Additional angles to calculate the deformation of RNA helices induced by bulge loops

Bulges are common features of folded RNA structures. The RNA axial kinking caused by bulges has been confirmed by many experiments. Usually, a kinking angle zeta and a bending angle theta are used to describe the kinking and twisting of RNA molecules containing bulges. Here, we present two additional angles (twist angle zeta(1), twist angle zeta(2)) to describe the deformation of RNA helices induced by bulge loops because only two angles (a kinking angle zeta and a bending angle theta) are not enough to define the deformation of RNA induced by bulges. (C) 2002 Elsevier Science B.V. All rights reserved.

Dynamics of RNA with A6 bulge loop

In order to understand the behavior of RNAs with large bulges In solution, molecular dynamics was performed on the RNA molecule in water with A6 bulge. The result of simulation showed that nonstacked conformation Is the main conformation in large bulges, and the backbone of large bulge is of great conformational flexibility, but bulges-induced bends are relatively rigid. The fluctuation in bulge has little influence on the bend angle of RNAs.