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From Proteopedia
proteopedia linkproteopedia linkBase 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]
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Examples of base stacking
- DNA double helix: In , 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 , 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 (between base pairs) and (within base pairs).
- RNA single strand bound to a protein: In this , some of the stacking interactions are disrupted by amino acid side chains (such as arginine, histidine and tyrosine) intercalating between adjacent bases.
References
- ↑ 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
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