I would suggest to use a speed-vac and reduce the volume without drying the sample, as drying will increase loss of DNA adhering to the walls of the tube.

I agree with Albino above, it would be better to use a speed-vac to reduce the volume than trying to lyophilise.

Alternatively you could try using a cut-off filter such as ones sold by Microcon.

http://www.millipore.com/catalogue/module/c113861

Goodluck!

Better to use a micropore column.

In the old days, we used to use siliconized eppendorf tubes to prevent DNA from sticking to plastic at these small volumes and low concentrations. This may reduce the potential for loss in a Speedy-Vac.

If lyophilization is the only option left with you its ok to lyophilize DNA, it wont effect the quality of DNA much. However, Speed Vac concentration is the quick and easy method.

Thanks for all the answers everyone.

My concern with evaporating to reduce volume is concentrating contaminants/inhibitors.

I'm considering eluting in water (instead of buffer AE supplied by the kit), lyophilizing, and then resuspending in a smaller volume of buffer AE.

The problem is, during the lyophilization, will the powder of DNA be lost due to the rotating and sudden stopping, instead of staying in the tubes?