http://2007.igem.org/wiki/index.php?title=Melbourne/Lab_Notebook_gv_2&feed=atom&action=history
Melbourne/Lab Notebook gv 2 - Revision history
2024-03-29T00:00:41Z
Revision history for this page on the wiki
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http://2007.igem.org/wiki/index.php?title=Melbourne/Lab_Notebook_gv_2&diff=41317&oldid=prev
PhillipDodson at 12:31, 26 October 2007
2007-10-26T12:31:32Z
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<td colspan='2' style="background-color: white; color:black;">Revision as of 12:31, 26 October 2007</td>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Melbourne/Lab GV Notebook| <Return to lab book summary>]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Prepared for site dirrected mutagenesis==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Prepared for site dirrected mutagenesis==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*resuspended primers supplied by geneworks to produce stock solution at 125ng/uL using filtered,autoclaved,milliQ water.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*resuspended primers supplied by geneworks to produce stock solution at 125ng/uL using filtered,autoclaved,milliQ water.</div></td></tr>
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PhillipDodson
http://2007.igem.org/wiki/index.php?title=Melbourne/Lab_Notebook_gv_2&diff=36776&oldid=prev
PhillipDodson at 13:06, 25 October 2007
2007-10-25T13:06:48Z
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<td colspan='2' style="background-color: white; color:black;">Revision as of 13:06, 25 October 2007</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>!pNL29T1-(GvpL-g351a)->!!6 || !! 6871|| 2112!! <-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>!pNL29T1-(GvpL-g351a)->!!6 || !! 6871|| 2112!! <-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*Results of PstI diagnostics: </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*Results of PstI diagnostics: <ins class="diffchange diffchange-inline">[[Image:Melbourne-gv mut1B.jpg|right|thumb|400px|PstI digest]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**pNL29 control was barely visable.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**pNL29 control was barely visable.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**Bands less than 300bp were not visable</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**Bands less than 300bp were not visable</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**See Gel</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**See Gel</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**Conclude that 5A and 6A are suitable templates for the second round of mutagenesis.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**Conclude that 5A and 6A are suitable templates for the second round of mutagenesis.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>*Results of EcoRI diagnostics:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>*Results of EcoRI diagnostics: <ins class="diffchange diffchange-inline"> [[Image:Melbourne gv mut 1A.jpg|right|thumb|400px|EcoRI & BamHI digests]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**pNL26 control barely visable.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**pNL26 control barely visable.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**Colonies 11A,B,C,D and 10A,B,C,D,E all show required pattern but the 33bp band is unlikely to be visible making the 10A..E test inconclusive, and the 220bp band in 11A..D is only barely visible in 11A..E making its diagnosis also risky.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>**Colonies 11A,B,C,D and 10A,B,C,D,E all show required pattern but the 33bp band is unlikely to be visible making the 10A..E test inconclusive, and the 220bp band in 11A..D is only barely visible in 11A..E making its diagnosis also risky.</div></td></tr>
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PhillipDodson
http://2007.igem.org/wiki/index.php?title=Melbourne/Lab_Notebook_gv_2&diff=22983&oldid=prev
PhillipDodson at 01:41, 5 October 2007
2007-10-05T01:41:06Z
