Base stacking

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Base stacking is a common arrangement of nucleobases found in the three dimensional structure of nucleic acids. 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.[1]


Examples of base stacking

  1. 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.
  2. RNA kissing loops: Loops on two separate RNA pieces are held together by stacking interactions (between base pairs) and hydrogen bonds (within base pairs).
  3. 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.    

References

  1. ↑ Yakovchuk P, Protozanova E, Frank-Kamenetskii MD. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 2006 Jan 31;34(2):564-74. doi: 10.1093/nar/gkj454. Print 2006. PMID:16449200 doi:http://dx.doi.org/10.1093/nar/gkj454


Short piece of DNA (Drew-Dickerson dodecamer, PDB ID 4c64) shown as cartoon (gray) with base pairs shown in alternating colors (skyblue and coral). Each base pair is sandwiched between two base pairs of the other color, excluding water and maximizing non-covalent interactions.
Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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