Automated DNA extraction from large volumes

1. Introduction 

Our laboratory has recently implemented automated DNA extraction using DNA-IQ™ and TECAN® robots. While most DNA-containing samples are easily amenable to automation, some still present a challenge to forensic laboratories faced with a broad range of substrates from which ever diminishing amounts of DNA must be recovered and analyzed for genetic fingerprinting purposes.

One such challenge is the recovery of DNA from substrates such as clothing from which only trace amounts of DNA are recovered. In such cases, it is necessary to remove relatively large tissue samples for analysis and to use 5ml or more of extraction buffer. Since our automated procedure is set up to handle a maximum of 400μl of extraction buffer per sample, it may require a dozen or more individual assays to purify the DNA with the added complication of having to pool the DNA-containing solutions eluted from the magnetic beads into a large and dilute final volume.

In order to reconcile automation and optimal DNA recovery from large substrates we have developed a method of direct cell lysis on the substrate followed by batch DNA concentration on magnetic beads in DNA-IQ™ extraction buffer.

2. Batch lysis and DNA concentration method for large volumes 

1.Approximately 25cm2 of substrate or tape lifts are cut up into 1cm2 pieces and placed in a 50ml screw-cap tube containing 5ml lysis buffer (10mM Tris–HCl pH 8.0, 10mM EDTA, 70mM NaCl, 1% Sarkosyl, 0.04mg/ml Proteinase K) and incubated overnight with rotation at 56°C.

2.Tube contents are transfered to a spin-basket tube (Vectaspin 20™) and centrifuged at 3000×g for 5min. The tissue is discarded and the solution transfered to a clean 50ml tube.

3.Two volumes of DNA-IQ™ extraction buffer are added together with 14μl magnetic beads. The tubes are fixed to a rotary shaker and vigorously agitated at 120rpm for 1h at room temperature.

4.The tubes are placed in a large volume DNA-IQ™ magnetic rack, the supernatant discarded and the magnetic beads transfered to a mini-tube on the robot and the DNA-IQ™ protocol for DNA extraction resumed as per the manufacturer's instructions.

3. Conclusions 

Batch extraction of DNA from large substrates allows recovery of 50–70% of the DNA obtained from cutting up the substrate into small pieces and processing each separately (Fig. 1). This greatly facilitates automation and in most cases is sufficient to obtain interpretable profiles. Another important advantage is the recovery of DNA in a small volume (25μl) rather than in multiples of 25μl which have to be reconcentrated before amplification.

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Fig. 1. Batch DNA extraction from 4μl blood dried on cotton squares in the presence of 14μl magnetic beads. Proteinase K is adjusted to 0.04mg/ml.

Reducing Proteinase K from 0.5mg/ml to 0.04mg/ml nearly doubled DNA recovery, possibly due to reduced interference of Proteinase K with DNA binding to the beads. Replacement of SDS with Sarkosyl (Fig. 2) reduces foaming without significant loss of yield.

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Fig. 2. Comparison of DNA recovered from three body fluids dried on cotton squares and extracted with 1% SDS (white) or 1% Sarkosyl (black) with the batch method. Control is the total amount of DNA extracted in small tubes and processed individually.

Conflict of interest 

None.