Dear Simon Butler, 

Although it is feasible, observing DNA on SEM is a little bit challenging. Try cleansing your silicon substrate with RCA method (just the basic part should be enough). It will make it more hydrophilic (never touch it, not even with gloves - use tweezers always). 

You can try adding some microliters of your purification product directly onto silicon and let it dry (or rest for some minutes - try both). Then use your gold enhancement kit. Be gentle, otherwise the DNA will detach. 

Be sure you are using a FE-SEM in order to get the best results. Use low kV and low current to avoid DNA damaging.

An easier alternative is using AFM (atomic force microscopy) if you have access.

Please let us know your progress. Good luck

Hi Wagner Correr

Thanks very much. Thats very helpful.

If you could spare a few more moments:

When you say the basic part of the RCA method do you mean just the initial particle clean?

Would you say that once DNA has been applied it is then possible to wash the slide with water in an enhancement step or would this just wash away the DNA?

Thanks again

Simon

Yes. I meant the first part: 5 parts of deionised water, 1 part of H2O2 , and 1 part of NH4OH. Place the silicon pieces inside and bring it to 70-80 ºC during 10 minutes. Rinse with deionised water. 

To wash the slide, you can carefully submerge it in water or, using a micropipete, put a drop on it and take it back gently. If there is too much turbulence you will detach the DNA.