Hi Chaker,

The appropriate buffer, largely used for DNA and RNA hybridization, is the SSC buffer. You can either prepare it or just purchase the 20X concentrated one from sigma.

here the link for the buffer

http://www.sigmaaldrich.com/catalog/product/sigma/s6639?lang=en®ion=TN

All the best

Hi Makram,

Thanks for the answer Makram. I tried that buffer with different concentration 2x and 4x but it looks there is no hybridization. I think the probe and the target have a secondary structure which inhibits the hybridization. I will send you DNA probe and target sequences and you can help me to find the best temperature for hybridization.

Regards

you can find a good link for Tm calculations online  

DNA Melting Temperature (Tm) Calculator -- EndMemo

Thanks Mohammed. I will check the EndMemo for Tm calculation. How are things with you in KSA?

very well alhamoudllah

Hope things going ok with u

The ssc should be diluted to 1X,. I will check the sequence. You may resolve the problem of the potential secondary structure by adding formaldehyde or Dmso. We will discuss in more details by email

All the best