Biomod/2011/IITM/AcidArtists/Work diary: Difference between revisions

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(New page: <html> <head> <style> →‎#bodyContent{text-align:center;}: ul.polaroids { width: 970px; margin: 0 0 18px -30px; } ul.polaroids li { display: inline; } ul.polaroids a{display: inli...)
 
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Revision as of 17:05, 2 November 2011

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<div id="brain_storming" style="width:80%;"> <pre> Work Diary August 

Week 3

Made our first structure using cadnano (i.e. smiley) Started our work on the Cadnano design of the aggregator molecule Week 4 Completed the final cadnano design of the aggregator molecule September Week 1 Ordered the staples for our prototype model Made an Excel sheet Week 2 Dilluted the staples to a final concentration of 200uM and storted at 40C Concentration measured using nanodrop and updated the excel sheet

Week 3 Isolated the plasmid pGEX-4T1 from E-coli using phenol chloroform method and stored at 40C Purity was checked using Gel Electrophoresis Concentration of Plasmid was measured using nanodrop Week 4 200uM concentration of staples stock was further diluted to 15uM. Scaffold stock having 0.1uM concentration was made


First PCR reaction set 10x folding Buffer = 5ul Scaffold = 10ul 1ul of each staple *16 = 16ul (Assuming Staples Stock Concentration is 15ul) DEPC water = 19ul Concentration of PCR reaction Mix Staples 300nM each 

Scaffold 20nM

PCR Program 1. T= 95 for 05:00min 2. T=90 for 01:00 min 3. -10C 4. Go to 2 repeat 65 times 5. Hold at 4 0C


Gel Electrophoresis 2% agarose gel was made Result No bands corresponding to the structure seen October Week 1 Made the PCR reaction mixture having the same concentration as that of the previous one 

Gel Electrophoresis

1% agarose gel was made Result No bands corresponding to the structure seen Week2 Made the new scaffold stock having 0.25uM concentration Made the PCR reaction mixture having the following concentration 10x folding Buffer = 5ul Scaffold = 8ul 2ul of each staple *16 = 32ul (Assuming Staples Stock Concentration is 15ul) DEPC water = 5ul Concentration of PCR reaction Mix Staples 600nM each 

Scaffold 40nM

Gel Electrophoresis 1% agarose gel was made Results: No bands corresponding to the structure seen Week 3 

Made the PCR reaction mixture having the following concentration

10x folding Buffer = 5ul Scaffold = 8ul 2ul of each staple *16 = 32ul (Assuming Staples Stock Concentration is 15ul) DEPC water = 5ul Concentration of PCR reaction Mix Staples 600nM each 

Scaffold 40nM

Gel Electrophoresis New Runnig buffer made using Mg(OAc)2 instead of MgCl2 1% agarose gel was made Results+ No bands corresponding to the structure seen Week 4 Made the PCR reaction mixture having the following concentration 10x folding Buffer = 5ul Scaffold = 8ul 2ul of each staple *16 = 32ul (Assuming Staples Stock Concentration is 15ul) DEPC water = 5ul Concentration of PCR reaction Mix Staples 600nM each 

Scaffold 40nM

PCR Program used 1) T= 95 for 05:00min 2) T=90 for 04:00 min 3) -10C 4) Go to 2 repeat 30 times 5) T = 60 C for 05:00 mins 6) -0.5 degree celcius 7) Goto 5 repeat 71 times 8) Hold at 4 0C

GEL Electrophoresis Runnig buffer having Mg(OAc)2 was used 0.3% agarose gel was made Results Bands corresponding to the structure seen</pre>

</div>


<div class="stack"> <img src="http://openwetware.org/images/9/9f/Stack.png" alt="stack"> <ul id="stack"> <li><a href=""><span>Reference Papers</span><img src="http://openwetware.org/images/1/13/Papers.png" alt="Papers"></a></li> <li><a href=""><span>Brain Stroming</span><img src="http://openwetware.org/images/3/3f/Brain.png" alt="Brain Storming"></a></li> <li><a href=""><span>Work Diary</span><img src="http://openwetware.org/images/2/2a/Diary.png" alt="Work diary"></a></li> <li><a href=""><span>Team</span><img src="http://openwetware.org/images/6/62/Team_iitm.jpg" alt="Team"></a></li> <li><a href=""><span>Project</span><img src="http://openwetware.org/images/f/f0/Home-sm.png" alt="Project"></a></li> </ul> </div>


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