DNA ligation

Curators

James Hadfield, CRUK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE.

Anyone should feel free to add themselves as a curator for this consensus protocol. You do not need to be a curator in order to contribute. This is a new initiative on OWW, please provide your thoughts on the idea of consensus protocol curators here.

Abstract

This is a consensus protocol. See the bottom of this article for specific protocols.

DNA ligation is the process of joining together two DNA molecule ends (either from the same or different molecules). Specifically, it involves creating a phosphodiester bond bond between the 3' hydroxyl of one nucleotide and the 5' phosphate of another. This reaction is usually catalyzed by a DNA ligase enzyme. This enzyme will ligate DNA fragments having blunt or overhanging, complementary, 'sticky' ends. Typically, it is easier to ligate molecules with complementary sticky ends than blunt ends. T4 DNA ligase is the most commonly used DNA ligase for molecular biology techniques and can ligate 'sticky' or blunt ends.

The two components of the DNA in the ligation reaction should be equimolar and around 100μg/ml. Most commonly, one wants to ligate an insert DNA molecule into a plasmid, ready for bacterial transformation. Typically, DNA and plasmid vector are individually cut to yield complementary ends, then both are added to a ligation reaction to be circularised by DNA ligase. If the plasmid backbone to insert DNA ratio is too high then excess 'empty' mono and polymeric plasmids will be generated. If the ratio is too low then the result may be an excess of linear and circular homo- and heteropolymers.

Materials

Reagents

• T4 DNA ligase
• 10x T4 DNA Ligase Buffer
• Deionized, sterile H₂O
• Purified, linearized vector (likely in H₂O or EB)
• Purified, linearized insert (likely in H₂O or EB)

Equipment

Vortex

Procedure

10μL Ligation Mix

Larger ligation mixes are also commonly used

• 1.0 μL 10X T4 ligase buffer
• 6:1 molar ratio of insert to vector (~10ng vector)
• Add (8.5 - vector and insert volume)μl ddH₂O
• 0.5 μL T4 Ligase

Calculating Insert Amount

[math]\displaystyle{ {\rm Insert\ Mass\ in\ ng} = 6\times\left[\frac{{\rm Insert\ Length\ in\ bp}}{{\rm Vector\ Length\ in\ bp}}\right]\times{\rm Vector\ Mass\ in\ ng} }[/math]

The insert to vector molar ratio can have a significant effect on the outcome of a ligation and subsequent transformation step. Molar ratios can vary from a 1:1 insert to vector molar ratio to 10:1. It may be necessary to try several ratios in parallel for best results.

Method

1. Add appropriate amount of deionized H₂O to sterile 0.6 mL tube
2. Add 1 μL ligation buffer to the tube.
   Vortex buffer before pipetting to ensure that it is well-mixed.
   Remember that the buffer contains ATP so repeated freeze, thaw cycles can degrade the ATP thereby decreasing the efficiency of ligation.
3. Add appropriate amount of insert to the tube.
4. Add appropriate amount of vector to the tube.
5. Add 0.5 μL ligase.
   Vortex ligase before pipetting to ensure that it is well-mixed.
   Also, the ligase, like most enzymes, is in some percentage of glycerol which tends to stick to the sides of your tip. To ensure you add only 0.5 μL, just touch your tip to the surface of the liquid when pipetting.
6. Let the 10 μL solution sit at 22.5°C for 30 mins
7. Denature the ligase at 65°C for 10min
8. Dialyze for 20 minutes if electroporating
9. Use disks shiny side up
10. Store at -20°C

Troubleshooting

Factors affecting efficiency

From Tom Ellis

A protocol analysis experiment for a typical DNA ligation (7.2 kb vector + 0.6 kb insert, sticky ends) gave optimal ligation efficiency when 50 ng of vector was ligated overnight at 16°C with a 2:1 insert:vector molar ratio and standard T4 ligase. Ligase was heat inactivated at 65°C for 20 mins before 2 μL (of 20 μL) was used to transform commercial heat-shock competent cells.

