What is Base Stacking?

Base stacking interactions in RNA are due to dispersion attraction, short-range exchange repulsion, and electrostatic interactions which also contribute to stability. GC stacking interactions with adjacent bases tend to be more favorable. (Note, though, that a GC stacking interaction with the next base pair is geometrically different from a CG interaction.) Base stacking effects are especially important in the secondary structure and tertiary structure of RNA; for example, RNA stem-loop structures are stabilized by base stacking in the loop region.

RNA folds when it changes its shape to make base pairs. RNA folds to increase its stability. Usually, RNA will try to create a stack to do that. A stack is a series of adjacent base pairs. Look at the image below, this stack contains adjacent G-C, A-U, and G-U pairs.

The stability of a stack depends on the strength and order of base pairs within.The intensity of white brightness between two bases represents the strength of the bond. Look at the brightness of arrows in the RNA as well as at the color palette located at the bottom.

G-C is the strongest pair (see the red-green pair on the right). U-A is the next strongest (see the blue-yellow pair on the left). G-U is the weakest pair (see the red-blue base in the middle).