User:Karmella Haynes/Notebook/BioBrick cloning/2013/03/19: Difference between revisions

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(Autocreate 2013/03/19 Entry for User:Karmella_Haynes/Notebook/BioBrick_cloning)
 
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==mm/dd/yy==
==03/19/13==
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* Line item 1
* Oligo annealing for new mammalian vector
* Line item 2




----
'''Minipreps'''<br>
* Check with E/P digests
{| {{table}} border="1" cellspacing="3" <!-- Digest check rxn. table -->
|- valign="top"
| bgcolor=#cfcfcf | Reagent
| bgcolor=#cfcfcf | Volume
| rowspan="7" | <u>Expected:</u><br>1. BB 1 = size<br>2. BB2 = size<br>
| rowspan="7" | <!-- [[Image:GelImage.jpg|400px|Hover name]]<br>15 μL/lane; 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder] -->
|-
| DNA(plasmid) || 2.0 μL
|-
| 10X buffer || 1.5
|-
| EcoRI || 1.0
|-
| PstI || 1.0
|-
| dH<sub>2</sub>O || 9.5
|-
| &nbsp; || 15 μL --> 37°C/ ~15 min.
|}


----
----
'''Assemblies'''
'''Oligo annealing'''
# BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size
* Note: made fresh 10x annealing buffer
# BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size
 


* Digests (Fermentas FD)
** Specific notes
{| {{table}} cellspacing="3" <!-- Digest rxn. table -->
|- valign="top"
| bgcolor=#cfcfcf | Reagent
| bgcolor=#cfcfcf | Volume
| rowspan="7" | <!-- [[Image:GelImage.jpg|270px|Hover name]]<br>30 μL/lane, 1% agarose; [http://openwetware.org/wiki/Image:KAH_Fermentas_GeneRuler_1kbplus.jpg Ladder] -->
|-
| DNA (plasmid) || up to 25 μL
|-
| 10x buffer || 3.0
|-
| enzyme 1 || 1.0
|-
| enzyme 2 || 1.0
|-
| dH<sub>2</sub>O || ---
|-
| &nbsp; || 30 μL --> 37°C/ ~30 min.
|}
* Measure conc.'s
{| {{table}} cellspacing="3" <!-- [DNA] table -->
|- bgcolor=#cfcfcf
| Sample || OD260 || 260/280 || ng/μL
|-
| 1. Digested part (a/b) || --- || --- || ---
|-
| 2. Digested part (c/d) || --- || --- || ---
|}
* Dephosphorylation (Roche)
{| {{table}} cellspacing="3" <!-- Dephos table -->
|-
| bgcolor=#cfcfcf | Reagent
| bgcolor=#cfcfcf | Volume
|-
| DNA (clean digest) || up to 17 μL (500 ng)
|-
| 10x buffer d.p. || 2.0
|-
| phosphatase || 1.0
|-
| dH<sub>2</sub>O || ---
|-
| &nbsp; || 20 μL --> 37°C/ 10 min.; 75°C/ 2 min.; [final] = 25 ng/μL
|}
* Ligations
{| {{table}} cellspacing="3" <!-- Ligations table -->
|- bgcolor=#cfcfcf
| Ligation || <font color="blue"><u>Plate results (lig : neg crtl)</u> mm/dd/yy</font>
|-
| 1. insert(a/b)/size, ## ng + vector(c/d)/size, ## ng || <font color="blue">new BioBrick #:1 (Pick #)</font>
|-
| 2. vector(c/d)/ ## ng || &nbsp;
|}
{| {{table}} cellspacing="3" <!-- Ligation rxn table -->
| &nbsp;            || 1    || 2    ||
|-
| Insert DNA        || ###  || ---  ||
|-
| Vector DNA        || ###  || ###  ||
|-
| 2x lgn buf (Roche) || ###  || ###  ||
|-
| T4 ligase (NEB)    || 1.0  || 1.0  ||
|-
| dH<sub>2</sub>O    || ###  || ###  ||
|-
| &nbsp;            || # μL || # μL ||
|}
----
'''Oligo annealing'''
# New BB 1
# New BB 1
# New BB 2
* oligo 1
* oligo 2
* oligo 3
* oligo 4


{| class="wikitable" border="0" cellspacing="3" <!-- Oligo annealing rxn table -->
{| class="wikitable" border="0" cellspacing="3" <!-- Oligo annealing rxn table -->
| DNA (oligos, 100 μM) || up to 18 μL (3 μL ea.)
| DNA (oligos, 100 μM) || 4x 3 μL ea. = 12.0
|-
|-
| 10x annealing buffer || 2.0
| 10x annealing buffer || 2.0
|-
|-
| dH<sub>2</sub>O || ---
| dH<sub>2</sub>O || 6.0
|-
|-
| &nbsp; || 20 μL --> 100°C (water bath)/ 5 min.; Cool to R.T. overnight
| &nbsp; || 20 μL  
|}
|}


Thermal Cycler (try new thermal cycling approach)<br>
Multigene Optimax Thermal Cycler
* 99.9 °C, 10 min.
* [99.9°C, temp. increment -2.0°C, 1 min.; 97.9°C, temp. increment -2.0°C, 1 min.] x35
* 25°C, ∞


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Revision as of 17:57, 19 March 2013

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03/19/13

  • Oligo annealing for new mammalian vector


Oligo annealing

  • Note: made fresh 10x annealing buffer
  1. New BB 1
  • oligo 1
  • oligo 2
  • oligo 3
  • oligo 4
DNA (oligos, 100 μM) 4x 3 μL ea. = 12.0
10x annealing buffer 2.0
dH2O 6.0
  20 μL

Thermal Cycler (try new thermal cycling approach)
Multigene Optimax Thermal Cycler

  • 99.9 °C, 10 min.
  • [99.9°C, temp. increment -2.0°C, 1 min.; 97.9°C, temp. increment -2.0°C, 1 min.] x35
  • 25°C, ∞


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