Base Pair - Base Stacking

Base Stacking

Base stacking interactions in DNA and RNA are due to dispersion attraction, short-range exchange repulsion, and electrostatic interactions, which also contribute to stability. Again, GC stacking interactions with adjacent bases tend to be more favorable. (Note, however, 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.