Hey John + Can,

thx for your answers and suggestions.

@ John: Yeah I pretty much had the same ideas and considerations as you and I think the real problem is the non-specific binding of SYBR on the membrane. A possibility would be to have a fluor. labeled oligo I guess.

I'll update this if I get any new results / insights.

I've got exactly the same problem and still no solution. I would need this as a loading CTRL. I think the DNA blotted is highly denaturated and mainly ssDNA (due to extraction method). A dsDNA antibody did not detect anything (other dots with "healthy" DNA were OK). Since the DNA seems to be mainly ssDNA any intercallating stain as EtBr or DAPI will give accurate results, that's why I switched to SYBR Gold binding to ds and ssDNA.

Nevertheless the manufacturer states that it should work.(http://probes.invitrogen.com/media/pis/td004.pdf)

5.2 Staining Nucleic Acids on Membranes

The success of this particular application is very dependent

on membrane type. HYBOND® membranes and other positively

charged nylon membranes give the best results. On such membranes

SYBR stains are far superior to ethidium bromide or methylene

blue. However, on nitrocellulose and on some neutral

nylon membranes the SYBR stains produce a high nonspecific

background that dramatically reduces sensitivity.

_____

Please let me know if there is any solution,

Best

Stephan

I would love to know the answer to this as well!

I would like to try the telomere dot blot protocol from this paper http://nar.oxfordjournals.org/content/39/12/e84.long, but it relies on using a product called Sybr Dx from Invitrogen which appears to have been discontinued.

Has anyone tried diluting the dye in 2xSSC instead of TAE? Would this even work? Or 0.5x TBE vs 1 x TAE??

Is there any way to block the membrane prior to staining that wouldn't interfere with hybridisation?

I use Sybr gold for staining 1% agarose gel and it can detect up to ~ 1pg. If you have more than few pico gram of DNA on the membrane, I would say you can easily detect the DNA with laser or blue light source. 

I see that's an old topic, but I was looking for some answers myself, so maybe someone else will find that useful too:

to stain nucleic acids on the membranes you can try

Methylene Blue staining

Wash blot with 5%Acetic acid 5min. Stain by washing with 0.1% Methylene Blue in 5% Acetic acid. Destain with DDW couple of times, until nice bands appear.

Although I don't know if the membrane will be fine to use for some further hybridization.