Base stacking: Difference between revisions

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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 Walls interactions.

'''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 Walls interactions. In terms of structural stability, the stacking interactions of bases play a larger role than the hydrogen bonds of the bases for nucleic acids in aqueous solution.<ref> PMID:16449200</ref>

== Examples of base stacking ==

# DNA double helix

In <scene name='80/804504/Dna/1'>double-stranded DNA</scene>, bases from two strands pair up to form base pairs, which are stacked along the helix axis of the double strand.

# RNA kissing loops

<scene name='80/804504/Kissing_loop/1'>Loops on two separate RNA pieces</scene> are held together by stacking interactions (between base pairs) and hydrogen bonds (within base pairs).

# RNA single strand bound to a protein

In this <scene name='80/804504/Intercalation/1'>complex of RNA bound to a protein</scene>, some of the stacking interactions are disrupted by amino acid side chains (such as arginine, histidine and tyrosine) intercalating between adjacent bases.

</StructureSection>

== References ==

Base stacking: Difference between revisions

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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 Walls interactions.
+'''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 Walls interactions. In terms of structural stability, the stacking interactions of bases play a larger role than the hydrogen bonds of the bases for nucleic acids in aqueous solution.<ref> PMID:16449200</ref>
 <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
+== Examples of base stacking ==
+# DNA double helix
+In <scene name='80/804504/Dna/1'>double-stranded DNA</scene>, bases from two strands pair up to form base pairs, which are stacked along the helix axis of the double strand.
+# RNA kissing loops
+<scene name='80/804504/Kissing_loop/1'>Loops on two separate RNA pieces</scene> are held together by stacking interactions (between base pairs) and hydrogen bonds (within base pairs).
+# RNA single strand bound to a protein
+In this <scene name='80/804504/Intercalation/1'>complex of RNA bound to a protein</scene>, some of the stacking interactions are disrupted by amino acid side chains (such as arginine, histidine and tyrosine) intercalating between adjacent bases.
 </StructureSection>
 == References ==
 <references/>