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<td colspan='2' style="background-color: white; color:black;">Revision as of 01:41, 5 October 2007</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Site dirrected Mutagenesis Round #1 ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Site dirrected Mutagenesis Round #1 ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Applied the [[Melbourne/Site directed mutagenesis|stratagene Site directed mutagenesis protocol]]to the following DNA and primer pairs, which when plated out on LB AMP plates producing the numbers of colonies shown. Several of these were picked and tubes marked with a character suffix as shown in table.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Applied the [[Melbourne/Site directed mutagenesis|stratagene Site directed mutagenesis protocol]]to the following DNA and primer pairs, which when plated out on LB AMP plates producing the numbers of colonies shown. Several of these were picked and tubes marked with a character suffix as shown in table.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| border="1"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| border="1"</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|+ Site dirrected Mutagenesis round #1</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|+ Site dirrected Mutagenesis round #1</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[Melb:Miniprep protocol|Minipreped remaining culture (4mL) giving 100uL.]] </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[Melb:Miniprep protocol|Minipreped remaining culture (4mL) giving 100uL.]] </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[Melbourne/equipement/Measure DNA|Measure DNA concentrations]] using 2uL of miniprep(100uL) diluted in 98uL of TE.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* [[Melbourne/equipement/Measure DNA|Measure DNA concentrations]] using 2uL of miniprep(100uL) diluted in 98uL of TE.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|| border="1"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{|| border="1"</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|+ DNA concentrations in ng/uL</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|+ DNA concentrations in ng/uL</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 73:</td>
<td colspan="2" class="diff-lineno">Line 75:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Digest Pattern</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Digest Pattern</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Expected effects</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Expected effects</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| border="1"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| border="1"</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|+ PstI digest</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|+ PstI digest</div></td></tr>
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<td colspan="2" class="diff-lineno">Line 81:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>!History!!Mutation tube !!FRAGMENTS</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>!History!!Mutation tube !!FRAGMENTS</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL29T1!!pNL29T1|| <del class="diffchange diffchange-inline"> </del>5983|| 2516|| 378|| 105</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL29T1!!pNL29T1 <ins class="diffchange diffchange-inline"> || </ins>|| 5983|| 2516|| 378|| 105</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL29T1-(GvpP-g441a)->!!3!!6088 || 2516 || 378!! <-</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL29T1-(GvpP-g441a)->!!3<ins class="diffchange diffchange-inline">|| </ins>!!6088 || 2516 || 378!! <-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL29T1-(GvpL-g318a)->!!4 || 5983|| 2516!!483!! <- </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL29T1-(GvpL-g318a)->!!4 <ins class="diffchange diffchange-inline">|| </ins>||5983|| 2516!!483!! <- </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL29T1-(Comp-g318a)->!!5|| 5983|| 2516!!483!! <- </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL29T1-(Comp-g318a)->!!5<ins class="diffchange diffchange-inline">|| </ins>||5983|| 2516!!483!! <- </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL29T1-(GvpL-g351a)->!!6|| 5983|| 2516|| 378|| 105</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL29T1-(GvpL-g351a)->!!6<ins class="diffchange diffchange-inline">|| </ins>||5983|| 2516|| 378|| 105</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL26P3!!pNL26P3|| <del class="diffchange diffchange-inline"> </del>3928 || 3137 || 2516 || 378 || 220 || 105 || 33</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL26P3!!pNL26P3|| <ins class="diffchange diffchange-inline"> ||</ins>3928 || 3137 || 2516 || 378 || 220 || 105 || 33</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!p26P3-(GvpQ-g183a)->!!10|| 3928 !! 3170 || 2516 || 378 || 220 || 105 !! <-</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!p26P3-(GvpQ-g183a)->!!10<ins class="diffchange diffchange-inline">|| </ins>||3928 !! 3170 || 2516 || 378 || 220 || 105 !! <-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!p26P3-(GvpP-g441a)->!!11!! 