Team:Heidelberg/Templates/MM week17p

== 2013-08-19 ==
* received BL21(DE3) from Gruss Lab, ZMBH
* grow in LB to OD=0.53, [[Heat-shock competent bacteria|prepare competent cells]]
* co-transform with pIK1.2(0.2 µl = 120 ng)+pMM64(1 µl = 15 ng), pIK2.6(0.2 µl = 60 ng)+pMM64(1 µl = 15 ng), plate on Cm+Amp+IPTG, grow at 37°C

== 2013-08-20 ==
* all colonies white
* pick 1 colony each, inoculate LB+Cm+Amp, grow at 37°C until cultures are opaque, add IPTG to 1mM, grow at 30°C
* no visible indigoidine production
* need to clone into a different backbone in order to be able to cotransform with pRB21
* inoculate LB+Kan with TOP10-pSB3K3-BBa_J04450, grow at 37°C

== 2013-08-21 ==
[[File:Heidelberg_Methylmalonyl-digest2013-08-21.png|150px|thumb|left|Lane 1: NEB 2-log; lanes 2-3: pSB3K3-BBa_J04450 digested with EcoRI+SpeI; lane 4: pIK1.2 digested with EcoRI+SpeI; lane 5: pIK2.6 digested with EcoRI+SpeI]]
* [[Preparing glycerol stocks|prepare glycerol stock]] of TOP10-pSB3K3-BBa_J04450
* perform miniPrep -> 10.1 ng/µl in 38 µl
* digest with EcoRI+SpeI: 380 ng of pSB3K3-BBa_J04450: use everything (50 µl total volume, 2x0.5 µl enzyme, expect 2.7kb & 1kb), 1200 ng of pIK1.2 (2 µl of miniPrep from 2013-08-09, 20 µl total volume, 2x0.5 µl enzyme, expect 6.7kb & 2.7kb), 900 ng of pIK2.6 (3 µl of miniPrep from 2013-08-09, 20 µl total volume, 2x0.5 µl enzyme, expect 4.4kb & 2.7kb)
* pSB3K3-BBa_J04450 looks as though it was not cut: inoculate 50 ml TB+Kan with TOP10-pSB3K3-BBa_J04450, grow at 37°C
* as control for indigoidine production from pMM64: co-transform BL21(DE3) with pMM64(1 µl = 15 ng)+pMM65(0.2 µl = 13 ng), plate on Amp+Kan+IPTG

== 2013-08-22 ==
[[File:Heidelberg_Methylmalonyl-digest2013-08-22.png|150px|thumb|right|Lane 1: pSB3K3-BBa_J04450 digested with EcoRI+SpeI, lane 2: NEB 2-log]]
[[File:Heidelberg_20130822 pRB19-21 pSB3K3.png|150px|thumb|left|Lane 1: NEB 2-log; lanes 2-9: pRB* plasmids; lane 10: 1 µl of pSB3K3-BBa_J04450 midiPrep]]
* no colonies of BL21(DE3)-pMM64-pMM65: co-transform BL21(DE3) with pMM64(1 µl = 15 ng)+pMM65(1 µl = 75 ng), plate on Amp+Kan+IPTG
* prepare midiPrep of pSB3K3-BBa_J04450: 2952.1 ng/µl
* digest 0.4 µl of midiPrep with EcoRI+SpeI (20 µl total volume, 2x0.5 µl enzyme)
* band too weak: 2 possibilities:
*# concentration measurement wrong
*# mispipeted
* => load 1 µl of midiPrep on gel -> concentration measurement about right
* large pSB3K3 fragment over 3 kb, consistent with miniPrep from 2013-08-21 -> 2.7 kb expected, sequence wrong on parts.igem.org
* gel-purify pSB3K3, 6 kb fragment of pIK1, 4 kb fragment of pIK2
* 18 µl of pSB3K3 (not measured), 12.3 ng/µl pIK1 in 21 µl; 7.9 ng/µl pIK2 in 21 µl
* ligate at RT for 1h:
{| class="wikitable"
|-
! what !! µl
|-
| pSB3K3 || 9
|-
| insert || 8
|-
| T4 ligase || 1 µl
|-
| T4 ligase buffer || 2 µl
|}
* heat-inactivate: 75°C for 5 min
* transform 10 µl of each ligation into TOP10, plate on Kan, grow at 37°C (pSB3K3+pIK2 = pIK6)

