July entries

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Amy N. Kristofferson 14:21, 29 July 2010 (EDT)

To do:

  • MP 41/42 stuff.
    • Map minipreps
    • Submit for sequencing
  • Pick colonies off 9145-1144


  • Look into adding his-tags to transposases for purification
  • Look into buffers that optimize transposase activity

iGEM10_046 and 051 Assembly analysis


IMG 5640.JPG

lanes 1-8: 42+44 (iGEM10_046) expected length: 6317bp Perfect: 4,7 MP: 4,7

lanes 9-12: 41+43 (iGEM10_049) expected length: 5978bp Perfect: 4 MP: 1,2 (4 was cotransformed)

Cotransformation results: Only 41+43d was cotransformed. Unfortunately, d was the only one that looked good on the colPCR. Oh well.

42+44: c,d,g (labeled 46c,d,g for iGEM10_046)
41+43: a,b,c (labeled 49a,b,c for iGEM10_049)

Tecan Assay: Testing Self-Lysis timing of 047/048 in LB and Toxicity of 020

Assembly of 1888+1858 with Mike's plasmid

Messed up yesterday's assembly, and realized I don't need to gel purify the digest of Mike's plasmid, because I'll be able to select for the correct plasmids, since the colonies will be green So I set up the following:

Bgl/XhoI digest of 1884+1858 e,f eluted PCR products

Bam/XhoI digest of Mike's plasmid (mel001 in pJco12)

Started at 12:55pm.

Ligation started at 2:20pm.

Transformed jtk030 cells and plated on amp.

Amy N. Kristofferson 14:10, 28 July 2010 (EDT)

To do:

  • Pick colonies off of 41/42+43/44 plates
  • Pick colonies for Tecan assay tomorrow (see Tim's email)

41/42+43/44 plates Analysis and colony picking

42+44: 18 colonies
42+43: 0 colonies
41+44: 0 colonies
41+43: tons of colonies

I'll pick 8 colonies off 42+44 (I have a feeling a lot of them are co-transformed), and 4 colonies off 41+43. Inoculate in LB-AK, colPCR?, streak on triple antibiotics.

Ran a 7KcolPCR

Restock 9145-1144

Transformed jtk030 cells.

1884+1858 ca998/iGEM048

Expected length: ~700bp. They all look great!

IMG 5603.JPG

I'll also digest Mike's plasmid (Mel001 p3co12) with Bam/XhoI. Started at 2:14pm.

Even though I haven't gotten sequencing results back, I'm going to digest sample c and d with Bgl/XhoI. Digest started at 3:06pm. Gel purified. Expected lengths: 700bp dropout, vector should be ~5700bp. (Single cut would produce ~6400bp) Hopefully the gp worked well... I cut out the upper band, which was too high to really distinguish the length.

Ligation started at 5:29pm.

Transformed jtk030 cells.

Found my digests in the incubator. Turns out I used the undigested eluted PCR product for the assembly. Whoops. Trashed the cells. I'll redo the digestion+ligation tomorrow.

Transposase Assay: Testing Transposase Expression time and Activity Time

  1. Day before, add one colony to 6mL of LB-CK.
  2. Day of assay, move 1000uL of cells into five flasks (can discard extra mL)
  3. Add 10uL of arabinose for each mL of cells at t=o, 1 hour, 2 hours, 3 hours
    1. t=0 was 10:58am. I added 10ul of ara to the tube marked t=0.
    2. t=1 was 11:56am. I added 10uL of ara to the tube marked t-1.
    3. t=2 was 12:58pm.
    4. t=3 was 1:58pm.
  1. After four hours have passed since you first added arabinose (3pm), add 1uL of atc per mL of cells. Allow 1 hour for lysis.
    1. Added 1uL of atc to every tube but the control at 3:00pm.
  2. After that one hour, add 3uL of 9145-1144 DNA to each tube.
    1. Added DNA at 4:00pm. There was no visible sign that the cells had lysed.
  3. Remove a 200uL sample of lysate after 30min, 1 hour, 1.5hour, 2hours.
    1. 4:30, 5, 5:30, 6pm (NOTE: I may have forgotten to add ADB to the lysate for the 5:00pm sample... I can't remember)
  4. Immediately after removal, spin down the lysate and zymo the supernatant.
  5. Transform lefty pir+ cells with the lysate. Plate on Amp and Gen.

Need to transform cells w/ 9145-1144 so we can get more DNA.

Transformed TG1 cells.

Rough test of Self Lysis Timing in TB

Yesterday, I inoculated iGEM10_047 and 048. I put 1 mL of each into two tubes, so I have a control tube and a tube to add atc to, with all the cells derived from one colony pick.

Added 1uL of Conor's 1000x atc at 11:25am. At 12:25pm, the cells still do not appear to have lysed.

Check cells at 11:55am. Based on visual inspection, there appears to be no change in OD.

Checked cells again at 1:00pm. The cells in 47 have clearly lysed, but it doesn't appear that the 48 cells have lysed yet.


47 (w/o tip) Left=control, right=atc
48 (w/ tip) left=control, right=atc.

Sequencing Results

iGEM10_042a is perfect. (ca998 sequencing redo produced a perfect partial)

Degradation Assay

Conor will do this tomorrow:

Add 1uL of atc to each 1mL sample of cells. Let cells lyse for an hour. Add 1uL of DNA. At each of the following intervals: 15min, 30min, 45min, 1 hour, 1.5, 2, 2.5, 3, remove 200uL of DNA, spin down, and zymo supernatant. After you have all your zymo'd samples, plate on Amp.

Amy N. Kristofferson 14:25, 27 July 2010 (EDT)

To do:

  • Grow up Payload delivery colonies in TB
  • Grow up transposase colonies

Picked two colonies of jtk030 cells transformed with iGEM10_047 and 048 and put them in TB-KA in the shaker upstairs. Tomorrow, I'll see how long it takes for the cells to undergo self-lysis. Each part has the exact same SL device under the same Ptet promoter, so they shouldn't vary.

PCR off 1884+1858 in 1601CK

I designed an oligo that will add a XhoI site to the NLS. So if I do a PCR with ca998 and my oligo igemTen048, hopefully I should get a band around 733bp long. I should only get this band if NLS is after RFP. It can't PCR off just RFP, because there would be no NLS to bind to. And just NLS is only 33bp, so that wouldn't even show up on the gel. Ran a 2K55.

Mapping of 1884 and 1858

I wasn't going to map these, but since sequencing of 1884+1858 a and b w/ g00101 both failed, I'm going to map them. The maps won't show whether or not the NLS tag is there, but it should show how good the MP is and if the backbone is good.

Eco/Bam Digest started at: 12:30pm

Expected lengths: 3142 (vector), 711 (part)

Lanes 1-8 correspond with samples a-h.

IMG 5571.JPG

Everything looks good. They could have had bad reads because they were cotransformed. I submitted 1884+1858c and d for sequencing.

Sequencing Results

iGEM10_020b in pmllCA is perfect
iGEM10_042a in pmllAC's fwd read was messed up. I submitted the exact same part w/ ca998 again.
iGEM10_041b in pmllCA is perfect

Next Assembly step: Creating iGEM10_045/046 and 049/050 (Self-Lysis T ver)

Assemble iGEM10_042/041 with iGEM10_43/044

I have left over righty digest of iGEM10_043/044, so I only have to set up a Lefty digest of iGEM10_042/041. NOTE: iGEM10_042 hasn't been sequence confirmed yet, but I'm going to go ahead with assembly and keep my fingers crossed.

I think I started it around 2:00pm.

Started ligation at 4:37pm. Used 2114+2275/2316 digests from construction of 47 and 48.

Amy N. Kristofferson 14:07, 26 July 2010 (EDT)

To do:

  • Transform cells w/ best igem20 map
  • order oligos
  • submit best igem20,41,42 map for sequencing
  • start next assembly step for 41, 42?


