Base stacking - Revision history

Karsten Theis at 16:39, 3 January 2022

2022-01-03T16:39:42Z

←Older revision		Revision as of 16:39, 3 January 2022
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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.<ref> PMID:16449200</ref>	+	'''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'>		<StructureSection load='' size='500' side='right' caption='' scene='80/804504/Dna/1'>

Karsten Theis at 12:52, 28 July 2020

2020-07-28T12:52:40Z

←Older revision		Revision as of 12:52, 28 July 2020
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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.<ref> PMID:16449200</ref>	+	'''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.<ref> PMID:16449200</ref>

	<StructureSection load='' size='500' side='right' caption='' scene='80/804504/Dna/1'>		<StructureSection load='' size='500' side='right' caption='' scene='80/804504/Dna/1'>
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	== Examples of base stacking ==		== 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.	+	# '''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 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>		# '''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>		<jmolRadioGroup>

Karsten Theis at 20:45, 27 August 2019

2019-08-27T20:45:08Z

←Older revision		Revision as of 20:45, 27 August 2019
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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. 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.		# '''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 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/6'>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>	+	# '''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>		<jmolRadioGroup>
	<item>		<item>

Karsten Theis at 02:47, 28 December 2018

2018-12-28T02:47:41Z

←Older revision		Revision as of 02:47, 28 December 2018
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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. 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.		# '''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/2'>stacking interactions</scene> (between base pairs) and<scene name='80/804504/Kissing_loop/4'> hydrogen bonds</scene> (within base pairs).	+	# '''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>	+	# '''RNA single strand bound to a protein''': In this <scene name='80/804504/Intercalation/6'>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>		<jmolRadioGroup>
	<item>		<item>

Karsten Theis at 13:46, 25 December 2018

2018-12-25T13:46:10Z

←Older revision		Revision as of 13:46, 25 December 2018
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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. 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.		# '''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''': <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''': Loops on two separate RNA pieces are held together by <scene name='80/804504/Kissing_loop/2'>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>		# '''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>		<jmolRadioGroup>

Karsten Theis at 21:47, 24 December 2018

2018-12-24T21:47:44Z

←Older revision		Revision as of 21:47, 24 December 2018
Line 5:		Line 5:
	== Examples of base stacking ==		== 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/4'>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.	+	# '''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''': <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. <jmol>		# '''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>

Karsten Theis at 21:45, 24 December 2018

2018-12-24T21:45:34Z

←Older revision		Revision as of 21:45, 24 December 2018
Line 5:		Line 5:
	== Examples of base stacking ==		== 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.	+	# '''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/4'>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''': <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. <jmol>		# '''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>

Karsten Theis at 01:04, 21 December 2018

2018-12-21T01:04:50Z

←Older revision		Revision as of 01:04, 21 December 2018
Line 10:		Line 10:
	<jmolRadioGroup>		<jmolRadioGroup>
	<item>		<item>
-	<script>background black; selectionhalos on; select ~~visible~~ and sidechain and arg</script>	+	<script>background black; selectionhalos on; select 288 and sidechain and arg</script>
	<text>Arginine</text>		<text>Arginine</text>
	</item>		</item>

Karsten Theis at 01:01, 21 December 2018

2018-12-21T01:01:05Z

←Older revision		Revision as of 01:01, 21 December 2018
Line 7:		Line 7:
	# '''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>

Karsten Theis at 18:21, 20 December 2018

2018-12-20T18:21:05Z

←Older revision		Revision as of 18:21, 20 December 2018
Line 1:		Line 1:
-	'''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, 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>	+	'''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.<ref> PMID:16449200</ref>

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