4148 || 3137 || 2516 || 378 !! <- || 105 || 33</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!p26P3-(GvpP-g441a)->!!11!! <ins class="diffchange diffchange-inline"> ||</ins>4148 || 3137 || 2516 || 378 !! <- || 105 || 33</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| border="1"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| border="1"</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|+ EcoRI and BamHI digest</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|+ EcoRI and BamHI digest</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!History!!Mutation tube<del class="diffchange diffchange-inline">\</del>Fragments: <del class="diffchange diffchange-inline">!! A !! B !!C </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!History!!Mutation tube<ins class="diffchange diffchange-inline">!!</ins>Fragments: <ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL29T1!!pNL29T1 || 6124|| 2112|| 747</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL29T1!!pNL29T1 <ins class="diffchange diffchange-inline">|| </ins>|| 6124|| 2112|| 747</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL29T1-(GvpP-g441a)->!!3 || 6124|| 2112|| 747</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL29T1-(GvpP-g441a)->!!3 <ins class="diffchange diffchange-inline">|| </ins>|| 6124|| 2112|| 747</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL29T1-(GvpL-g318a)->!!4 || 6124|| 2112|| 747</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL29T1-(GvpL-g318a)->!!4 <ins class="diffchange diffchange-inline">|| </ins>|| 6124|| 2112|| 747</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL29T1-(Comp-g318a)->!!5 || 6124|| 2112|| 747</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL29T1-(Comp-g318a)->!!5 <ins class="diffchange diffchange-inline">|| </ins>|| 6124|| 2112|| 747</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>!pNL29T1-(GvpL-g351a)->!!6|| 6871|2112<del class="diffchange diffchange-inline">|| </del>-</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>!pNL29T1-(GvpL-g351a)->!!6 || <ins class="diffchange diffchange-inline">!! </ins>6871<ins class="diffchange diffchange-inline">|</ins>| 2112<ins class="diffchange diffchange-inline">!! <</ins>-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Results of PstI diagnostics: </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Results of PstI diagnostics: </div></td></tr>
</table>
PhillipDodson
http://2007.igem.org/wiki/index.php?title=Melbourne/Lab_Notebook_gv_2&diff=22981&oldid=prev
PhillipDodson at 01:33, 5 October 2007
2007-10-05T01:33:41Z
<p></p>
<p><b>New page</b></p><div>==Prepared for site dirrected mutagenesis==<br />
*resuspended primers supplied by geneworks to produce stock solution at 125ng/uL using filtered,autoclaved,milliQ water.<br />
*Produced working solutions at 125ng/2uL by diluting 10uL of stock with 190uL of filtered,autoclaved,milliQ water.<br />
*Produced NZY broth 100mL autoclaved<br />
*Produced 1mL of 10mM IPTG filter sterilised<br />
*Produced 1mL of 2% XGAL in DMF(Dimethylformamide) filter sterilized<br />
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==Site dirrected Mutagenesis Round #1 ==<br />
*Applied the [[Melbourne/Site directed mutagenesis|stratagene Site directed mutagenesis protocol]]to the following DNA and primer pairs, which when plated out on LB AMP plates producing the numbers of colonies shown. Several of these were picked and tubes marked with a character suffix as shown in table.<br />
{| border="1"<br />
|+ Site dirrected Mutagenesis round #1<br />
|-<br />
!Mutation Number !!Template DNA (10ng)!! Sence Primer !! Antisence Primer !!#Colonies !! Picks named<br />
|-<br />
!1 || pWhitescript || control #1 || control #2 || Blue and White on XGAL&IPTG plates || <br />
|-<br />
!2|| pNL29T1 || GvpL-g213a || GvpL-g213a-R || None|| <br />
|-<br />
!3|| pNL29T1 || GvpL-g318a || GvpL-g318a-R || 3|| 3A,3B,3C<br />
|-<br />
!4|| pNL29T1 || JMY-g318a || JMY-g318a-R || 26|| 4A,4B,4C<br />
|-<br />
!5|| pNL29T1 || Comp-g318a || Comp-g318a-R || 60|| 5A,5B,5C<br />
|-<br />
!6|| pNL29T1 || GvpL-g351a || GvpL-g351a-R || 1|| 6A<br />
|-<br />
!7|| pNL29T1 || GvpL-g696a || GvpL-g696a-R || None|| <br />
|-<br />
!8|| pNL29T1 || GvpA-t57c || GvpA-t57c-R || None|| <br />
|-<br />
!9|| pNL29T1 || GvpQ-g150a || GvpL-Q-g150a || None|| <br />
|-<br />
!10|| pNL29T1 || GvpQ-g183a || GvpQ-g183aa-R || 6|| 10A,10B,10C,10D,10E<br />
|-<br />
!11|| pNL29T1 || GvpP-g441a || GvpP-g441a-R || 200|| 11A,11B,11C,11D<br />
|-<br />
!12|| PUC18 || N/A || N/A|| 30 Blue on Xgal&IPTG Plates|| <br />
|-<br />
!13|| N/A || N/A || N/A || None|| <br />
|-<br />
!14|| pNL29T1 || GvpL-g213a || GvpL-g213a-R || None|| <br />
|-<br />
!15|| IPTG & Xgal|| N/A|| N/A || None|| <br />
|}<br />
* Picked colonies from Plates and [[Melb:Growing up cells|culture overnight ]]<br />
