Flexibility Difference Between Double-Stranded RNA and DNA as Revealed by Gel Electrophoresis

Abstract

A systematic study of agarose gel electrophoresis of double-stranded RNA in the kilobase range of sizes was performed. The dsRNA to dsDNA relative mobility was found to depend on gel concentration: in low density gels RNA moves slower and in high density gels - faster than DNA of the same molecular size. The electrophoretic differences were interpreted within the reptation theory to be mainly due to the molecular stiffness differences. The dsRNA persistence length was roughly estimated to be about twice as great as that of DNA.

Effects of local changes in the helix flexibility on electrophoretic migration of DNA in agarose gel

“…A further indication that chain stiffness is important for the migration in agarose gels is the observation that dsRNA migrates slower than dsDNA of the same size [29, 301. The main cause for the difference is probably that the persistence length of RNA is about twice that of DNA at the same ionic strength [30], since the effective charge of the two polynucleotides should be similar. The interpretation of the results is difficult because dsRNA can only be obtained in a relatively narrow size range (less than about 20 kbp), where the mode of migration is a complex mixture of sieving and coil deformation effects.…”

Double strand RNA-mediated RNA interference through feeding in larval gypsy moth, Lymantria dispar (Lepidoptera: Erebidae)

“…2B, lanes 2-6) and LacZ (2C) as control. Slower mobility of dsRNA was observed which is common when comparing dsRNA to dsDNA (Livshits et al, 1990). The dsRNA was observed to be stable over the period of feeding.…”

Two Novel Mycoviruses Related to Geminivirus Isolated from the Soil-Borne FungiMacrophomina Phaseolina(Tassi) Goid. andMucor RacemosusBull

“…The resultant nucleic acid was separated in an 0.8 % agarose gel, stained with ethidium bromide and visualized with UV transillumination. For obtaining pure mycovirus DNA, nucleic acid solutions were treated with RNase under low and high salt concentrations (23,37).…”