Hello everyone! One of my students asked me a question about DNAse step during RNA isolation. She asked me how is it possible, that DNAse is responsible for hydrolyzing phosphodiester bonds in DNA, and it does not degrade the same bonds in RNA, although it is a less stable molecule? I haven't found any precise answer, so I would be very grateful for your help!
Best regards,
Joanna
DNase is of course an enzyme and you can think about it just like you can think about any other enzyme. There are many enzymes that catalyze the same reaction but act on different substrates. The active site region must recognize the correct substrate in order to catalyze the reaction and this is what provides substrate specificity. The same thing is true here. RNA and DNA have different backbones and it is as simple as whether the enzyme recognizes the substrate (RNA or DNA). This is further compounded that DNA is generally double stranded and RNA singled stranded, so they will "look" very different to an enzyme. It is true that some nucleases will cleave both, but most are specific.
Looking at DNase 1 structure bound to DNA, the 2' hydroxyl of RNA is geometrically blocked. In particular a tyrosine packs against the ribose sugar which would directly collide with the 2' hydroxyl of RNA. So this collision should preclude excision of RNA but allow DNA 2' deoxyribose devoid of oxygen in its 2' position. In general geometric or steric collisions provide exquisite specificity in molecular biology by blocking non-target interactions.
It is a question on structure. You might say it is unstable, but the substances are not alike. There might be some evidence a DNAse might degrade RNA, but unlikely. To degrade DNA you use DNAse, and for RNA you use RNAse. Structure, and chemical similarity, but unlikely
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