iGEM Part Plasmid Assembly

NOTE: The following page is under revision. The GGA procedures and protocols below may not be optimal for your experiments. If you are new to GGA, please check with Dr. Mishler prior to using any of the following procedures.

Things to add:

• BsaI-VF2 works
• T4 DNA ligase works
• Altered time/temperature for digestion/ligation reaction steps.
• Promega vs NEB T4 DNA ligase as well as ligase buffer. Only difference between buffers is 300mM tris (pH 7.8 Promega) vs 500 mM tris (pH 7.5 NEB). "optimized protocol from the CIDAR MoClo 2016 papers" suggest the promega enzyme/buffer are better, but not data are presented that back this assertion. They may have just done an experiment favoring those enzymes b/c that is what they are used to and the two sets of buffer+enzymes worked similarly.
• Link to the above paper (methods and supplemental methods) https://pubs.acs.org/doi/full/10.1021/acssynbio.5b00124
• Links (?) to new protocols/information...

Part Plasmid Assembly Protocol using BsmBI restriction enzyme and T4 DNA ligase.

Total volume will be 20 μL; You will need 10 fmol of entry vector (pYTK001) and 20 fmol of your DNA insert(s).

• 17.7ng pYTK001 plasmid [try to keep volume to 1-2μL]
• 20 fmol of insert DNA = 650 * insert length * 20x10^-6 ng [try to keep volume to less than 10 μL]
• 2 μL of 10× T4 DNA ligase buffer (Promega? NEB?)
• 1 μL of BsmBI
• 1 μL of T4 DNA ligase (Promega? NEB?)
• x μL water up to 20 μL total.

This reaction should then run at...

http://barricklab.org/twiki/bin/view/Lab/ProtocolsBTKMakeANewPartPlasmid

Below is the "Dr. Mishler recommends" Golden Gate Assembly reaction for FRI/iGEM students.

Alternative Golden Gate Assembly Reaction (FRI/iGEM variant)

The reason for this alternative procedure is based on some summer experiments, showing that one reason we may have high background is that we are using BsmBI at non-ideal conditions.

This first gel shows pYTK001 being cut with BsmBI and pYTK095 being cut with BsaI at either 37°C or 42°C with either T4 DNA ligase buffer, cutsmart buffer, or NEB 3.1 buffer. This last buffer is the preferred BsmBI buffer. BsmBI is most active at 55°C (NEB catalog). All buffers and enzymes are from NEB (New England Biolabs)

• Gel of BsmBI digestion under different reaction conditions.:

From left to right: (Note: Not sure how to get the text to move over a bit more...-DM)

1. 1 KB ladder
2. uncut pYTK095
3. pYTK095 + cutsmart buffer at 37°C
4. pYTK095 + T4 DNA ligase buffer at 37°C
5. pYTK095 + cutsmart buffer at 42°C
6. pYTK095 + T4 DNA ligase buffer at 42°C
7. uncut pYTK001
8. pYTK001 + cutsmart buffer at 37°C
9. pYTK001 + T4 DNA ligase buffer at 37°C
10. pYTK001 + 3.1 buffer at 37°C
11. pYTK001 + cutsmart at 42°C
12. pYTK001 + T4 DNA ligase buffer at 42°C
13. pYTK001 + 3.1 buffer at 42°C

Based on the above reactions, a protocol was developed using NEB buffer 3.1, supplemented with ATP and DTT to allow for T7 DNA ligase activity. The results can be seen in the PDF below. There are three sets of reactions: The first lane for each set is DNA only, then DNA in a GGA reaction without ligase, and finally DNA in a GGA reaction with ligase. In each set the presence of the ligase results in the formation of higher band products. The procedure was to incubate for 30 minutes with BsmBI at 42°C followed by incubating with T7 DNA ligase at 25°C for 30 additional minutes.

• GGA_test2_6_23_2016.pdf: Test of BsmBI and T7 DNA ligase procedure using NEB buffer 3.1

This initial protocol was simply a proof of principle. From this protocol, we are currently using the following protocol.

Total volume will be 20 μL; You will need 17.7 ng of pYTK001 and 20 fmol of your DNA insert(s).

• 17.7ng pYTK-001 plasmid [try to keep volume to 1-2μL]
• 20 fmol of insert DNA = 650 * insert length * 20x10^-6 ng [try to keep volume to less than 10 μL]
• 2 μL of 10× 3.1 buffer
• 2 μL of 10 mM ATP
• 1 μL of 100 mM DTT
• 1 μL of BsmBI
• x μL water up to 20 μL total.

