There is little knowledge about the 3D folding of complex pseudoknots with interrupted stems, which may lead to bending or distortions of the RNA A-helix. Loops L 1 and L 3 need to cross the major and minor groove of stems S 2 and S 1 , respectively. To disallow sterically infeasible configurations for long interrupted stems, we make the following assumptions (41) . For interrupted stems with more than 10 bp (including bulges and internal loops), the loops bridging the stems must have a minimum length: loop L 1 must be ! 2 nt and loop L 3 must be ! 6 nt.