View source for Base stacking

'''Base stacking''' is a common arrangement of nucleobases found in the three dimensional structure of [[Nucleic Acids|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.<ref> PMID:16449200</ref>

<StructureSection load='' size='500' side='right' caption='' scene='80/804504/Dna/1'>

== Examples of base stacking ==

# '''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. Zooming in to a detailed view of a <scene name='80/804504/Dna/5'>G:C base pair</scene>, 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 <scene name='80/804504/Kissing_loop/5'>stacking interactions</scene> (between base pairs) and<scene name='80/804504/Kissing_loop/4'> hydrogen bonds</scene> (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. <jmol>
  <jmolRadioGroup>
    <item>
      <script>background black; selectionhalos on; select 288 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/>

</StructureSection>