Designed the following oligo: igemTen048 gctagCTCGAGttaAACTTTACGTTTTTTTTTCGGCGG 38 rev xhoI 1858 {<NLS!}

ColPCR results

IMG 5551.JPG

Expected length: about 900bp. They all look good. Mapping won't show me much, since the NLS is so small (~30bp). So I'm going to sumbit two samples for sequencing, using the g00101 oligo. If they're cotransformed, I'll get back a mixed read.

IMG 5550.JPG

Expected lengths for iGEM10_042: 2895bp (lanes 1-4) and iGEM10_041: 3126bp (lanes 5-8)

Results: 42a,b,c and 41b,d look good. I'll map all the minipreps anyway.

Miniprep Mapping

They all look good! iGEM10_020 is a little faint, but I'm going to send off a sample of each to be sequenced.

IMG 5559.JPG

I ran the same gel out for a few more minutes... You can see the sizes of the 42 and 41 digests better now...

IMG 5561.JPG

Lane Part Digest Expected length
1 42a Eco/XhoI 3768, 1672
2 42b Eco/XhoI
3 41b Eco/XhoI 3998, 1672
4 41d Eco/XhoI
5 20b Eco/Bam 6246 (part), 2745 (vector)
6 20d Eco/Bam
7 20e Eco/Bam
8 20f Eco/Bam

started at 12:00pm.

Transformed jtk030 with iGEM10_020b=

Started rescue at 2:25pm. Labeled "Sequenced MP of iGEM10_020b." I'll grow up colonies tomorrow so I can perform the Transposase Assay on Wednesday.

Sequencing submissions

Submitted iGEM10_020b in pmllCA, iGEM10_042a in pmllAC, iGEM10_041b in pmllCA, and jh1884+1858 in 1601CK A,B for sequencing.

Bam/XhoI digest started at 1:50pm.

Amy N. Kristofferson 14:07, 24 July 2010 (EDT)

To do:

  • Run gel of colPCRs from Friday and Sat.
  • Map Minipreps of 1884+1848.
  • Miniprep any iGEM10_020's that aren't co-transformed.
  • Miniprep the 41/42 samples w/ good colPCR results.
  • figure out what to do w/ ef1a and atub

Colony picking: 42/41PCR+pMLL4AC and iGEM10_020

Picked 8 colonies of iGEM10_020 and checked for cotransformation. Didn't run a colPCR b/c the part is too big. Picked 4 colonies of 42/41PCR+pMLL4AC and started a 4K colPCR. Had to make more colPCR MM.

Miniprepped all 1884+1858 samples

Labelled 1884+1858a-h and placed in Amy #2. I need to map them.

Sequencing Results for iGEM10_019b

The part looks great! I'm glad I continued on with assembly.

iGEM84 iGEM10_019b ca998 Perfect partial. First 900bp look great
iGEM85 iGEM10_019b g00101 Perfect partial. Last 900bp look great

Amy N. Kristofferson 13:45, 23 July 2010 (EDT)

To do:

  • analytical gel of PCR of 42+41
    • if it looks good, digest eco/bam and ligate w/ pMLL4AC.
  • MP iGEM10_019b,d
    • Map
    • Submit for sequencing
    • Start next stage of assembly
  • Pick colonies from 1884, 1858. ColPCR, innoculate. No need to check for co-transf (same color)Tomorrow, miniprep and eco/bam into 9145. (xhoI site right after Bam)
  • Pick lots of colonies from ef1a/atub+2093 plate.
  • Redo-transformation of 47 and 48 (nothing grew on Tahoura's plates)


  • Pick colonies of igem47,48. Rough test to see how long it takes bacteria to lyse in TB

Colony Picks

1884+1858: expected colPCR length: 912bp efla/atub+2093 expected colPCR lengths: 1952, 2190bp

Ran col3k pcr.

Assembly: iGEM10_020 and Eco/Bam 41 and 42 PCR products into pMLL4AC


eco/bam: 41, 42

R: bgl/xhoI of igem019-gel purify (mapping at same time): 6181, 1607. Cut out top band.

L:bam/xhoI of igem001

digests started at 12:46pm

Gel purified 19b,d: There was a band at around 6000bp, but I couldn't see one at 1607, but that could be because I ran the gel for a long time. I gel purified the top band anyway and I'll continue on with the next step of assembly. I could map again, but I think my analytical colPCR combine with sequencing results will be a pretty good confirmation.

Zymo'd 41, 42, and 1.


41/42+pMLL4AC, transform into lefty 19b/d with 1, transform into jtk030

Started at 2:55pm.

Rescue started at 3:41pm.

PCR of ca998/g00101 off iGEM10_042 and 041 in hybrid vector

Analytical Mapping:

Lane 1: iGEM10_042, expected length: 2863bp
Lane 2: iGEM10_041, expected length: 3093bp

IMG 5520.JPG

The PCRs look successful. I'm going to Eco/Bam the PCR product and ligate with pMLL4AC.

Cotransformation Results for iGEM10_019 and ef1a/atub+2093

iGEM10_019: only sample c was co-tranformed, but I'm only going to miniprep b and d, since I forgot to streak sample a on the antibiotics plate.

All of the samples for ef1a/atub+2093 were co-transformed. I'll pick a lot more colonies today, colPCR, inoculate, and streak for cotransformation.

Amy N. Kristofferson 14:37, 22 July 2010 (EDT)

To do:

  • Plate at 4:35pm
  • Run colony PCR on gel
  • See if i have any ef1a MPs that mapped well that I could submit for sequencing. I want one w/o the double T deletion. However, it's prob before the atg used as a start codon, so it may not affect anything. We'll see...
  • On a second glance, mapping data for ig114/2271+2017 could be ok. Maybe do with iGEM10_043/044 (four reactions total) and submit them for sequencing?

Nuclear Localization check

pjc012 backbone

Bgl/XhoI transfer of CDS of our protein

his6tag prom-rbs-his6-my gene!

rfp+nls: 1884+1858 in 1601KC

Transformed into jtk049. Started rescue at 3:35pm. Plated on KC.

Tomorrow, pick colonies. Can do colPCR off plasmid (1601 series).

Next day: miniprep, map, sequence? PCR on bgl/xhoI sites.

may need to pcr a new bam/xhoI around GFP-Nls and then cut into mike's plasmid

Sequencing Results for iGEM10_047, 48, 51, 52 (SL/VB Assembly Product with L-Lysozyme Self Lysis

All parts look perfect for about the first and last 1000bp.

iGEM72 iGEM10_048a in AK ca998 Perfect partial. Good for first 1000bp
iGEM73 iGEM10_048a in AK g00101 Perfect partial. Good for last ~1000bp
iGEM74 iGEM10_051a in AK ca998 Perfect partial. Good for ~900bp, \"mutations\" are conserved.
iGEM75 iGEM10_051a in AK g00101 Perfect partial. Good for last ~950bp..
iGEM76 iGEM10_052a in AK ca998 Perfect partial. Good for first ~900bp
iGEM77 iGEM10_052a in AK g00101 Perfect partial. Good for last ~950bp..

Picking ef1a/atub-Bjh2093 in pMLL/1601KC hybrid vector colonies

  • Pick four colonies of each.
  • ColPCR w/ ca998/g00101
  • Inoculate in LB-KC

Picking iGEM10_019 colonies

The plate looks great. It's covered in fairly healthy looking colonies.

  • Pick 4 colonies off of iGEM10_019 plate.
  • Run ColPCR w/ conor's oligos from Gibson:
igemTen021 gtcgactgtctcttatacacatctcaaccgGATCTCTGGCAGTTCCCTAC 50 \"fwd for iGEM10_017 + iGEM10_016
Gibson fusion\"
igemTen024 cGTCGACTGTCTCTTATACACATC 24 rev for iGEM10_016 Gibson fusion

If both 17 and 16 (a part of 18) are there, the colPCR will produce a band ~888bp long.

