Base stacking
From Proteopedia
(Difference between revisions)
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# '''DNA double helix''': In <scene name='80/804504/Dna/3'>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. | # '''DNA double helix''': In <scene name='80/804504/Dna/3'>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/2'>Loops on two separate RNA pieces</scene> are held together by stacking interactions (between base pairs) and hydrogen bonds (within base pairs). | # '''RNA kissing loops''': <scene name='80/804504/Kissing_loop/2'>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/2'>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. | + | # '''RNA single strand bound to a protein''': In this <scene name='80/804504/Intercalation/2'>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. <jmol> |
| + | <jmolRadioGroup> | ||
| + | <item> | ||
| + | <script>background black; selectionhalos on; select visible and sidechain and arg</script> | ||
| + | <text>Arginine</text> | ||
| + | </item> | ||
| + | <item> | ||
| + | <script>background black; selectionhalos on; select visible and sidechain and his</script> | ||
| + | <text>Histidine</text> | ||
| + | </item> | ||
| + | <item> | ||
| + | <script>background black; selectionhalos on; select visible and sidechain and tyr</script> | ||
| + | <text>Tyrosine</text> | ||
| + | </item> | ||
| + | <item> | ||
| + | <script>background white; selectionhalos off</script> | ||
| + | <text>off</text> | ||
| + | <checked>true</checked> | ||
| + | |||
| + | </item> | ||
| + | |||
| + | </jmolRadioGroup> | ||
| + | </jmol> | ||
| + | |||
== References == | == References == | ||
<references/> | <references/> | ||
</StructureSection> | </StructureSection> | ||
Revision as of 01:01, 21 December 2018
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]
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