User:Karmella Haynes/Notebook/BioBrick cloning/Entry Base: Difference between revisions

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==mm/dd/yy==
==11/18/09==
* Outline of experiments/ tasks
* Unfinished line item
* &#x2713; Finished line item


----
'''Assemblies'''
# BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size
# BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size


'''Task 1'''<br>
> Digests (Fermentas FD)<br>
> Line item 1<br>
--> Specific notes<br>


{| class="wikitable" border="0" cellspacing="5"
{| class="wikitable" border="0" cellspacing="3" <!-- Digest rxn table -->
|-
|-
| '''Reagent'''
| <u>Reagent</u> || <u>Volume</u>
| '''Volume'''
| '''Conc.'''
|-
|-
| reagent 1
| DNA (plasmid) || up to 25 μL
| vol 1
| conc 1 or &nbsp;
|-
|-
| reagent 2
| 10x buffer || 3.0
| vol 2
| conc 2 or &nbsp;
|-
|-
| dH<sub>2</sub>O
| enzyme 1 || 1.0
| vol 3
| &nbsp;
|-
|-
| &nbsp;
| enzyme 2 || 1.0
| total vol
|-
| &nbsp;
| dH<sub>2</sub>O || ---
|-
| &nbsp; || 30 μL --> 37°C/ ~30 min.
|}
 
 
> Measure conc.'s
{| class="wikitable" border="0" cellspacing="3" <!-- [DNA] table -->
|-
| <u>Sample</u> || <u>OD260</u> || <u>260/280</u> || <u>ng/μL</u>
|-
| 1. KAH81 (X/P) || 0.519 || 1.67 || 25.9
|-
| 2. huPcCD (E/S) || 1.590 || 1.76 || 79.5
|-
| 3. mPcCD (E/S) || 1.604 || 1.76 || 79.5
|-
| 4. flyPcCD (E/S) || 0.903 || 1.66 || 45.2
|-
| 5. fshPcCD (E/S) || 1.482 || 1.74 || 74.1
|-
| 6. hCBX8 (E/S) || 0.691 || 1.74 || 34.5
|-
| 7. flyPc (E/S) || 0.118 || 1.44 || 5.9
|-
| 2. KAH74 (E/X) || 0.188 || 1.37 || 9.4
|}
 
 
> Dephosphorylation (Roche)
{| class="wikitable" border="0" cellspacing="3" <!-- Dephos table -->
|-
| <u>Reagent</u> || <u>Volume</u>
|-
| 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
|}
|}


> Reaction conditions




<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
> Ligations (*Note: use insert + old backbone in calculations)
{| class="wikitable" border="0" cellspacing="3"
| <u>Ligation</u> || <u>Plate results (lig : neg crtl)</u> 11/19/09
|-
| 1. KAH81(X/P)/2640, 33 ng + KAH48(S/P)/~3200, 20 ng || KAH86 >10:1 (Pick 2)
|-
| 2. KAH48(S/P)/ 20 ng || &nbsp;
|-
| 3. huPcCD(E/S)/3386*, > 42 ng + KAH74(E/X)/4061, 25 ng || KAH87 >10:1 (Pick 2)
|-
| 4. mPcCD(E/S)/3386*, > 42 ng + " || KAH88 >10:1 (Pick 2)
|-
| 5. flyPcCD(E/S)/3386*, > 42 ng + "  || KAH89 >10:1 (Pick 2)
|-
| 6. fshPcCD(E/S)/3386*, > 42 ng + "  || KAH90 >10:1 (Pick 2)
|-
| 7. hCBX8(E/S)/1170, > 42 ng + "  || KAH91 >10:1 (Pick 2)
|-
| 8. hCBX8(E/S)/1170, > 42 ng + "  || KAH92 >10:1 (Pick 2)
|-
| 9. KAH74(S/P)/ 20 ng || &nbsp;
|}
|}


__NOTOC__
{| class="wikitable" border="0" cellspacing="3"
| &nbsp; || 1 || 2 || 3 || 4 || 5 || 6 || 7 || 8 || 9
|-
| Insert DNA        || 1.4 || --- || 1.7 || 1.7 || 1.7 || 1.7 || 0.5 || 2.5 || ---
|-
| Vector DNA        || 0.6 || 0.6 || 2.5 || 2.5 || 2.5 || 2.5 || 2.5 || 2.5 || ---
|-
| 2x lgn buf (Roche) || 5.0 || 5.0 || 5.5 || 5.5 || 5.5 || 5.5 || 5.5 || 5.5 || 5.5
|-
| T4 ligase (NEB)    || 1.0 || 1.0 || 1.0 || 1.0 || 1.0 || 1.0 || 1.0 || 1.0 || 1.0
|-
| dH<sub>2</sub>O    || 2.0 || 3.4 || 0.3 || 0.3 || 0.3 || 0.3 || 1.5 || --- || 2.0
|-
| &nbsp; || 10 μL || 10 μL || 11 μL || 11 μL || 11 μL || 11 μL || 11 μL || 11.5 μL || 11 μL
|}
 