  • Inoculate in LB-AK

ColPCR results from above colony picks

IMG 5509.JPG

Lane 1-4: iGEM10_019 w/ igemTen21/24, I wanted 888bp band, so they all look great!
Lane 5-8: ef1a+2093 w/ ca998/g00101, expected 1952, all bad--last two are probably cotransformed w/ ef1a parent vector
Lane 9-12: atub+2093 w/ ca998/g00101, expected 2190, all bad

Even though my ef1a/atub+2-93 colPCR results don't look so hot, I'll miniprep the ones that weren't co-transformed and map them tomorrow.

IMG 5510.JPG

ColPCR results for ig114/2271+2017 picks

This analytical backbone PCR seems useless, since a 900bp band was supposed to reveal the presence of the p15 origin of rep, a sign that the part was in the hybrid vector but my negative control, a part in pMLL4AC, also produced a 900bp band! My only choice of analysis then is mapping, but all of the colony PCRs look very crazy. Maybe I'll just miniprep and map them all anyway. Another route I could do would be to perform an Eco/Bam transfer into a vector w/ diff antibiotics, and then do another Eco/Bam transfer into the PMLL4AC. That's just going take a long time...


IMG 5487.JPG

Lane Part Don\'t want
1--4 2271+2017 ~900bp band
4--8 ig114+2017
9 2345 In pMLL4AC


IMG 5488.JPG

' ' '
Lane Part Expected length
1--4 2271+2017 2895
4--8 ig114+2017 3126

Minipreped everything and started an analytical Eco/XhoI digest at 5:21pm.

IMG 5510.JPG

iGEM name Digest Expected length Expected length if still in hybrid
iGEM10_042 Eco/XhoI 3768, 1672 4702, 1672
iGEM10_041 Eco/XhoI 3998, 1672 4932, 1672

One of these is clearly still in its hybrid vector, but I don't know what's going on with the single bands. I'm going to Fusion PCR off ___ using ca998 and g00101. Then I'll Eco/Bam that into PMLL4AC.

Amy N. Kristofferson 13:04, 21 July 2010 (EDT)

ig114/2271+2017 vector transfer redo

Pick 4 colonies for ig114/2271+2017. Normal colPCR seems to be a waste of time, but I'll try it anyway. I'm also going to do my backbone analysis PCR. Negative control: Bjh2345 in PMLLAC.

Assembly of iGEM10_018 and 017 to make iGEM10_019

Manual R/L Digest of iGEM10_018 and 017. Started at 10:00am. Zymo'd. Ligation started at 1:08pm. Transform into Righty cells. Rescue started at 1:50pm Plated on KA. Labelled plate iGEM10_019.

One Pot Assembly of atub/ef1a with jh2093

DNA used: Rigthy: Bjh2093 in 1601AC Lefty: ef1a PMLLKA b (7/14 miniprep) and atub PMLLKA b (7/14 miniprep) All samples are methylated.

NOTE: I'm intentionally creating a hybrid vector! I think this will save time. Just make sure not to transform into Righty, because then I won't be able to Eco/Bam the product into a good vector. Also, this ef1a has a two base pair deletion, so it may not be functional.

Digest started at 1:32pm. Heat kill at 2:49pm. Add ligase at 3:15pm. Add jtk030 cells and heat shock at 3:45pm. Start rescue. Plate at 4:49pm.

  • Set up the digestion:
1uL lefty plasmid(methylated)
1uL righty plasmid (methylated)
0.3 uL XhoI
0.3 uL BglII
0.3 uL BamHI
6.1uL Water
  • Digest for 1 hour at 37C
  • Heat kill at 65 for 20 min
  • Add 0.3uL T4 Ligase
  • Ligate at room temperature for 30 minutes
  • Put on ice for transformation
  • Transform, rescue, plate on dual antibiotic plates

Amy N. Kristofferson 13:45, 20 July 2010 (EDT)

None of the colonies picked yesterday from the iGEM10_047, 48, 51, 52, or 16+2294 were co-transformed. And since the ColPCR didn't reveal much of anything, I'm just going to miniprep the first two samples of each, except for iGEM10_047. iGEM10_047's d sample looked great on ColPCR, so I'll miniprep sample a and d instead of a and b. Also, somehow all 12 of the colonies that I picked for the transfer of 2271/ig114+ 2017 from the hybrid into PMLL4AC seemed to still be in the hybrid vector, based on my analytical pcr (they all had bands around 900bp). I'll miniprep four of each anyway and map them. If they're not the right side, I'll do the transfer over again.

To do:

  • Minipreps
  • Ask Tim about Ef1a sequence.

Picking colonies w/ Payload and Payload delivery

30µL into ea mL TB media (use TB for growing up for assay)

Miniprep Map

IMG 5443.JPG

Tube Mapping iGEM name Digest Expected length Expected length if still in hybrid Good?
1,2 2271+2017 w/ PMLL4AC iGEM10_042 Eco/XhoI 3768, 1672 4702, 1672 Possibly. Upper band looks good. Perhaps lower band too faint
3,4 ig114+2017 g.p. a w/ PMLL4AC iGEM10_041 Eco/XhoI 3998, 1672 4932, 1672 Possibly. Upper band looks good. Perhaps lower band too faint
5,6 2345 in PMLL4 b w/ 2114+2316 g.p. a iGEM10_047 Eco/Bam 5533, 2877 a,b
7,8 2345 in PMLL4 b w/ 2114+2275 a (7/14) iGEM10_048 Eco/Bam 6102, 2877 a,b*
9,10 1968 in PMLL4 b w/ 2114+2316 g.p. a iGEM10_051 Eco/Bam 5763, 2877 a,b
11,12 1968 in PMLL4 b w/ 2114+2275 a (7/14) iGEM10_052 Eco/Bam 6332, 2877 a.b
13,14 16a w/ 2294 Eco/Bam 3166, 2745 righty methylated!! good for one cut, but need to do Eco/XhoI

Submitted a sample a for each of the 2345/1968 assemblies for sequencing, except I submitted sample d for iGEM10_047.

16+2294 is righty methylated. That's why I only got one band. It's the right sized band though. I'll map it with Eco/XhoI. Started digest at 4:10pm.

IMG 5457.JPG

Lane 1: 16+SLa
Lane 2: 16+SLb

Expected lengths: 4644, 1466

Analysis: I think the top band is parent vector. Don't know why sample B has three bands... very strange. I submitted a for sequencing.

Redo of Hybrid vector transfer

Those oligos shouldn't PCR off the genome (http://archaea.ucsc.edu/cgi-bin/hgPcr?hgsid=462798&org=Escherichia+coli+K12&db=eschColi_K12&wp_target=genome&wp_f=cggttatccacagaatcaggg+&wp_r=gcgctgatgtccggcggtgc&Submit=submit&wp_size=8000&wp_perfect=15&wp_good=15&boolshad.wp_flipReverse=0)

I'm going to make more of pMLL4AC Eco/Bam digest from Tim's stock in plate 2, well F7 (pMLL4AC Bth8062). Started digestion at 2:04pm. Drop out is 813bp. Vector should be 2745bp.

Use 3uL of digested pMLL4AC instead of 1uL when ligating.

Unfortunately, there's only about 1.75uL of digest PMLL4AC vector left, so I used it to redo the ligation w/ eco/bam digested ig114+2017. I started the ligation at 1:51pm. Started rescue at 3:04pm.

Redo of ligation with new pre-digested and gel purified PMLL4-AC w/ FFGFP dropout. Started ligation at 4:45pm. Started rescue at 5:30pm.

Amy N. Kristofferson 14:51, 19 July 2010 (EDT)

Everything grew up very well. The only concern I have is that the colonies with 2345 in the part have a transparent loop around the colony, possibly suggesting that self-lysis is starting. I'll have to careful when I miniprep these.

