I have an assay in which I digest ssRNA with RNase A but not dsRNA (A-form). I was wondering if RNase A would be able to digest Z-form dsRNA in the same conditions?
Unlikely, as zRNA is double-stranded and RNAse A is specific for single-stranded RNA. It may be that the z-form is not entirely stable and "breathing ends" will be chopped off by RNAse A - what may eventually lead to the degradation of the zRNA molecule - but the action is still on ssRNA(-ends) and not on the actual ds(z-)RNA.
What conditions do you use to digest ssRNA with RNase A ?
In Khramtsov NV, Woods KM, Nesterenko MV, Dykstra CC, Upton SJ. Virus-like, double-stranded RNAs in the parasitic protozoan Cryptosporidium parvum. Mol Microbiol 1997;26:289–300
"RNase A digestion, 37°C for 30 min at different enzyme concentrations, was carried out in the high- and low-ionic strength buffers 2 × SSC (1 × SSC: 0.15 M NaCl, 15 mM sodium citrate pH 7.4) and 0.01 × SSC respectively."
In those condition, dsRNA is not degraded in 2 × SSC, but is degraded in 0.01 × SSC...
and
"We report here evidence obtained by these different spectroscopic techniques that poly(G-C).poly(G-C) undergoes a transition from the A-form to a left-handed Z-form in conditions of high ionic strength and at temperatures above 35 degrees C."
Then if one uses the Khramtsov's protocol, for example, then the ionic strength must be a parameter to take into account because it interferes both with the action of the RNAse A and with the change in the conformation of the dsRNA to Z form ...
I hope I don't add too much confusion, but I'm not sure !!!