Ligation efficiency was marginally decreased by

1. Doing a 1 hr ligation at room temperature
2. Using 100 ng vector
3. Using insert:vector molar ratios of 5:1 and 1:1

Ligation efficiency was noticably decreased (x100) by

1. Sticky end ligation with a larger insert (5.2 kb vector + 2.6 kb insert)
2. Blunt end ligation

Ligation efficiency was severely decreased (x10000) by

1. Using DNA fragments that have been exposed to UV during the gel extraction procedure (can avoid by blind excision, or by using a black-light or 365nm UV transilluminator instead of the usual 312nm type)
2. Using the NEB Quick Ligation Kit (heat inactivation of PEG in the buffer ruins transformation, without heat inactivation the ligation probably would've been fine)

For additional troublshooting, check out the NEB FAQ page for T4 ligation: [1]

Notes

1. Make sure the buffer is completely melted and dissolved. The white precipitate is BSA according to NEB. Make sure the buffer still smells strongly like "wet dog" (to check if the DTT is still good).
2. Because ligase buffer contains ATP, which is unstable and degraded by multiple freeze/thaw cycles, you may want to make 10-20ul aliquots from the original tube. Ligase buffer may be spiked with additional ATP.
3. If you are having trouble with your ligation, NEB offers FAQ's (Quick Ligation T4 DNA ligase) and tips to help.
4. Prior to the ligation, some heat their DNA slightly (maybe ~37°C) to melt any sticky ends which may have annealed improperly at low temperatures.
5. Tom Knight has read that ligase can inhibit transformation [1]. By heat-inactivating the ligase, this inhibition can be avoided. However, according to the NEB FAQ, heat-inactivation of PEG (which is present in the ligation reaction) also inhibits transformation, therefore a spin-column purification is recommended prior to transformation if you are having problems.
6. Treating PCR products with proteinase K prior to restriction digest dramatically improves the efficiency of subsequent ligation reactions. [2]
7. Using SYBR Safe DNA Gel Stain is a safer, non-carcinogenic alternative to ethidium bromide.
8. T4 DNA Ligase is very sensitive to shear, so spinning your ligation mix or vortexing it to mix it can affect your yields. Instead try mixing with the pipette tip or slowly resuspending the solution.
9. If there is a lot of self-ligation look into Phosphatase treatment of linearized vector.

Acknowledgments

This protocol is primarily based on Endy:DNA ligation using T4 DNA ligase.

References

1. Michelsen BK. Transformation of Escherichia coli increases 260-fold upon inactivation of T4 DNA ligase. Anal Biochem. 1995 Feb 10;225(1):172-4. DOI:10.1006/abio.1995.1130 |
2. Crowe JS, Cooper HJ, Smith MA, Sims MJ, Parker D, and Gewert D. Improved cloning efficiency of polymerase chain reaction (PCR) products after proteinase K digestion. Nucleic Acids Res. 1991 Jan 11;19(1):184. DOI:10.1093/nar/19.1.184 |
3. Olivera BM and Lehman IR. Linkage of polynucleotides through phosphodiester bonds by an enzyme from Escherichia coli. Proc Natl Acad Sci U S A. 1967 May;57(5):1426-33. DOI:10.1073/pnas.57.5.1426 |

   DNA ligation by Escherichia coli DNA ligase

Specific protocols

• Endy:DNA ligation using T4 DNA ligase -- Using T4 DNA Ligase
• Knight:DNA ligation using NEB Quick Ligation Kit -- 5min ligation.
• Knight:TOPO TA cloning -- For PCR products.
• Silver:Ligation -- A protocol for sticky end ligations using the Roche Kit.
• Richard_Lab:Ligation -- Uses T4 Ligase
• BE.109:DNA ligation -- A ligation protocol for classroom use in a laboratory class taught at MIT. Uses T4 DNA ligase but has interesting tips and tricks.

• Corum:T4_Ligation

Discussion

You can discuss this protocol.