I pick colonies, ran a normal colony pcr for all of them, ran an analytical pcr to make sure the parts I transfered out of the hybrid vector aren't still in the hybrid vector, inoculated and check for co-transformation for the assembly plates. Here are my notes:

  • pick four colonies off each plate.
  • run colPCRs w/ ca998/g00101 for all of them
  • run colPCRs w/ th395/th396 on ig114+2017 and 2271+2017 vector transfers and original minipreps to check for hybrid

Timing wise:

  • make colPCR MM for 5 rxns w/ th395/396.
  • set up tubes for colPCR (need 28 tubes for regular, and 8+2=10 for th395/396 version)
  • set up plate for co-transformation check: 5x4 grid
  • cross out gfp colonies on ig114/2271+2017 plates
  • set up two 24-well plates. Need 2AC-4AK-1AC LB.
  • pick colonies, colPCR (don't forget to double dip for the 2017s!), inoculate, co-transf. plate
  • don't forget to add template DNA from original minipreps for th395/6 PCR for comparison check.

Analytical PCR results for Transfer from hybrid vector

This is a gel from a colPCR with oligos th395/th396 of four colonies picked from 2271+2017 and ig114 7/16/10 plates. If the plasmid is still a hybrid, it will contain the p15 origin of replication, and will PCR off a ~900bp DNA. This gel suggests that all the colonies I picked contained the hybrid vector. Tim said that if I need to do the transfer over again, I should use more pMLL vector (~3uL). For now, I'll pick more colonies.

IMG 5412.JPG

Tube Part
1a-4a iGEM10_042
5a-8a iGEM10_041
9a 2271+2017 in hybrid vector
10a ig114+2017 g.p. in hybrid vector


This results aren't very good. But I think that's to be expected when parts are about 6k or greater. I'm going to mostly ignore these results and miniprep a couple samples from each reaction anyway.

The analytical PCR makes it seem like all the hybrid transfers are still in the hybrid vector... :(

IMG 5428.JPG

IMG 5432.JPG

ColPCR tube DNA iGEM name oligos Expected length Good?
1--4 2271+2017 w/ PMLL4AC iGEM10_042 ca998/g00101 2895
5--8 ig114+2017 g.p. a w/ PMLL4AC iGEM10_041 ca998/g00101 3126
9--12 2345 in PMLL4 b w/ 2114+2316 g.p. a iGEM10_047 ca998/g00101 5733 d
13--16 2345 in PMLL4 b w/ 2114+2275 a (7/14) iGEM10_048 ca998/g00101 6302
17--20 1968 in PMLL4 b w/ 2114+2316 g.p. a iGEM10_051 ca998/g00101 5963
21--24 1968 in PMLL4 b w/ 2114+2275 a (7/14) iGEM10_052 ca998/g00101 6532
25--28 16a w/ 2294 ca998/g00101 3366
29--36 2271+2017 w/ PMLL4AC th395/396
Small gel: 1--8 ig114+2017 g.p. a w/ PMLL4AC th395/396

Amy N. Kristofferson 15:20, 16 July 2010 (EDT)

To do:

-Eco/Bam digest ig114+2017 g.p. and 2271+2017 g.p. Run on gel and gel purify. Ligate to pMLLAC pre-digested vector. (calculated expected lengths before running gel, to make sure it's worth the trouble. Bands might be so similar that maybe just a zymo is better)

-ligate g.p. 2294 with g.p. 16a.

-assemble SL-L with vacuole buster:

  • Bjh2345 in pMLL4-AC with iGEM10_043 and iGEM10_044 (I'm going to use my 2114+2275 miniprep from 7/13, even though it hasn't been sequenced yet. It mapped well, but this doesn't say much since Pcon is so small. Even so, I'm do the reaction anyway and trash it if the sequence comes back bad, like the last one did.)
  • Bjh1968 in pMLL4-AC with iGEM10_043 and iGEM10_044

NOTE: can't use one pot because iGEM10_043 and iGEM10_044 are NOT methylated. I transformed jtk030 cells to make them. I'll have to do separate righty and lefty digests.

Sequence Analysis of Ef1a/Atub

iGEM57-ef1a ef1a animal promoter (iGEM10_021 in PMLLKA) miniprepped 7/14 ca998 Deletion of two T\'s at around 410bp. Would cause a frame shift, so it\'s useless.
iGEM58 atub animal promoter (jh2342 in pMLLKA) miniprepped 7/14 ca998 Perfect partial. The read was very short. Only the first 200bp or so were good.

So where to go from here?

I'll submit atub for sequencing with g00101. As for ef1a, since my ef1a in the AK vector (was supposed to be KA... argh) sequenced perfectly. I'll just Eco/Bam Transfer it? Then I'll get colonies tomorrow, and I can ColPCR/inoculate and then miniprep on Tuesday. OR I could pick more colonies today. However, even if I map well, the part could have mutations...

Transfer of 2271/ig114+2017 to PMLLAC from pMLL/1601 hybrid

Eco/Bam digest of 2271+2017 g.p. a, ig114+2017 g.p. a.

Gel purify part:

2271+2017 in pMLL/1601 vector Eco/Bam: 3670, 2704 Lower band includes parts.

ig114+2017 in pMLL/1601 vector Eco/Bam: 3670, 2934 Lower band includes parts

When I pick colonies, I'll run two ColPCRs: ca998/g00101 and th395/th396. If the plasmid is still a hybrid, it will contain the p15 origin of replication, and will PCR off a ~900bp DNA. I'll also run the ColPCR on colonies that I know contain the hybrid so that I can compare. This will allow me to do less minipreps. I'll still map them though, to confirm the vector size.

TH395   gcataGAATTCcggttatccacagaatcaggg        fwd for EcoBAM p15A, pBth7011
TH396   ctaggGGATCCgcaccgccggacatcagcgc         rev for EcoBam p15A, pBth7011

Second Step of Assembly for SL/VB: L-1968/2345 to iGEM10_043/044

Bam/XhoI: 2345 in PMLL4 b, 1968 in PMLL4AC (T1, L) Bgl/XhoI: 2114+2316 g.p. a, 2114+2275 a (7/14)

Transposase Assay: ligating gel purified 16a to gel purified 2294 in CORRECT KA vector

Details of today's Digestions, Ligations, Transformations, and Platings

Tube DNA Enzymes
1 2271+2017 g.p. a Eco/Bam
2 ig114+2017 g.p. a Eco/Bam
3 2345 in PMLL4 b L: Bam/XhoI
4 1968 in PMLL4AC (T1, L) L: Bam/XhoI
5 2114+2316 g.p. a R: Bgl/XhoI
6 2114+2275 a (7/14) R: Bgl/XhoI
Tube DNA Transform into Plate on
1 2271+2017 w/ PMLL4AC Lefty AC
2 ig114+2017 g.p. a w/ PMLL4AC Lefty AC
3 2345 in PMLL4 b w/ 2114+2316 g.p. a jtk030 AK
4 2345 in PMLL4 b w/ 2114+2275 a (7/14) jtk030 AK
5 1968 in PMLL4 b w/ 2114+2316 g.p. a jtk030 AK
6 1968 in PMLL4 b w/ 2114+2275 a (7/14) jtk030 AK
7 16a w/ 2294 Righty CA

Submit 2114+2275a 7/13 miniprep for sequencing


iGEM60 2114+2316a 7/13 miniprep fwd ca998
iGEM61 2114+2316a 7/13 miniprep rev g00101

Results: Great! This part is as it should be.

Sequencing Results for ig114+2017

iGEM59 ig114+2017 g.p. ca56 Perfect partial: shows the correct junction between Pbad and SL-T. These three reads don\'t all overlap, but I think it\'s safe to assume the part is Perfect.

I'm going to Eco/Bam Transfer the part, because it's currently in a pMLL-jh1601 fusion backbone.

