User:Karmella Haynes/Notebook/BioBrick cloning/2015/10/08: Difference between revisions

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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Karmella's BioBrick Cloning</span>
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;">Karmella's BioBrick Cloning</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
|style="background-color: #F2F2F2" align="center"|[[File:Report.png|frameless|link={{#sub:{{FULLPAGENAME}}|0|-11}}]][[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|[[File:Resultset_previous.png|frameless|link={{#lnpreventry:{{FULLPAGENAME}}}}]][[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}}
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| Sample || OD260 || 260/280 || ng/μL
| Sample || OD260 || 260/280 || ng/μL
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| 1. MV11 (S/N) || ### || ### || ###
| 1. MV11 (S/N) || 0.024 || 1.746 || 24.15
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| 2. H3-1-40 PCR || 0.03 || 1.879 || 29.8 [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/BioBrick_cloning/2015/06/23 06/23/15]
| 2. H3-1-40 PCR || 0.03 || 1.879 || 29.8 [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/BioBrick_cloning/2015/06/23 06/23/15]
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* Ligations
* Ligations (10/12/15)
** > 2:1 ratio calculations...
** > 2:1 ratio calculations...
** 433 bp largest insert / 10305 bp vector * 2 * 50 ng vector = 4.2 ng
** 433 bp largest insert / 10305 bp vector * 2 * 50 ng vector = 4.2 ng
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| Insert DNA        || 0.5  || ---   
| Insert DNA        || 0.5  || ---   
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| Vector DNA        || 3.5 || 3.5  
| Vector DNA        || 2.0 || 2.0  
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| 2x lgn buf (Roche) || 5.0  || 5.0  
| 2x lgn buf (Roche) || 5.0  || 5.0  
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| T4 ligase (NEB)    || 1.0  || 1.0   
| T4 ligase (NEB)    || 1.0  || 1.0   
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| dH<sub>2</sub>O    || --- || 0.5
| dH<sub>2</sub>O    || 1.5 || 2.0  
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| &nbsp;            || 10.0 μL || 10.0 μL  
| &nbsp;            || 10.0 μL || 10.0 μL  
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RESULTS (10/09/15)
RESULTS (10/13/15)
* tba
* tba


Latest revision as of 01:14, 27 September 2017

Karmella's BioBrick Cloning Main project page
Previous entry      Next entry

10/09/15

  • Cas-tone- H3 inserts into MV12 (new MV11-GFP)


Cas-tone Project

  • STAGE 1 - pcDNA-dCas9-VP64 vector re-design
    • DONE - Knock-out VP64 from C-terminus - replace AscI-VP64:HA:STOP-EcoRI-XbaI with AscI-HA:STOP-XbaI dsOligo
    • DONE - Knock-out FLAG from N-terminus - replace SpeI-CMV:3xFLAG:NLS-SacII with PCR-amplified (SpeI)/XbaI-CMV-SpeI-NotI-SacII; use reverse primer to add SacII
  • STAGE 2 - Histone parts
    • DONE - Order primers (annotated in Benchling)
    • DONE PCR-amplify histone parts as XbaI-Kozak-histone part-a-NotI. Note: Do no use Kozak BioBrick, since this will add extra amino acids onto conserved histone N-terminal tail. Instead, use the Kozak-like seq. from the Addgene plasmid, +3 extra Kozak bases (included in primer)
  • STAGE 3 - Cas-fusion
    • Insert Kozak-histone parts (X/N) into dCas9 plasmid + GFP reporter "MV12" (S/N)
  • STAGE 4 - gRNA
    • Put pre-existing gRNA (from luc experiment) into pSPgRNA


Assemblies

  1. H3-1-40_MV12: H3-1-40/(X/N)/129 + MV12/(S/N)/10305
  2. H3-1-60_MV12: H3-1-60/(X/N)/189 + "
  3. H3-1-80_MV12: H3-1-80/(X/N)/250 + "
  4. H3-1-116_MV12: H3-1-116/(X/N)/373 + "
  5. H3-1-136_MV12: H3-1-136/(X/N)/433 + "


  • Digest of vector (Fermentas FD)
    • SpeI/NotI
Reagent Volume
DNA (plasmid) 25.0
10x buffer 3.0
SpeI 1.0
NotI 1.0
dH2O ---
  30 μL --> 37°C/ ~30 min.
  • Gel purification
    • Sigma GenElute kit. Elute & back elute w/ 30 μL elution sln.


  • DpnI digest & clean-up of PCR products


  • Measure [DNA] for vector and inserts
Sample OD260 260/280 ng/μL
1. MV11 (S/N) 0.024 1.746 24.15
2. H3-1-40 PCR 0.03 1.879 29.8 06/23/15
3. H3-1-60 PCR 0.04 1.974 39.7 06/23/15
4. H3-1-80 PCR 0.047 1.865 46.8 06/23/15
5. H3-1-116 PCR 0.06 1.887 59.57 06/23/15
6. H3-1-136 PCR 0.062 1.932 62.0 06/23/15


  • Digest & dephos inserts
    • Done on 06/23/15
    • Final concentration = 25 ng/μL.


  • Ligations (10/12/15)
    • > 2:1 ratio calculations...
    • 433 bp largest insert / 10305 bp vector * 2 * 50 ng vector = 4.2 ng
    • 129 bp smallest insert / 10305 bp vector * 2 * 50 ng vector = 1.3 ng
Reagent Rxn1-5 Rxn6
Insert DNA 0.5 ---
Vector DNA 2.0 2.0
2x lgn buf (Roche) 5.0 5.0
T4 ligase (NEB) 1.0 1.0
dH2O 1.5 2.0
  10.0 μL 10.0 μL

RESULTS (10/13/15)

  • tba



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