Mix well by pipetting.

• Incubate at 42°C for 30 minutes.

• Then, add 1 μL of T7 DNA ligase and incubate at 16°C for 30 minutes. This is followed by 25 cycles of incubation at 42°C for 5 minutes and 16°C for 5 minutes. This is then followed by a 15-30 minute incubation at 55°C and a 10 minute incubation at 80°C.

Rationale for each step: The initial cutting for 30 minutes will generate cleaved product similar to lane 13 in the gel above. However, this higher temperature will result in some loss of T7 DNA ligase activity. Thus, we add the ligase after this initial incubation. We then conduct a 30 minute incubation at a low temperature (traditional standard molecular biology protocol for DNA ligases). After these initial incubations, we cycle, maximizing the chances for success. The final two high temperature incubations are meant to 1) maximize BsmBI cutting of uncut pYTK001 (minimizing background) at 55°C, and 2) to kill all enzymatic activity at 80°C.

• Use 2 μL assembly reaction for electroporation.
• After recovery, plate on LB/CAM.

Results and Troubleshooting

Below are three plates from summer 2016. ATF1 (bba_J45014) was added to pYTK001, an entry vector for golden gate assembly. This required removing an internal BsmBI cut site, and then adding the resulting ATF1 gene to pYTK001 using BsmBI.

The first plate is a negative control. The golden gate assembly was performed with no gene, just pYTK001. The second plate is a positive control using a gBlock from Peng. The last plate is the actual experimental golden gate assembly where ATF1 inserted into pYTK001.

• The Negative control GGA using only pYTK001 with no insert.:
  

Since pYTK001 contains sfGFP with a promoter. The only colonies seen are fluorescent green. These are uncut or religated pYTK001 plasmid, and this is our level of background.

• The Positive control GGA using a gBlock from Peng with pYTK001.:
  

The number of colonies is much higher on this plate, and most are not fluorescent. These non-fluorescent colonies should be the correctly assembled plasmid containing the gBlock

• ATF1-pYTK001 GGA transformation on LB/CAM plate.:
  

The number of colonies and non-fluorescent colonies on this plate resembles the number seen on the positive control plate. This assembly reaction is assessed as "having worked". However, the colonies must be picked, grown overnight, and then the plasmid extracted and sequenced to confirm that the assembly did indeed work.

gBlocks vs PCR products as sequences being assembled.

• gBlocks - This high quality dsDNA tends to easily be assembled into an entry vector, such as pYTK001. This DNA can be resuspended and thrown straight into a GGA reaction.
• PCR products - This DNA can vary in quality, and tends to be more troublesome in two ways.
  
  
  1. Since the DNA is synthesized via PCR, there will frequently be point mutations. Thus, when picking colonies from a plate after GGA, try to pick at least 3 colonies. With ATF1-pYTK001 (see the plates above), 5 colonies were picked, 3 had point mutations.
  2. We have noticed that the PCR products made and purified in the FRI lab may be "less stable" or perhaps "degrades more quickly". It is unclear if this is a true difference, but regardless multiple PCR products were partially or fully degraded within 1 month of purification and storage at -20 degrees. Thus, it is STRONGLY recommended that immediately after purifying the PCR products, you should Qubit the products, and then begin your assembly reaction. Example: when creating an ATF1 PCR product that was compatible for golden gate assembly, the ATF1 gene first needed to be PCR'd into two discreet products to remove a restriction site. These two PCR products were then used in an GGA reaction with pYTK001 to create a single plasmid. However, the first couple of times this was attempted, the PCR products were made ~1 week before being used in the assembly reaction. These assemblies failed, and upon inspection (~1 week later), the PCR products were partially or wholly degraded. On the final attempt (which appears to have worked), the PCR products were purified on the same day that they were assembled into the pYTK001 entry vector. This is not conclusive, but it suggests that the quality of PCR products, which can naturally degrade over time (due to freeze/thaw cycles, nuclease contamination, or being left out at room temp), is absolutely critical. Even partial degradation could be sufficient to fully prevent successful GGA as the partially degraded products may still have one of their two cut sites available. These sites would be cleaved and could then be ligated to the pYTK001 plasmid. However, lacking a second viable cut site, this product would be an off pathway product (i.e. you can convert it into the desired final product).

Contributors

• Dennis Mishler

This link will take you back to the main Golden Gate Assembly page.
http://barricklab.org/twiki/bin/view/Lab/GoldenGateAssemblyProtocolsMainPage