Amy N. Kristofferson 14:55, 15 July 2010 (EDT)

To do:

  • reinterpret mapping results w/ SL with 1601 plasmid
  • Design oligo for sequencing of 2271+2017
  • gel purify SL. Ligate to gp'd 16a
  • sequence analysis of ef1a and atub

Important Mini-meeting update: Issue with SL Assembly probably resulted from use of 2017 in 1601 vector

Mapping Yesterday's Minipreps

IMG 5363.JPG

Ran out the gel a bit more, and I think it shows that the two 2271+2017 samples mapped well:

IMG 5365.JPG

Lane Miniprep Digest Expected Lengths ' Cut out Good?
1 2114+2275a Eco/XhoI 4627, 1466 good
2 2114+2275b Eco/XhoI 4627, 1466 good
3 2271+2017a Eco/XhoI 3768, 1672 too big
4 2271+2017b Eco/XhoI 3768, 1672 too big
5 ig114+2017e Eco/XhoI 3998, 1672 too big
6 ig114+2017f Eco/XhoI 3998, 1672 too big
7 ef1a in PMLLKA b Eco/Bam 2868, 897 good
8 atub in PMLLKA b Eco/XhoI 2405, 1598 good
9 atub in PMLLKA c Eco/XhoI 2405, 1599 bad
10 jh2294 in PMLLKA BglII/XhoI 3777, 1607 Upper band good

Sequencing Results for the rest of the Minipreps from my first batch of colony picks from Gel-Purified Assembly

Submission Name Part Oligo Analysis
iGEM51 2114+2275 g.p. F ca998 BAD- a bunch of junk. No alignment with sequence.
iGEM52 2114+2275 g.p. R g00101 Perfect partial. The last 1000bp or so of the part is perfect
iGEM53 2271+2017 g.p. F ca998 Perfect Partial- first ~1000bps of the part is right
iGEM54 2271+2017 g.p. R g00101 Perfect Partial- last ~700bp of part look good
iGEM55 ig114+2017 g.p. F ca998 About 1000bp aligned, except for mutation: @ 291bp, mutation: @ 449bp
iGEM56 ig114+2017 g.p. R g00101 Perfect Partial: last 700bp sequenced perfectly

The boundaries of parts 2114+2275 and ig114+2017 look good. I'm going to PCR off the middle to check if the insides are go too. I used ca56 for ig114+2017 (binds to pbad promoter). I designed a primer for the middle of

Amy N. Kristofferson 13:24, 14 July 2010 (EDT)

To do:

  • Redo cotransformation of Tera'a Payloads with Payload delivery devices in 1601K. DON'T FORGET MG!!!
  • Run colony PCRs for KA transfer
  • Run colony PCRs for SL/VB Assembly colony picks
    • Miniprep everything that wasn't co-transformed

Sequencing Submissions: the rest of my gel-purified assembly minipreps

iGEM51-56= each part w/ ca998 and g00101

Cotransformation Redo

Rescue started at 11;32am.

Sequencing Results for 2114+2316 (iGEM10_043): Great news! Successfully put Pcon in front of VBa

I submitted the part with ca998 and g00101, and the results clearly show that the Pcon is in front of the vacuole buster. Woo hoo!

KA transfer

Christoph Miniprepped everything he needed.

I miniprepped the remaining 1mL of 10 or bjh2294-PMLLKA (eluted with 25uL to keep normal MP concentration), ef1a-PMLLKA b, atub-PMLLKA b,c.

Parent Vector bleed-through results: All samples from 1,2,3,4,6,7,8,12,13,16 are good. The only samples with co-transformation were 15a and 9a,b,d.

IMG 5329.JPG
IMG 5331.JPG
IMG 5332.JPG
IMG 5334.JPG

Colony PCR- ca998+g00101

Tube Lane Quick Ref part expected length good?
1--4 1,3,5,7 1 sbb09 235 all good
4--8 9,11,13,15 2 sbb07 1631 a,b,d
9--12 2,4,6,8 3 sbb06 441 all good
13--16 10,12,14,16 4 sbb04 1988 all good
17--20 17,19,21,23 6 sbb19 797 all good
21--24 25,27,29,31 7 sbb12 434 all good
25--28 18,20,22,24 8 sbb10 1226 all good
29--32 26,28,30,32 9 sbb42 291 all good
33--36 33,35,37,39 10 Bjh2294 2707 a,d
37-40 41,43,45,47 12 sbb04 1988 a,c
41-44 34,36,38,40 13 sbb19 797 a,d
45-48 42,44,46,48 15 sbb10 1226 all good
49-52 49,51,53,55 16 sbb42 291 a,b,c
53-68 57,59,61,63,50,52,54,56,58,60,62,64 (52,54,56-64) 5 Bjh1906 247 all good, except h
69-76 65,67,69,71, 73,75,77,79, 66, 68, 70,72 (65-73, 75,77,79) 11 Bjh2245 297 all good, except a, j
77-80 74,76,78,80 ef1a 1088 b
81-84 81,83,85,87 atub 1326 b,c,d

NOTE: lanes 49-96 refer to the middle gel. Just subtract 48 from the lanes in the table to see what number to refer to on the actual gel.

Colony PCR-th313+iGEM10

Note: the results for 5 are in the middle right gel shown above.

IMG 5327.JPG

Tube Lane Quick Ref Part Expected length Good?
1--12 89,91,93,95 and 82-96 even 5 Bjh1906 about 1650 all good, excect h
13-24 small gel: 1-12 11 Bjh2245 about 1651 b,c,e

SL/VB Assembly Colony Picks

Cotransformation results: 2h and 6a were co-transformed. Everything else had no growth on the triple antibiotics plate.

IMG 5336.JPG

IMG 5337.JPG

Column Part Plate Date Lane Expected lengths for ColPCR Good lanes Good wells Miniprep
1 2114+2275 8-Jul 1-15odd 3622 possibly 11,13,15 a,b,c (I accidentally added the samples in the inverse order to the gel) a,b
2 2114+2275 7-Jul 2-16even 3622
3 2271+2017 8-Jul 17-31 odd 2895 possibly 17, 19 a,b a,b
4 2271+2017 6-Jul 18-32even 2895
5 ig114+2017 8-Jul 33-47 odd 3125 43 f e,f
6 ig114+2017 6-Jul 34-48even 3125

Amy N. Kristofferson 18:16, 13 July 2010 (EDT)

Co-transform jh2348/2291-1601K with Tera's Payload

Added 100uL of H2O to 1uL of DNA from Tera's Ef1a and Atub payload constructs.
Added 10uL of H2O to 1uL of DNA from my minipreps of 2348/2291-1601K.

Added 1uL of each of those dilutions to 70uL of MG1655 cells.

Mg needs to be added for all steps of cloning the PDD's
1M MgSO4
10µL into rescue step (after heatshock)
400µL spread on plate (if +Spec, add 20µL and spread)
30µL into ea mL TB media (use TB for growing up for assay)

Started rescue at 4:06pm.

KA Vector transfer: ColPCR (parts and vector backbone check), inoculate, grow up

I picked colonies, inoculated and ran a colony pcr for all the parts we moved into the new, CORRECT KA vector.

Important notes:

  • 5 and 11 were originally in AK vectors. 10 was also in an AK vector, but I gel purified it. Even so, I will run an analytical PCR of my minipreps of 10, and I ran an analytical Colony PCR with th313 and g00101 for my 5 and 11 colonies. I picked 12 colonies of 5 and 11.
  • I also check for parent vector bleed-through by plating all the parts on spec, except for 9 (plated on triple antibiotics since it came from CK) and efla+atub (PCR products)
  • All the inoculations are in the shaker.
  • The colony PCRs are in the black PCR machines. They'll probably be done around 6pm.

SL/VB Assembly: Picking colonies from 7/6, 7/7, and 7/8 plates

Picked 8 colonies from Assembly attempt #2 (one pot) and assembly attempt #3 (gel purification) for 2114+2275, ig114+2017 and 2271+2017. Inoculated, checked for co-transformation, and set up ColPCR.

Amy N. Kristofferson 14:43, 12 July 2010 (EDT)


Christoph just ran and analytical digest/gel that proved that the vector in the tube that was supposed to contain KA actually contained AK vector instead of KA. I need to Eco/Bam transfer the parts into a new KA vector. Also, this explains why the assembly with the Self-Lysis Device didn't work. We need to Eco/Bam transfer it into a KA vector too.

