Knight:Annealing and primer extension with Klenow polymerase

This protocol uses annealing and primer extension to generate a short fragment of DNA (~100 bp). The DNA fragment is prepared for cloning by restriction digest.

Materials

• Two oligos which overlap by ~20 bp and have restriction enzyme sites at the 5' ends as in the diagram below. See restriction digest notes for information on cutting near the ends of linear DNA fragments. See notes for more information on primer ordering.

Oligo 1:    5' ---RE site-------------------------------- 3'
Oligo 2:                                        3' --------------------------------RE site--- 5'

• Klenow 3'[math]\displaystyle{ \rightarrow }[/math]5' exo^- polymerase
• dNTPs (25 mM each dNTP in stock)
• Restriction enzyme(s)
• Restriction enzyme buffer
• BSA

Calculating amount of oligo for reaction

This should be checked for errors -Reshma 19:03, 12 May 2005 (EDT)

[math]\displaystyle{ \rm{X\ L\ oligo} = \frac{\frac{Y\ g\ oligo}{(330\ g/mol\ of\ nt)(W\ nt/oligo)}\ mol\ of\ oligo}{Z\ mol/L\ oligo\ stock} }[/math]

Procedure

1. Dilute the two oligos to a concentration of 10 or 25 μM using H₂O
2. Mix the following in a 0.6 mL sterile tube
   • 10 μL 10X restriction enzyme buffer
   • 1 μL 100X BSA
   • X μL oligo 1 (typically 1 μg or more)
   • Y μL oligo 2 (typically 1 μg or more)
   • (87 - X - Y) μL deionized sterile H₂O
3. Anneal the two oligos together by either placing the mixture in a thermal cycler (MJ Research, PTC-200) at 94°C for 5 mins, a cool down for 0.1°C/sec to 65°C, 65°C for 5 mins, then a cool down for 0.1°C/sec to 37°C. Alternatively, the tube can be placed in a beaker of boiling water and let cool to room temperature.
4. Add 1 μL Klenow 3'[math]\displaystyle{ \rightarrow }[/math]5' exo^- polymerase to mixture.
   Vortex polymerase before pipetting to ensure it is well-mixed.
5. Add 1 μL dNTPS (equal to 0.25 mM final concentration of each dNTP).
   Recommend using a thermal cycler for the following incubation steps.
6. Incubate 1 hr at 37°C.
7. Heat inactivate polymerase by incubating at 75°C for 20 minutes.
   See Restriction Digest for more information on the following steps.
8. Add 1 μL restriction enzyme(s) to mixture.
9. Incubate for a minimum of 2 hrs.
10. Heat inactivate restriction enzyme by incubating at 80°C for 20 mins.
11. Purify DNA as necessary

Notes

• Once oligos become about around 50-60 bp in length, there can often be problems with errors or deletions in the primers. Therefore, it might be worth ordering your primers with an extra purification step such as PAGE. Invitrogen custom primers offers this service for an extra fee.
• Klenow is tolerant of a broad range buffer conditions. This includes NEBuffer for EcoRI in which it will exhibit a rate of polymerization of approximately equal to 50% of that in its recommended buffer. For greater reproducibilty, you could add DTT to the reaction, since DTT is absent from EcoRI reaction buffer. Courtesy of Paul Walsh at NEB Technical Support.
• When using Klenow(exo-) for this type of reaction, there is much less risk of "overdoing" the reaction than when using regular Klenow. Incubating at 37C for one hour, using one unit of Klenow(exo-) per pmol of DNA should result in the desire 90bp duplex. Courtesy of Paul Walsh at NEB Technical Support.

References

W. P. Stemmer, A. Crameri, K. D. Ha, T. M. Brennan, and H. L. Heyneker. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene, 164(1):49–53, 1995. PubMed