Effects of secondary structures in RNA on interlocking probabilities.

In 1967 Wang and Schwartz reported on the formation of interlocked rings between linear or circular DNA molecules by the enzyme topoisomerase. We propose viewing the secondary structured loop in RNA (or single stranded DNA) as analogous to a circular DNA molecule. Formation of a catenane between such an RNA loop with a DNA molecule may constitute a probe of the secondary and general three dimensional structure of the RNA molecule. The experimental results may be compared with the theoretical calculation. We suggest here a method for estimating linkage probabilities and calculate them for several cases for which secondary structures of the RNA have been proposed.