart> and <bbpart>BBa_J23066</bbpart> first. | * First, we will try out the UC Berkley riboregulators <bbpart>BBa_J23078</bbpart> and <bbpart>BBa_J23066</bbpart> first. | ||
* This is '''the exact experimental''' [[IGEM:Peking/2007/Count-Procedure-Riboregulator | '''procedure''']]. | * This is '''the exact experimental''' [[IGEM:Peking/2007/Count-Procedure-Riboregulator | '''procedure''']]. | ||
===Supplement by Yu Tao=== | |||
*For conveniency, we abbreviate this section as '''''"Lock & Key"'''''. (I learn this from UC Berkeley team.) | |||
*As is mentioned, the crRNA is the ''Lock'', and we use the '''"2 primer" strategy''' (as indicated by Yang Yifan) to synthesize the ''Lock''. | |||
*As for ''Key'' which is not mentioned above, we first tried '''"3 primer" strategy'''(similar to '''"2 primer" strategy''', but we divided ''Key'' into 3 overlap parts so that we were able to synthesize the shorter parts at a relatively lower price), but failed. Now we'd better try the '''"2 primer" strategy'''. | |||
==Construct the tandem oriT region== | |||
* For each conjugation plasmids, we want to construct oriT-taRNA-dbTerm-oriT. | |||
* And Plac to the 5' and GFP to the 3' to test conjugation and deletion. | |||
* Use pSB1A3 as backbone. | |||
* This is '''the exact experimental''' [[IGEM:Peking/2007/Count-Procedure-tandem-oriT | '''procedure''']]. | |||
==Put the relaxase under the crRNA control== | |||
==Assemble the tandem oriT together== | |||
==Hop count experiement== | |||
This is our goal. |
Latest revision as of 02:26, 31 August 2007
Conjugation Test
- We want to do a conjugation efficiency test with wild type F to verify the protocol.
- And then test the conjugation efficiency with all the plasmids at hand.
- This is the exact experimental procedure
Helper plasmids construction
- To construct helper plasmids, we need to knock out the oriT.
- To put conjugation under control, we need to knock out the relaxase.
- The Knockout method: (Anting please explain your method here)
Make more independent riboregulators(Lock & Key section)
- We choose to use <bbpart>pSB1A2</bbpart> and <bbpart>BBa_R0010</bbpart>(Plac) to express the taRNA(<bbpart>J23066</bbpart>), and <bbpart>pSB3K3</bbpart> and <bbpart>BBa_R0040</bbpart> to express <bbpart>BBa_E0040</bbpart>, whose translation is under the control of crRNA.
- crRNA is synthesized as two partially overlap ~70bp long primers, and 5 cycles PCR can make it to a dsDNA with some BioBrick cloning sites flanked. ("2 primer strategy"--sunnyboy 05:26, 31 August 2007 (EDT))
- crRNA should be cut by XbaI at 5' and PstI at 3' and cloned into BBa_R0040 to get the full length BioBrick prefix and suffix.--YangYifan 04:19, 9 July 2007 (EDT)
- First, we will try out the UC Berkley riboregulators <bbpart>BBa_J23078</bbpart> and <bbpart>BBa_J23066</bbpart> first.
- This is the exact experimental procedure.
Supplement by Yu Tao
- For conveniency, we abbreviate this section as "Lock & Key". (I learn this from UC Berkeley team.)
- As is mentioned, the crRNA is the Lock, and we use the "2 primer" strategy (as indicated by Yang Yifan) to synthesize the Lock.
- As for Key which is not mentioned above, we first tried "3 primer" strategy(similar to "2 primer" strategy, but we divided Key into 3 overlap parts so that we were able to synthesize the shorter parts at a relatively lower price), but failed. Now we'd better try the "2 primer" strategy.
Construct the tandem oriT region
- For each conjugation plasmids, we want to construct oriT-taRNA-dbTerm-oriT.
- And Plac to the 5' and GFP to the 3' to test conjugation and deletion.
- Use pSB1A3 as backbone.
- This is the exact experimental procedure.
Put the relaxase under the crRNA control
Assemble the tandem oriT together
Hop count experiement
This is our goal.