Miniprep - Alkaline Lysis for BACs

by A. Untergasser (contact address and download at www.untergasser.de/lab)
Version: 1.0 - Print Version (.PDF)

ATTENTION: This is a low priced protocol. Use it preferably!

  1. Pick colony and grow in 3 ml LB over night at 37°C
  2. Spin down 1.5 ml for 2 min at 8000 rpm (6000 G) store the rest at 4°C
  3. Resuspend pellet in 150 µl ALS-I buffer
  4. Incubate on ice for 5 min
  5. Add 300 µl ALS-II buffer
  6. Mix carefully by inverting the tube 8 times
  7. Incubate on ice for 5 min
  8. Add 225 µl ALS-III buffer
  9. Mix carefully by inverting the tube 8 times
  10. Spin down immediately for 6 min at 13000 rpm (18000 G)
  11. Transfer 600 µl supernatant to a tube containing 360 µl isopropanol
  12. Mix well by inverting the tube several times
  13. Spin down for 10 min at 13000 rpm (18000 G)
  14. Remove the supernatant and add 700 µl of 70% ethanol
  15. Mix well by inverting the tube several times
  16. Spin down for 5 min at 13000 rpm (18000 G)
  17. Remove the supernatant and dry at room temperature for 1 min
  18. Add 50 µl TER and incubate at 60 °C for 5 min

Buffers:

ALS-I: ALS-II:
0.9 g Glucose 0.8 g NaOH
2.5 ml TrisHCl (Stock: 1 M; pH 8.0) 10 ml SDS (Stock: 10 %)
2 ml EDTA (Stock: 0.5 M; pH 8.0)    
add water to 100 ml, store at 4 °C add water to 100 ml,
store at room temperature
   
ALS-III: TER:
29.5 g potassium acetate 10 µl TrisHCl (Stock: 1 M; pH 8.0)
11.5 ml glacial acetic acid 2 µl EDTA (Stock: 0.5 M; pH 8.0)
should have pH 4.8 2 µl RNAse A
add water to 100 ml, prepare fresh add water to 1 ml, store at 4 °C
   
Stock Solutions:
1 M TrisHCl (pH 8.0) 10 % (w/v) SDS
0.5 M  EDTA (pH 8.0) 10 mg / ml RNAse A

Buffer-Concentration:

ALS-I: ALS-II:
50 mM Glucose 0.2 M NaOH
25 mM TrisHCl (pH 8.0) 1 % SDS
10 mM EDTA (pH 8.0)  
 
  
ALS-III: TER:
3 M potassium acetate 10 mM TrisHCl (pH 8.0)
11.5 % v/v glacial acetic acid 1 mM EDTA (pH 8.0)
should have pH 4.8 0.02 mg / ml RNAse A

Commented Protocol:

1. Pick colony and grow in 3 ml LB over night at 37°C

3 ml LB are fine if you prep 1.5 ml, use 4 ml if you want to prep 3 ml. Then you have still enough to inoculate a maxiprep, 500 µl for a glycerol stock or similar things...

2. Spin down 1.5 ml for 2 min at 8000 rpm (6000 G) store the rest at 4°C

Most other protocols recommend longer and higher centrifugation steps, but this step gives you a pellet that is easy to resuspend and would not fall off during the following steps. Do not pipet off the supernatant - open the eppi, discard all liquid inside and beat the eppi hard and several times upside-down on a piece of paper towel! The pellet will stand it and the liquid is efficient and fast removed.

3. Resuspend pellet in 150 µl ALS-I buffer

You have to resuspend each pellet with a fresh tip. Do not leave any pieces of the pellet undissolved, or the lyses will be incomplete.

4. Incubate on ice for 5 min

5. Add 300 µl ALS-II buffer

Just open all eppis, use one tip and pipet into all eppis.

6. Mix carefully by inverting the tube 8 times

Invert the tubes carefully or the BACs will break and you get fractioned DNA.

7. Incubate on ice for 5 min

Do not extend the time, longer denaturation time can result in useless DNA. With some strains the solution clears after some time.

8. Add 225 µl ALS-III buffer

Just open all eppis, use one tip and pipet into all eppis.

9. Mix carefully by inverting the tube 8 times

Close the eppis and invert carefully the whole eppi-rack.

10. Spin down immediately for 6 min at 13000 rpm (18000 G)

This is the biggest difference to the normal alkaline lysis which incubates samples some time on ice at this step.

11. Transfer 600 µl supernatant to a tube containing 360 µl isopropanol

12. Mix well by inverting the tube several times

Invert carefully the whole eppi-rack.

13. Spin down for 10 min at 13000 rpm (18000 G)

You can see a pellet!!!

14. Remove the supernatant and add 700 µl of 70% ethanol

Be careful!!! Try to keep an eye on it during the removal of the supernatant to now loose it. It does not sick very well to the eppi, that is why I always pipet of the supernatant, just to be sure.

15. Mix well by inverting the tube several times

Invert carefully the whole eppi-rack.

16. Spin down for 5 min at 13000 rpm (18000 G)

Be careful!!! Try to keep an eye on it during the removal of the supernatant to now loose it. It sticks even less to the eppi, that is why I always pipet of the supernatant.

17. Remove the supernatant and dry at room temperature for 1 min

If you extend this to 15 min it would not be a problem as well. Do not use a speedvac for a long time, because if the DNA is overdried it is difficult to dissolve it later.

18. Add 50 µl TER and incubate at 60 °C for 5 min

Allow some time to dissolve but do NOT pipet up and down (to prevent shearing of the DNA). Do not use water here!!! If you dont add RNAse A at this step then you can not digest the DNA and load it on gel. The big amounts of RNA will outshine your bands.

Known Issues:

References and Comments:

This is in my hands the best protocol for prepping BACs. For regular use I prefer the Rapid Boiling Method, because all happens there in the eppi you start with and it is far less pipetting from one eppi to the other.

I did it as described before many times and never had any problems.

How to cite this page in publications:

This document can be cited like this:

Untergasser A. “Miniprep - Alkaline Lysis for BACs” Untergasser's Lab. Summer 2006. (include here the date when you accessed these page).
<http://www.untergasser.de/lab/protocols/miniprep_alkaline_lysis_for_bacs_v1_0.htm>.

Please Do Not Reprint This Article:

This article is copyrighted. Please do not reproduce this article in whole or part, in any form, without obtaining my written permission.