Digesting the new pMLL-KA backbone

Marianna gave us 10uL of her CMED7 in KA part. The dropout will be 324bp. To digest all of it, I multiplied the Analytical Mapping protocol by 2.5:

10uL of Water
10uL of CMED7-PMLLKA Miniprep
2.5uL NEB
1.25uL EcoRI
1.25uL of BamHI
Total: 25uL
Load 12.5uL into 2 wells. Gel Purify. Elute each with 12.5uL of H20.

Started digest at 4:30pm.

Ligation of ef1a and atub (bjh2342) eco/bam zymo'd digest

Ligated ef1a and atub eco/bam zymo'd digests (from my previous insertion into the supposed KA vector) with the new gel purified Eco/Bam digested KA vector. Started at 7:05pm. Transformed jtk030, MC1061 pir+ cells. In retrospect, I could have used Lefty.

Checking vector backbones of SL/VB Eco/Bam transfers

Set up a 2K55 PCR reaction with Taq MM, 1uL of 1/10 th313 oligo (in the middle of AmpR) and iGEM10 (rev oligo right before EcoR1 site) to verify the order on antibiotics on the backbone. This reaction PCR's off the AmpR gene to right before the EcoRI site. So if the vector is actually A-, the PCR product will contain a bit of AmpR and plasmid backbone and will be 865bp. If the plasmid is -A, the PCR product will contain a bit of AmpR, lots of plasmid backbone and the other antibiotic. In the case of CA, this amounts to 1808bp.

See Eco/Bam page in Excel notebook.

This data suggest that all the backbones that should be A- are indeed A- and that all the backbones that are -A are indeed -A. So the antibiotics shouldn't be the problem. For whatever reason, nothing turned up in the 2345 lane. I'll run the PCR again just to double check.

IMG 5281.JPG

Lane Part Color Expected length Good?
1 Bjh2345 AC 865 no-empty lane
2 Bjh2271 AK 865 yes
3 Bjh1968 AC 865 yes
4 Bjh2316 AK 865 yes
5 Bjh2275 AK 865 yes
6 Bjh2114 CA 1808 yes
7 ig114 AK 865 yes

IMG 5303.JPG

Lane Part Color Expected length Good? 1 Bjh2345a AC 865 no-empty lane 2 Bjh2345b AC 865 good 3 Bjh2345c AC 865 good

Threw out Bjh2345a. Must be a bad miniprep. I should probably map b and c. I guess I haven't yet...

Analytical digests of SL/VB Gel Purf. Assembly Minipreps

Eco/XhoI IMG 5280.JPG

Eco/BamHI IMG 5301.JPG

Tube Part Digest Color Expected Lengths (part, plasmid) Good? Second Digest Expected lengths Good?
1 2114+2316a Eco/Xho CK 4058, 1466 yes started at 3:45
2 2114+2316c Eco/Xho CK 4058, 1467 yes
3 2114+2275 Eco/Xho CK 4627, 1466 Eco/Bam (lane 1) ? ?
4 2271+2017 Eco/Xho AC 3768, 1672 Eco/Bam (lane 2) ? ?
5 ig114+2017 Eco/Xho AC 3998, 1672 Eco/Bam (lane 3) ? ?
6 iGEM16a+2294 Eco/Xho CA 4644, 1466

Payload Delivery: Analytical Mapping of 2348 and 2291 in 1601K

Both parts look great! I'm going to give them to Jin.

IMG 5302.JPG

Tube/Lane part Digest Expected length Good?
1 1601K-jh2348 Eco/Bam 4632, 2475 yes
2 1601K-jh2291 Eco/Bam 5927, 2475 yes

Eco/Bam Transfer from Bad KA to Good KA backbone

Lane Part short description expected lengths cut out
1 1601K-jh2348 payload 4632, 2475
2 1601K-jh2291 payload 5927, 2475
3 bjh2294 conor\'s self lysis 2868, 2516 lower
4 bjh1906 eco/bam plate: B11 46, vector (~2.8k) zymo\'d (too small to purify)

Amy N. Kristofferson 21:13, 10 July 2010 (EDT)

Must do today:

  • Miniprep good colony pcr/cotransformations from yesterday
  • Pick colonies for Tahoura

If I have downtime, could start items in the above To Do list

From yesterday's colony picks, only the first colony picked from 16a H3 was cotransformed. No idea how that happened, since I gel purified the digests before ligating.

Amy N. Kristofferson 13:37, 9 July 2010 (EDT)

Colony PCR of SL/VB and 16a+SL Assembly


Very odd. Even though I gel purified the correct bands, it appears that only 2114+2316 worked correctly. I'm going to check to make sure that everything is in the correct vector, because I don't know what else could be causing a problem. Since I'm miniprepping a the couple correct products, might as well miniprep and map a few others to try and figure out what the problem may be.

IMG 5252.JPG

Colony PCR ' ' ' ' '
Tube Combo Expected length Good? Cotransformed? Miniprepped
1 2114+2316 3053 yes yes
2 \"
3 \" yes yes
4 \"
5 2114+2275 3622 yes
6 \"
7 \"
8 \"
9 2271+2017 2895 yes
10 \"
11 \"
12 \"
13 ig114+2017 3125 yes
14 \"
15 \"
16 \"
17 16a+H3 3566 yes
18 \" yes
19 \"
20 16a+F3 3566

Animal Promoter: Analytical Mapping of atub and ef1a promoter in pMLLKA

Started an Eco/Bam digest of the 4 minipreps I made of each promoter (all of which had GREAT colony PCRs) at 10:35am. They will be ready to run on a gel at 11:05am.

IMG 5245.JPG

Once it has been verified that these parts map well, I'll submit them for sequencing and then begin the next step of assembly.

Lane Part Digest Expected Lengths '
1 iGEM10_021 in PMLLKA Eco/Bam 2868, 897 all good
2 Bjh2342 in PMLLKA Eco/XhoI 2868, 1125 all good

Submitted ef1a-a and atub-b

Sequencing submission:

iGEM35 ef1a animal promoter (iGEM10_021 in PMLLKA)
iGEM36 atub animal promoter (jh2342 in pMLLKA)

Amy N. Kristofferson 14:36, 8 July 2010 (EDT)

Cotransformation check

None of the 2271+2017 or ig114+2017 colonies were cotransformed, but ALL of the iGEM10_018 (16a+SL) were cotransformed.

Colony PCR results for 2271+2017, ig114+2017 atub and ef1a promoter, iGEM10_16a

Can disregard the results for 16a+SL since all samples were cotransformed. 2017 combo inoculations are useless since nothing showed up on the colony pcr. Very strange, since they weren't co-transformed. GOOD NEWS: atub and ef1a look great.

IMG 5201.JPG

Tube Part Lane Expected length Good
1--8 2271+2017 1-15odd 2895
9--16 ig114+2017 2-16even 2925
17--24 atub 17-31 odd 1326 19, 25, 29, 31
1a-8a ef1a 18-32even 1088 all good
9a-24a 16a+SL 31-39 3566 tube 16a looks good (40th well, 8th sample), but they\'re all cotransformed.

Redo of SL/VB and 16a+SL digests with Gel Purification

To avoid co-tranformation and hopefully encourage the creation of the parts I want, I'm going to run a preparative gel, select the appropriate bands and gel purify.

Performed a Lefty (Bam/XhoI digest), Righty (Bgl/XhoI digest), and one-pot digest on all the parts in my SL/VB promoter as well as iGEM10_016a and Bjh2294 in PMLL-KA can be found in the Cheshire Chat plate in H3 and F3. I'll gel purify the Lefty digests of Bjh2345, Bjh2271, Bjh1968, Bjh2114, ig114, 16a and the Righty digests of Bjh2316, Bjh2275, and the two self-lysis devices. The other digests are just to make sure everything was methylated correctly and that the one-pot reaction works on these vectors.

