Base stacking

Base stacking is a common arrangement of nucleobases found in the three dimensional structure of DNA. Bases (or base pairs) are planar, and these planes stack at contact distance (about 3.4 Angstrom), excluding water and maximizing Van der Waals interactions. In terms of structural stability of nucleic acids in aqueous solution, the stacking interactions of bases play a larger role than the hydrogen bonds formed by the bases.

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Examples of base stacking DNA double helix: In double-stranded DNA, bases from two strands pair up to form base pairs, which are stacked along the helix axis of the double strand. Zooming in to a detailed view of a G:C base pair, the extent of the stacking contacts are determined by the sequence. G:C base pairs contribute more to the thermal stability of DNA than A:T base pairs because they stack better. RNA kissing loops: Loops on two separate RNA pieces are held together by stacking interactions (between base pairs) and hydrogen bonds (within base pairs). RNA single strand bound to a protein: In this complex of RNA bound to a protein, some of the stacking interactions are disrupted by amino acid side chains (such as arginine, histidine and tyrosine) intercalating between adjacent bases.

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