== 2013-08-23 ==
[[File:Heidelberg_Methylmalonyl-colony-PCR2013-08-23.png|150px|thumb|left|Colony-PCR of TOP10 transformed with pSB3K3 ligated with pIK1/pIK2 and primers RB43+VR. Lane 1: NEB 2-log; lanes 2-6: pIK1; lanes 7-11: pIK2]]
[[File:Heidelberg_Methylmalonyl-colony-PCR2013-08-23_2.png|150px|thumb|left|Colony-PCR of TOP10 transformed with pSB3K3 ligated with pIK2 and primers RB43+VR. Lane 1: NEB 2-log; lanes 2-11: pIK2]]
* pick 5 colonies each, run colony-PCR with primers RB43+VR (expected: 1kb, using iTaq, 20 µl total volume):
{| class="wikitable"
|-
! Cycles !! temperature [°C] !! Time [s]
|-
| 1 || 95 || 300
|-
| rowspan="3"| 35 || 95 || 30
|-
| 54 || 30
|-
| 72 || 90
|-
| 1 || 72 || 600
|-
| 1  || 10 || inf
|}
* no amplificate
* have another look at sequences (motivated by DelRest results): 1 bp missing in pIK1.2: frame shift in permeability device => send pIK1.3 to sequencing with primers VF2, VR, IK25
* pick 30 colonies of pSB3K3-pIK2, run colony-PCR with primers RB43+VR (pool 3 colonies in 1 PCR reaction, iTaq, 20 µl total volume)
* no positives => ligation did not work, most likely due to low DNA concentrations
* need to repeat: inoculate 2x5 ml 2xYT+Cm with TOP10-pIK2.6

== 2013-08-24 ==
[[File:Heidelberg_Methylmalonyl-digest2013-08-24.png|150px|thumb|right|Lane 1: NEB 2-log; lane 3: pSB3K3 digested with EcoRI+SpeI; lane 5: pIK2.6 digested with EcoRI+SpeI]]
* make miniPrep of pIK2.6: 97 ng/µl in 37.5 µl
* digest 3 µg pSB3K3 (1 µl of midiPrep from 2013-08-22), 1.7 µg pIK2.6 (17 µl of miniPrep) with EcoRI+SpeI (20 µl total volume, 0.5 µl of each enzyme)
* treat pSB3K3 digest with antarctic phosphatase (37°C, 60 min)
* run gel, gel-purify -> 18 µl pSB3K3 (not measured), 15.0 ng/µl pIK2.6 in 20.5 µl
* ligate at RT for 1h:
{| class="wikitable"
|-
! what !! µl
|-
| pSB3K3 || 9
|-
| pIK2.6 || 8
|-
| T4 ligase || 1 µl
|-
| T4 ligase buffer || 2 µl
|}
* heat-inactivate: 75°C for 5 min
* transform 10 µl of ligation into TOP10, plate on Kan, grow at 37°C

== 2013-08-25 ==
[[File:Heidelberg_Methylmalonyl-colony-PCR2013-08-24_1.png|150px|thumb|left|Colony-PCR of TOP10 transformed with pSB3K3 ligated with pIK2 and primers RB43+VR. Lane 1: NEB 2-log; lanes 2-11: pIK2]]
* pick 10 colonies, run colony-PCR with primers RB43+VR (expected: 1kb, using iTaq, 20 µl total volume):
{| class="wikitable"
|-
! Cycles !! temperature [°C] !! Time [s]
|-
| 1 || 95 || 300
|-
| rowspan="3"| 35 || 95 || 30
|-
| 54 || 30
|-
| 72 || 90
|-
| 1 || 72 || 600
|-
| 1  || 10 || inf
|}
* no amplificate
* VR primer might not be binding to pSB3K3: http://www.ccbi.cam.ac.uk/iGEM2006/index.php/Primer_List#BioBrick_verification_primers , https://2009.igem.org/Team:Groningen/Notebook/22_July_2009
* pick another 10 colonies, run colony-PCR with primers VF2+IK25 (expected: 1kb, iTaq, 20 µl total volume):
[[File:Heidelberg_Methylmalonyl-colony-PCR2013-08-24_2.png|150px|thumb|right|Colony-PCR of TOP10 transformed with pSB3K3 ligated with pIK2 and primers VF2+IK25. Lane 1: NEB 2-log; lanes 2-11: pIK2]]
{| class="wikitable"
|-
! Cycles !! temperature [°C] !! Time [s]
|-
| 1 || 95 || 300
|-
| rowspan="3"| 35 || 95 || 30
|-
| 54 || 30
|-
| 72 || 90
|-
| 1 || 72 || 600
|-
| 1  || 10 || inf
|}
* definite product, but at 1.3 kb => pSB3K3 was longer than expected in digest, might be a result from that
* unspecific bands probably due to melting temperature of IK25 being at 67°C
* inoculate 2xYT+Kan, grow at 37°C
* pSB3K3 used was from plate 5 => transform TOP10 with pSB3K3 from plate 2, well 6 F