Notes on protocols: Used Manual 2ab Assembly protocols for Lefty and Righty Mastermixes. Used my One-pot recipe, except with 0.4uL of each enzyme. Also, the DNA taken from the Cheshire Cat Plate was diluted by half b/c it was eluted with 100uL, so we had to adjust the amounts of NEB2 and enzyme used so that the recipe in the R/L digests turned out to be 1.6uL NEB2 and 1.5uL of each enzyme total, since our using 8uL of DNA instead of 4uL of DNA would otherwise have diluted the buffer and enzyme.

Digests started at 3:35pm.

From left to right: Lefty Digests, Righty Digests

IMG 5233.JPG

Triple Digests

IMG 5234.JPG


Lane Part vector Purify L Fragments (if no methylation for R\'s) R Fragments (if no methylation, for L\'s) One Pot fragments (if not methylated) Proper methylation?
1 ig114a pMLL7-AK L-Upper 2925, 1196 2440, 1681 1681, 1244, 1196 Yes
2 Bjh2114 pMLL9-CA L-Upper 1518, 1270 1476, 1312 1476, 1270, 42 Yes
3 Bjh2271 pMLL7-AK L-Upper 2695, 1196 2210, 1681 1681, 1196, 3891 Yes
4 iGEM10_016a pMLL5-CK L-Upper 2333, 1196 2054, 1475 N/A (not methylated)
5 Bjh2316a pMLL7-AK R-Upper 4491, 1196 4006, 1681 2810, 1681, 1196 Yes
6 Bjh2275a pMLL7-AK R-Upper 5060, 1196 4575, 1681 3379, 1681, 1196 Yes
7 Bjh2294 F3 pMLL9-CA R-Upper 4114, 1270 3777, 1607 2507, 1607, 1270 Yes
8 Bjh2294 H3 pMLL9-CA R-Upper 4114, 1271 3777, 1608 2507, 1607, 1271 Yes

NOTE: lane 2 in the lefty gel is Bjh2294 H3, and everything else is pushed over one lane

Summary: Everything is methylated as it should be. I cut out all the right bands and purified them. Also, this shows that triple digestion isn't very efficient and cause a lot of parent vector bleedthrough (the top band of all the lanes). Also, note how dilute the SL DNA is... I'll still elute with the standard 8.5uL to concentrate the DNA, but this is still a potential problem.

Ligation and Transformation of SL/VB and 16a+SL purified digests

Started ligation at 6:45pm. Will transform into jtk030 (pir +, MC1061 cells). I forgot to digest 2017, so I used a righty digest that I had done previously. Started rescue at 8:10pm.

Amy N. Kristofferson 13:45, 7 July 2010 (EDT)

All the samples from 16a,b + SL were cotransformed, and since Jin mentioned that making a mastermix for the onepot reaction may result in there not being enough enzyme per reaction, I'm going to do it over again without making a mastermix AND using 0.5uL of enzyme instead of o.3uL of enzyme. This should cut back on parent vector bleedthrough as well.

There are a significant number of colonies on the plate for the 2271+2017 and ig114+2017 redo. I'll pick colonies/colony pcr/inoculate/check for cotransformation for 8 colonies from each. Also, since all the colony PCR's failed for my re-picking of 2114+2275, I'm going to redo the one-pot reaction for that as well.

The ligation of the atub promoter to the KA vector (Bjh2342-pMLL6-KA) was very successful, since I got a lot of colonies. I'll inoculate and run colony PCR (no need to check for co-transformation. Since my two colony picks of ef1a seemed to fail on the colony PCR yesterday, I'm going to pick a bunch more, inoculate, and run colony PCR again.

SL/VB Assembly: Redo of One Pot (with more enzyme) for 2114 combos

  • One Pot (used 0.4uL of enzyme):
    • 2114+2275
    • 2114+2316
      • Will be ready for ligase at 2:00pm. Added ligase at 2:00pm. Will be ready for transformation into RIGHTY cells at 2:30pm. Rescue started at 3:30pm.

iGEM10_020 Assembly: redo of 16a+SL assembly, starting with new L/R digests

  • Redo of L/R digest of 16a and 6+24
    • Put in incubator at 12:14pm. Ready for Zymo at 1:14pm. Zymo'd and added ligase at 2:00pm. Will be ready for transformation into RIGHTY cells at 2:30pm. Rescue started at 3:30pm.

Possibly successful assemblies (Animal Promoter, SL/VB and iGEM20

  • Picked colonies (8 each)/inoculate/cotransformation check
    • 2271+2017
    • ig114+2017
    • 16a+SL (pick at least 12 NEW colonies)
    • atub and ef1a (no cotransformation check)

Miniprep of Payload Delivery Vectors

Miniprepped Payload Delivery stuff (in shaker w/ Mg LB)

Sequencing Results for iGEM10_017b, 2114+2316b,Bjh2345 PMLL4

Sequencing results:

  • iGEM10_017b: the first 990bp or so of the 1546bp part are perfect, so I think it's safe to say that this miniprep is good to use for future assembly.
  • 2114+2316b: this proved to have the Pcon, but no vacuole buster in the part. At first I thought this was odd, since the part miniprepped well, but it makes sense now. The part had a bad colony PCR since only the 43bp pCon was in the vector. The part had what looked like a good miniprep map since the vector was the same size as the part, and I when I saw a band, I assumed it was the part AND the vector. My mistake.
  • Bjh2345 PMLL4: bad read. Do again, but make sure concentration is accurate?

Amy N. Kristofferson 13:49, 6 July 2010 (EDT)

Colony PCR results for all colonies picked today

Note: they ALL look horrible. Bands in the 16a lanes are probably from cotransformation with 16a vector, since that part is about 850bp.

IMG 5172.JPG

Lane Part Expected length
1 2114+2275 repick 3622
2 \"
3 \"
4 \"
5 \"
6 \"
7 \"
8 \"
9 16a+SL 3566
10 \"
11 \"
12 \"
13 16b+SL 3566
14 \"
15 \"
16 \"
17 ef1a 1088
18 \"

Transposase Assembly: Colony PCR of iGEM10_016a,b with Self Lysis Device

Picked 4 colonies of each. Ran Colony PCR. Inoculated. Plated to check for co-transformation.

Animal Promoter: Colony PCR of Ef1a

Picked 2 colonies. Ran Colony PCR. Inoculated.

Conor Eco/Bam digested and zymo'd the atub promoter (Bjh2842). Started ligation with PMLL6-KA vector at 4:45pm. Transformed into jtk049 cells. Started rescue at 5:55pm.

Payload Delivery

Since the payload delivery device contains the Self Lysis device under a promoter that's induced in low levels of Mg, I need to grow up my colonies in LB containing 30mM Mg to prevent Lysis. In the future, I should also rescue/plate on Mg. I selected clear colonies.

Tomorrow, I will miniprep the inoculations and map the minipreps next to the parent vector containing the part, so I can make sure the whole part is in the new vector. (Jin said recombination events can occur which could shorten the part)

SL/VB Promoter Assembly

Redo one pot reaction with 2271+2071 and ig114+2071

Conor set up two one pot reactions and put them in the thermocycler under my ONEPOT program. Added ligase at 4:45pm. Will transform into LEFTY cells. Started rescue at 5:55pm.

Picked more colonies for 2114+2275, since miniprep mapping failed

Pick 8 more colonies from 2114+2275. Ran colony PCR, inoculate, check for cotransformation.

Summary of Results so far

Part Transformation Miniprep Map Colony PCR for that Miniprep To do
2114+2316 good good bad Seq
2114+2275 good bad bad repick colonies
2271+2071 bad N/A N/A redo one-pot
ig114+2071 ok bad good redo one-pot
2345-pMLL4 good good bad Seq

For whatever reason, my Colony PCR results and miniprep results don't seem to ever correspond.

Amy N. Kristofferson 19:16, 5 July 2010 (EDT)

SL/VB Promoter Assembly: Mapping the minipreps produced from Round 1 and 2345 Redo

Started digestion at 5:18pm. Will be ready for the gel at 5:48pm.

