Yes, it makes sense as far as you have in the dNTPs mix digoxigenin-dUTP (DIG-11-dUTP) to polymerise a labeled PCR product. i.e. http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Roche/Bulletin/1/11636090910bul.pdf 

Yes, this technique is called Southern-blot, and the probe ised can be obtained by PCR od plamid digestion and purification. We normally obtain the probe by PCR as following:

1. Desing specific primers that amplifies about 400-600 bp of your interest gene (Tm of primers should be about 55-60 ºC). There is a good tool in NEB web for this purpose.

2. Purify genomic or plasmid DNA from E. coli (it depends where is your target gene). For plasmid extraction there are different kits available, however classical minipreps also works well. Quantify DNA concentration by agarose electroforesis.

3. Using 0.1 - 1 ng of plasmid, or 10 - 100 ng of genomic DNA, make 2-3 PCR reactions of 50 ul each. You can use Phusion polymerase if the target gene does not amplifies by Taq.

4. Check the PCR product by agarose electrophoresis. If you have only one band of the expected size, go to step 5. If there are more than one band, load the complete PCR product in a new gel, cut the band of the expected weight and extract from the agarose with a kit. We use the kit from ZymoGen kit for this.

5. Purification/concentration of the PCR product. There are different kits available, we have good yield with the Sigma-PCR clean kit. However is also a good chance to fenolize and precipitate the PCR product, because you can redisolve it in 5-10 ul to have a very concentrated sample.

6. Quantify the sample by agarose electrophoresis or nanodrop. Dilute to 100 ng/ul is the best option, however, 50 ng/ul also works well.

7. Put 15 ul of the DNA sample (1.5 ug of DNA) in a new tube with screw cap. Incubate 10 min at 100ºC to denaturalize DNA and pass the tube very quiquly to an ice-ethanol bath (about -10ºC), to avoid renaturalization.

8. Start with the DIG DNA labeling kit (http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Roche/Bulletin/1/11175033910bul.pdf) by adding 2 ul of DIG hexanucleotide mix, 2ul of DIG DNA labeling mix and 1 ul of Klenow enzyme. Mix by vortex pulse and incubate O/N at 37ºC

9. Check the efficiency of the labeled probe. For this, prepare at least 6 ten-fold dilutions of the probe. Put 1 ul drops in a nitrocelulose membrane. Croslink DNA to the membrane with an UV croslinker (as we observed, it  improves the signal, however, it is not really neccesary). You can also use nylon membrane without croslink.

10. Put the membrane in water for 30 secs, pass to maleic buffer for 5 min, and incubate in 1% bloking reagent in maleic buffer for 1 hour.

11. Incubate 30 min with antibody anti-DIG-AP (1:5000 of antibody diluted in 1% bloking buffer in maleic buffer, that is, 2 ul of antibody in 10 ml of buffer)

12. Four washes of 10 min maleic buffer, and start with the detection method of your choice. We use NBT/BCIP (http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Roche/Bulletin/1/11681451001bul.pdf) for this because is cheaper, however, CDP-Star (https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Datasheet/c0712dat.pdf) is also a good option, because is a chemiluminiscent substrate.

If all works well, you shoud see signal until 10-5 or even 10-6 dilution. However, in some cases the efficiency of the labeling is not so good, and  probes with signal at the 10-3 or 10-4 dilution also works well in shouthern-blots, however, we never use probes with lower efficiencies.

At this moment, you can start with the southern blots using your probe. Good luck!

Thank you very much!!!