----
'''Oligo annealing'''
# NLS myc stop (KAH011)
# K-stop (KAH012)
# Adapter BglII/EcoRI
# Adapter PstI/BglII
 
 
{| class="wikitable" border="0" cellspacing="3"
| DNA (oligos, 100 μM) || up to 18 μL
|-
| 10x annealing buffer || 2.0
|-
| dH<sub>2</sub>O || ---
|-
| &nbsp; || 20 μL --> 100°C (water bath)/ 5 min.; Cool to R.T. overnight
|}




Revision as of 07:13, 20 November 2009

Project name <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page

11/18/09

  • Unfinished line item
  • ✓ Finished line item

Assemblies

  1. BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size
  2. BioBrick name: 5' part/(a/b)/size + 3' part/(c/d)/size

> Digests (Fermentas FD)
--> Specific notes

Reagent Volume
DNA (plasmid) up to 25 μL
10x buffer 3.0
enzyme 1 1.0
enzyme 2 1.0
dH2O ---
  30 μL --> 37°C/ ~30 min.


> Measure conc.'s

Sample OD260 260/280 ng/μL
1. KAH81 (X/P) 0.519 1.67 25.9
2. huPcCD (E/S) 1.590 1.76 79.5
3. mPcCD (E/S) 1.604 1.76 79.5
4. flyPcCD (E/S) 0.903 1.66 45.2
5. fshPcCD (E/S) 1.482 1.74 74.1
6. hCBX8 (E/S) 0.691 1.74 34.5
7. flyPc (E/S) 0.118 1.44 5.9
2. KAH74 (E/X) 0.188 1.37 9.4


> Dephosphorylation (Roche)

Reagent Volume
DNA (clean digest) up to 17 μL (500 ng)
10x buffer d.p. 2.0
phosphatase 1.0
dH2O ---
  20 μL --> 37°C/ 10 min.; 75°C/ 2 min.; [final] = 25 ng/μL


> Ligations (*Note: use insert + old backbone in calculations)

Ligation Plate results (lig : neg crtl) 11/19/09
1. KAH81(X/P)/2640, 33 ng + KAH48(S/P)/~3200, 20 ng KAH86 >10:1 (Pick 2)
2. KAH48(S/P)/ 20 ng  
3. huPcCD(E/S)/3386*, > 42 ng + KAH74(E/X)/4061, 25 ng KAH87 >10:1 (Pick 2)
4. mPcCD(E/S)/3386*, > 42 ng + " KAH88 >10:1 (Pick 2)
5. flyPcCD(E/S)/3386*, > 42 ng + " KAH89 >10:1 (Pick 2)
6. fshPcCD(E/S)/3386*, > 42 ng + " KAH90 >10:1 (Pick 2)
7. hCBX8(E/S)/1170, > 42 ng + " KAH91 >10:1 (Pick 2)
8. hCBX8(E/S)/1170, > 42 ng + " KAH92 >10:1 (Pick 2)
9. KAH74(S/P)/ 20 ng  
  1 2 3 4 5 6 7 8 9
Insert DNA 1.4 --- 1.7 1.7 1.7 1.7 0.5 2.5 ---
Vector DNA 0.6 0.6 2.5 2.5 2.5 2.5 2.5 2.5 ---
2x lgn buf (Roche) 5.0 5.0 5.5 5.5 5.5 5.5 5.5 5.5 5.5
T4 ligase (NEB) 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
dH2O 2.0 3.4 0.3 0.3 0.3 0.3 1.5 --- 2.0
  10 μL 10 μL 11 μL 11 μL 11 μL 11 μL 11 μL 11.5 μL 11 μL

Oligo annealing

  1. NLS myc stop (KAH011)
  2. K-stop (KAH012)
  3. Adapter BglII/EcoRI
  4. Adapter PstI/BglII


DNA (oligos, 100 μM) up to 18 μL
10x annealing buffer 2.0
dH2O ---
  20 μL --> 100°C (water bath)/ 5 min.; Cool to R.T. overnight



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