* [[Melbourne/Glycerol Stocks|Produced glycerol stocks]] from 900uL of each overnight culture.<br />
* [[Melb:Miniprep protocol|Minipreped remaining culture (4mL) giving 100uL.]] <br />
* [[Melbourne/equipement/Measure DNA|Measure DNA concentrations]] using 2uL of miniprep(100uL) diluted in 98uL of TE.<br />
{|| border="1"<br />
|+ DNA concentrations in ng/uL<br />
|-<br />
!History!!Mutation tube\colony: !! A !! B !!C !!D !!E<br />
|-<br />
!pNL29T1-(GvpP-g441a)->!!3|| 141 || 93 |112 <br />
|-<br />
!pNL29T1-(GvpL-g318a)->!!4 || 108 || 116 |218<br />
|-<br />
!pNL29T1-(Comp-g318a)->!!5|| 141 || 78 |119 <br />
|-<br />
!pNL29T1-(GvpL-g351a)->!!6|| 212 <br />
|-<br />
!pNL26P3-(GvpQ-g183a)->!!10|| 305 || 253 ||258 || 392 || 272<br />
|-<br />
!pNL26P3-(GvpP-g441a)->!!11|| 221|| 190 ||259||204 <br />
|}<br />
* Diagnostic digests were performed using<br />
**A) 21.5uL of each in Buffer3 with 1uL PstI (20U) at 37degC for 2h30min. (25uL reaction)<br />
**B) 21.5uL of each p29T1 based colony in Buffer2 with 1uL EcoRI (20U) and 1uL BamHI (20U) at 37degC for 2h30min. (26uL reaction)<br />
**C) 21.5uL of each pNL26P3 based colony and in Buffer2 with 1uL EcoRI (20U) at 37degC for 2h30min. (25uL reaction)<br />
* Prepared two 20 lane 100mL [[Melbourne/Preparing an agarose gel|agarose gel]]<br />
*[[Melbourne/Loading a DNA gel|Loaded]] 20uL of digest <br />
*Digest Pattern<br />
*Expected effects<br />
{| border="1"<br />
|+ PstI digest<br />
|-<br />
!History!!Mutation tube !!FRAGMENTS<br />
|-<br />
!pNL29T1!!pNL29T1|| 5983|| 2516|| 378|| 105<br />
|-<br />
!pNL29T1-(GvpP-g441a)->!!3!!6088 || 2516 || 378!! <-<br />
|-<br />
!pNL29T1-(GvpL-g318a)->!!4 || 5983|| 2516!!483!! <- <br />
|-<br />
!pNL29T1-(Comp-g318a)->!!5|| 5983|| 2516!!483!! <- <br />
|-<br />
!pNL29T1-(GvpL-g351a)->!!6|| 5983|| 2516|| 378|| 105<br />
|-<br />
!pNL26P3!!pNL26P3|| 3928 || 3137 || 2516 || 378 || 220 || 105 || 33<br />
|-<br />
!p26P3-(GvpQ-g183a)->!!10|| 3928 !! 3170 || 2516 || 378 || 220 || 105 !! <-<br />
|-<br />
!p26P3-(GvpP-g441a)->!!11!! 4148 || 3137 || 2516 || 378 !! <- || 105 || 33<br />
|}<br />
{| border="1"<br />
|+ EcoRI and BamHI digest<br />
|-<br />
!History!!Mutation tube\Fragments: !! A !! B !!C <br />
|-<br />
!pNL29T1!!pNL29T1 || 6124|| 2112|| 747<br />
|-<br />
!pNL29T1-(GvpP-g441a)->!!3 || 6124|| 2112|| 747<br />
|-<br />
!pNL29T1-(GvpL-g318a)->!!4 || 6124|| 2112|| 747<br />
|-<br />
!pNL29T1-(Comp-g318a)->!!5 || 6124|| 2112|| 747<br />
|-<br />
!pNL29T1-(GvpL-g351a)->!!6|| 6871|2112|| -<br />
|}<br />
*Results of PstI diagnostics: <br />
**pNL29 control was barely visable.<br />
**Bands less than 300bp were not visable<br />
**Colonies 5A,5B,5C,and 3C all showed bands at 483bp and not at 378bp as required although 5B and 3C appear slightly larger than the other two.<br />
**Colony 6A shows no band at 747bp and a band at 6871bp as required.<br />
**Colonies 4A,and 4B contain a band at 378bp indicating failure of mutagenesis.<br />
**The following colonies show additional bands of unknown origin: 3B and 4C (700bp) , 3A (8500bp) of unknown origin.<br />
**See Gel<br />
**Conclude that 5A and 6A are suitable templates for the second round of mutagenesis.<br />
*Results of EcoRI diagnostics:<br />
**pNL26 control barely visable.<br />
**Colonies 11A,B,C,D and 10A,B,C,D,E all show required pattern but the 33bp band is unlikely to be visible making the 10A..E test inconclusive, and the 220bp band in 11A..D is only barely visible in 11A..E making its diagnosis also risky.<br />
**See Gel<br />
**Conclude that 10B and 11A may be suitable templates for the second round of mutagenesis.<br />
**Conclude that Primers generated by the stratagene program Comp-g318a outperformed (60 colonies of which 2/3 provided correct product ) both offset primers JMY-g318a (26 colonies of which 2/3 gave template DNA)primers and hand designed primers Gvp-g318a (3 colonies of which when using the stratagene PCR protocol. <br />
{|| border="1"<br />
|+ Sucess of primers gnerated different ways:<br />
|-<br />
!Primers name!!Design protocol !! no colonies !! #correctly mutated !!#unknown !! # template <br />
|-<br />
!(Comp-g318a)|| Statagene ||60 || 2 || 1 || -<br />
|-<br />
!(JMY-g318a) || Offset ||26 || - || 1 || 2<br />
|-<br />
!(GvpL-g318a)|| Hand design ||3 || - || 3 || -<br />
|}<br />
<br />
*It was however also noted that the success of the PCR with the hand generated primers was negatively correlated with the melting temperature of the primers. <br />
*It was therefore decided to increase the initial melting time from 1 to 2 minutes and increase subsequent melting times from 50 seconds to 1 minute in the next round of mutagenesis.</div>
PhillipDodson