IMG 5161.JPG

Tube Part Methylated? Digest Color Expected Lengths (part, plasmid) Good? Sequence Next step
1 2114+2316a R Eco/Xho CK 4058, 1466 good yes
2 2114+2316b possibly good yes
3 2114+2275b R Eco/Xho CK 4627, 1466 BAD Pick more colonies
4 2114+2275c BAD
5 ig114+2017 L Eco/Bam AC 2925, 2745 BAD redo
6 2345 in pMLL4a L Eco/Bam AC 2680, 2745 good yes
7 2345 in pMLL4b good
8 2345 in pMLL4c good

Transposase Assembly: Ligation of iGEM10_016a,b Lefty digest with 6+24 Righty digest

Started ligation at 4:05pm. Ligated unmethylated 6+24 digested with BglII+XhoI with both unmethylated iGEM10_016a+b, which had been digested with BamHI+XhoI. Tubes are labelled 16a+SL and 16b+SL (SL meaning Self Lysis, which is part 6).

After ligation is over, I will transform into RIGHTY cells. Started rescue at 5:05pm. Plated on CA.

Animal Promoter: Ligate Ef1a Eco/Bam digest of PCR product with PMLL6-KA

Started ligation at 4:05pm. Ligated Ef1a Eco/Bam digest of PCR product with pre-digested PMLL6-KA.

After ligation is over, I will transform into LEFTY cells. Started rescue at 5:05pm. Plated on KA.

Payload: Ligation of Bjh2348 and 2291 with Pjh1601K

Started ligation at 4:05pm. Ligated Eco/Bam digests of Bjh2291 and 2348 with my Eco/Bam digested Pjh1601K plasmid.

After ligation is over, I will transform into jtk049 cells, because they don't need to be methylated. Started rescue at 5:05pm. Plated on K.

Amy N. Kristofferson 13:00, 2 July 2010 (EDT)

Transposase Assay Take 2: Testing time for Transposase expression and time for transposase activity

  1. Each inoculation contains about 4mL of cells. Move 1000uL of cells into four flasks.
    1. Each flask contains 900uL of cells.
  2. Add 10uL of arabinose for each mL of cells at t=o, 1 hour, 2 hours, 3 hours.
    1. Since arabinose is 100x, will add 9uL of arabinose to each flask
    2. Added first 9uL at 10:49am.
    3. Added second 9uL at 11:49am
  3. After four hours have passed since you first added arabinose, add 1uL of atc per mL of cells. Allow 1 hour for lysis.
    1. Will add 0.9uL of atc, since 900uL of cells are being used and the concentration of the atc is 1000x.
  4. After that one hour, add 5uL of DNA to each tube.
  5. Remove a 200uL sample of lysate after 30min, 1 hour, 1.5hour, 2hours.
  6. Immediately after removal, spin down the lysate and zymo the supernatant.
  7. Transform lefty pir+ cells with the lysate. Plate on Amp and Gen.

Unfortunate update: Sequencing proved that iGEM10_020b is a dud. Gibson didn't work because one of our junctions contained palidromic terminal repeats, so the oligos designed based off those junctions didn't have a unique binding site. Oh well. We'll proceed with manual 2ab assembly.

iGEM10_20 2ab Assembly

Mapping of iGEM10_016 minipreps a and b

An Eco/Bam digest of iGEM10_16 in PMLL5-CK should result in bands at 2662 and 867.

Note: iGEM10_017 has already been mapping. (see below) Results were slightly confusing, so I'll submit it for sequencing...? iGEM10_001 was also mapped, and looks good. 1a-c are all good options.

Started digestion at 4:55pm.

IMG 5144.JPG

Both have bands at the appropriate places, but 16b has a lot more parent vector remaining, for whatever reason, so 16a is probably the best choice.

Assembly of iGEM10_018

Lefty Digest of iGEM10_16

Righty Digest of Self Lysis Device (6+24 taken from well G10 of ROMEO plate) Started at 4:42pm. Zymo'd and stored in my working box.

SL/VB Promoter Manual Assembly: Analysis of One-Pot reaction

2114+2316 and 2114+2275 both successfully transformed righty pir+ cells. The plates are covered in colonies. 2271+2017 and ig114+2071 weren't as successful. The former had no colonies, while the latter had 11, which is surprising, because I used barely any DNA.

I will pick four colonies from each, colony pcr, inoculate, and check for cotransformation.

IMG 5143.JPG

Cotransformation results:

IMG 5145.JPG

The ones with letters in the corners were chosen for minipreps.

Tube Combo Expected length Good? co-transformed? miniprep?
1 2114+2316 3053 yes no yes
2 \" no yes
3 \"
4 \" no
5 ig114+2017 3125 yes no yes
6 \" yes
7 \" yes
8 \"
9 2345 in pMLL4 2880 no yes
10 \" no yes
11 \" no yes
12 \" no
13 2114+2275 3622
14 \" no yes
15 \" no yes
16 \"

Moving into jh1601K

Performed an Eco/Bam Digest of jh1601K. Put in incubator at 11:09am. Trashed that digest. Realized I need to do a gel purification, so I'll do the digest again with 4uL of plasmid.

Started digest again at 4:54pm.

2345 Redo from 24+PMLL4 digests

The plate is covered in colonies. I will pick 8 colonies, inoculate, and check for cotransformation.

Amy N. Kristofferson 13:40, 1 July 2010 (EDT)

Eco/Bam transfer 2348 and 2291 into 1601K

Started Digest at 12:19pm.

Zymo'd and stored in my working box.

2345 Redo: Ligating Tim's ebid 24 and EB pMLL4-AC

Since my Colony PCR turned out so horribly yesterday, and 2345 is the Self Lysis Device we've been using for all our construction, I'm just going to use Tim's digests and ligate them together.

Started ligation at 11:48am.

I transformed the plasmid into lefty pir+ cells. Started rescue around 12:30pm. Plated on AC at 2:13pm.

One Pot Assembly of Jin's Parts

I'm going to redo the construction of the following with a one pot reaction, since they're all methylated.

Lefty Digest Righty Digest Transform into Plate on Short Description '
2114 2316 R CK pCon.VacuoleBusterA
2114 2275 R CK pCon.VacuoleBusterB
2271 2017 L AC Pbad.SelfLysisT
ig114 2017 L AC Ptet.SelfLysisT

Started digest at 11:10am, for all but ig114+2017. I added the speck of 2017 (~.2uL) left at around 11:36am. Started the 20 min heat kill for all but ig114+2017 at 12:30pm. Accidently set the heat kill program for 20 sec instead of minutes and added ligase. Hopefully that won't hurt anything. Put all four tubes in the PCR machine to heat kill at 12:53pm. Added ligase at 1:41pm. Started rescue at 2:42pm.

These numbers have been based on Qiagen minipreps of Jin's pBjh1601 assembly vectors:

  • Set up the digestion:
1uL lefty plasmid(methylated)
1uL righty plasmid (methylated)
0.3 uL XhoI
0.3 uL BglII
0.3 uL BamHI
6.1uL Water
  • Digest for 1 hour at 37C
  • Heat kill at 65 for 20 min
  • Add 0.3uL T4 Ligase
    • Ligate at room temperature for 30 minutes
  • Put on ice for transformation
  • Transform, rescue, plate on dual antibiotic plates


  • This requires the use of BglII and BamHI methylating strains!
  • 10X "NEB2+ATP" is a homemade buffer present as aliquots in 500uL

tubes labeled with a red slash

  • You can make up a mastermix of the enzymes/buffer/water and

distribute the plasmids into it

  • The leftmost thermocyler in 327 has a program JCA/1123 that runs the

1hr at 37 and heat kill steps of the procedure

Eco/Bam digest of EF1a PCR product

Started digest at 11:55am. Zymo'd the product.

I need to figure out what assembly vector to put it in and then map and sequence the part to make sure it's correct.