Purification of DNA fragments from agarose gels with theNucleoTrap extraction kit:

High Speed Protocol


ATTENTION: Before using the NucleoTrap extraction kit, add ethanol to buffer NT3 (volume is given on the bottle).

All buffers should be stored at room temperature!

1. With a clean scalpel or razor blade excise the DNA fragment with care in order to minimize excess agarose. Determine the weight of the gel slice and transfer it to a clean tube.

2. For each 100 mg of agarose gel add 300 l buffer NT1. For highly concentrated agarose gels, add an additional 300 l for each percent over 1%. (For example, for a 2% gel use 600 l, for a 3% gel use 900 l, and so on.)

3. Vortex the NucleoTrap suspension thoroughly until a homogenous mixture results. Add 10 l of the NucleoTrap suspension to the sample. For samples containing more than 2.5 g of DNA, add an additional 4 l of the NucleoTrap suspension per additional g.

4. Incubate the sample for 6 minutes at 50C. Vortex the sample briefly every 2 minutes.

5. Centrifuge the sample for 30 seconds at >10,000 x g and discard the supernatant.

6. Add 500 l of buffer NT2 to the DNA containing pellet. Vortex briefly, centrifuge the sample for 30 seconds at >10,000 x g, and remove the supernatant completely.

7. Add 500 l of buffer NT3 to the sample. Vortex briefly, centrifuge the sample for 30 seconds at >10,000 x g, and remove the supernatant completely. Repeat this washing step. Remove the buffer NT3 after the second washing step and centrifuge the pellet again.

8. Air dry the pellet for 5 minutes. (Do not vacuum dry because over dried pellets lead to lower recoveries.)

9. Add 20l (60% recovery rate) - 50l TE, pH 8.5 or another low salt media (e.g. sterile water, pH 8-8.5) to the sample. Resuspend the pellet by vortexing and incubate the mixture for 5 minutes at 50C, vortexing the mixture 2 to 3 times during this elution. Centrifuge the sample for 30 seconds at >10,000 x g and transfer the DNA containing supernatant to a clean tube. Repeating this step with the pelleted resin could increase the yield by ~10%.

Alternative elution step for DNA larger than 5 kb.

To increase the yields of large DNA on NucleoTrap, try using 5 l instead of 10 l of the NucleoTrap suspension. Also incubate the pellet from step 8 in elution buffer at 60C for 15 minutes prior to elution.

An alternative product Nucleobond AX is capable of isolating plasmids up to 300 kb in size in high purity for transfections, transgenic applications or for automated sequencing.

Having specific problems? Please refer to the Nucleobond AX Trouble Shooting Guide.

Back to the Nucleobond AX applications guide


Updated 1/20/98