Hi, Pei,

If you wish to do IF and detect only DNA, then you should use only DNA binding dyes such as - DAPI, 7-AAD, Hoechst.

RNA is prone to degradation, so if in your processing you have not taken care to prevent RNA degradation, then it must already de degrading.

Regards,

Prasad

Hi Xie,

DNA modifications in what sense are you talking about? Do you mean you want to see DNA methylation? Or do you mean to check some nucleosomal turns or telomere shortenings?

For simply DNA, DAPI is a good dye. But then it's DNA and no modfications can be detected. If you want to check methylation, then use a suitable Antibody raised against 5mC. It shall bind to the methylated domains (preferable CpGs) and secondary Ab with Alexa/Fluor can give you a good radiance. If you want to check telomeres like shortening, then you can use FISH.

But with tissue intact, I must say I think removal of RNA is not possible, without extruding the DNA out.

Hope this will help. If you have any further query, kindly ping.

Best,

Somnath.

Thank you for your generous, I will try these methods.