Isostable DNA Duplexes - Revision history

Dragos: Removed the pi-pi stacking interaction between adenine and 6-ethynylpyridone.

2024-09-06T07:36:27Z

Removed the pi-pi stacking interaction between adenine and 6-ethynylpyridone.

← Older revision		Revision as of 09:36, 6 September 2024
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	[[File:Hypoxanthine Cytosine base pair new.png\|right\|thumb\|Non-canonical base pair between hypoxanthine and cytosine.]]		[[File:Hypoxanthine Cytosine base pair new.png\|right\|thumb\|Non-canonical base pair between hypoxanthine and cytosine.]]
	[[File:6-Ethynylpyridone Adenine base pair.png\|right\|thumb\|Non-canonical base pair between adenine and 6-ethynylpyridone ~~featuring the pi-pi stacking interaction of the ethynyl group~~.]]		[[File:6-Ethynylpyridone Adenine base pair.png\|right\|thumb\|Non-canonical base pair between adenine and 6-ethynylpyridone.]]
	The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic or analytical tests. To overcome this problem, the concept of 'isostable DNA' was developed. In isostable DNA, the thermal stability of duplexes is independent of the G/C content. One way to accomplish this is to use non-canonical nucleobases. For example, guanine may be replaced by hypoxanthine to weaken the base pair with C, or thymine may be replaced by 6-ethynylpyridone as nucleobase surrogate to get a more stable base pair.		The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic or analytical tests. To overcome this problem, the concept of 'isostable DNA' was developed. In isostable DNA, the thermal stability of duplexes is independent of the G/C content. One way to accomplish this is to use non-canonical nucleobases. For example, guanine may be replaced by hypoxanthine to weaken the base pair with C, or thymine may be replaced by 6-ethynylpyridone as nucleobase surrogate to get a more stable base pair.

Dragos: Added images of two non-canonical base pairs.

2024-09-03T13:44:15Z

Added images of two non-canonical base pairs.

← Older revision		Revision as of 15:44, 3 September 2024
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	== Isostable DNA Duplexes ==		== Isostable DNA Duplexes ==

	The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic or analytical tests. To overcome this problem, the concept of 'isostable DNA' was developed. In isostable DNA, the thermal stability of duplexes is independent of the G/C content. One way to accomplish this is to use non-canonical nucleobases. For example, guanine may be replaced by hypoxanthine to weaken the base pair with C, or thymine may be replaced by 6-ethynylpyridone as nucleobase surrogate to get a more stable base pair.		[[File:Hypoxanthine Cytosine base pair new.png\|right\|thumb\|Non-canonical base pair between hypoxanthine and cytosine.]]
			[[File:6-Ethynylpyridone Adenine base pair.png\|right\|thumb\|Non-canonical base pair between adenine and 6-ethynylpyridone featuring the pi-pi stacking interaction of the ethynyl group.]]
			The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic or analytical tests. To overcome this problem, the concept of 'isostable DNA' was developed. In isostable DNA, the thermal stability of duplexes is independent of the G/C content. One way to accomplish this is to use non-canonical nucleobases. For example, guanine may be replaced by hypoxanthine to weaken the base pair with C, or thymine may be replaced by 6-ethynylpyridone as nucleobase surrogate to get a more stable base pair.


	== References ==		== References ==

Dragos: Improved formatting.

2024-08-05T10:41:13Z

Improved formatting.

← Older revision		Revision as of 12:41, 5 August 2024
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	== ~~'''~~Isostable DNA Duplexes~~'''~~ ==		== Isostable DNA Duplexes ==


	The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic or analytical tests. To overcome this problem, the concept of 'isostable DNA' was developed. In isostable DNA, the thermal stability of duplexes is independent of the G/C content. One way to accomplish this is to use non-canonical nucleobases. For example, guanine may be replaced by hypoxanthine to weaken the base pair with C, or thymine may be replaced by 6-ethynylpyridone as nucleobase surrogate to get a more stable base pair.		The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic or analytical tests. To overcome this problem, the concept of 'isostable DNA' was developed. In isostable DNA, the thermal stability of duplexes is independent of the G/C content. One way to accomplish this is to use non-canonical nucleobases. For example, guanine may be replaced by hypoxanthine to weaken the base pair with C, or thymine may be replaced by 6-ethynylpyridone as nucleobase surrogate to get a more stable base pair.

	== ~~'''~~References~~'''~~ ==		== References ==
	[1] H.K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N.T: Thuong, Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents. ''Nucleic Acids Res.'' '''1999''', ''27'', 1492-1498. https://doi.org/10.1093%2Fnar%2F27.6.1492		[1] H.K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N.T: Thuong, Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents. ''Nucleic Acids Res.'' '''1999''', ''27'', 1492-1498. https://doi.org/10.1093%2Fnar%2F27.6.1492

Dragos: Cleaned up the page formatting, redid the numbering of the references and added links to the cited papers.

2024-08-05T10:27:52Z

Cleaned up the page formatting, redid the numbering of the references and added links to the cited papers.

← Older revision		Revision as of 12:27, 5 August 2024
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			== '''Isostable DNA Duplexes''' ==

	'''Isostable DNA Duplexes'''


	The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic or analytical tests. To overcome this problem, the concept of 'isostable DNA' was developed. In isostable DNA, the thermal stability of duplexes is independent of the G/C content. One way to accomplish this is to use non-canonical nucleobases. For example, guanine may be replaced by hypoxanthine to weaken the base pair with C, or thymine may be replaced by 6-ethynylpyridone as nucleobase surrogate to get a more stable base pair.		The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic or analytical tests. To overcome this problem, the concept of 'isostable DNA' was developed. In isostable DNA, the thermal stability of duplexes is independent of the G/C content. One way to accomplish this is to use non-canonical nucleobases. For example, guanine may be replaced by hypoxanthine to weaken the base pair with C, or thymine may be replaced by 6-ethynylpyridone as nucleobase surrogate to get a more stable base pair.

			== '''References''' ==
			[1] H.K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N.T: Thuong, Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents. ''Nucleic Acids Res.'' '''1999''', ''27'', 1492-1498. https://doi.org/10.1093%2Fnar%2F27.6.1492

	~~'''References'''~~		[2] C. Ahlborn, K. Siegmund, C. Richert, Isostable DNA. ''J. Am. Chem. Soc.'' '''2007''', ''129'', 15218-15232. https://doi.org/10.1021/ja074209p

	a) H.K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N.T: Thuong, Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents. ''Nucleic Acids Res.'' '''1999''', ''27'', 1492-1498.

	~~b) C~~. Ahlborn, K. Siegmund, C. Richert, Isostable DNA. ''J. Am. Chem. Soc.'' '''2007''', ''129'', 15218-15232.

	c) M. Minuth, C. Richert, A nucleobase ~~analog~~ that pairs strongly with adenine. ''Angew. Chem. Int. Ed.'', '''2013''', ''52'', 10874-10877.		[3] M. Minuth, C. Richert, A nucleobase analogue that pairs strongly with adenine. ''Angew. Chem. Int. Ed.'', '''2013''', ''52'', 10874-10877. https://doi.org/10.1002/anie.201305555

Richert: Created page with " '''Isostable DNA Duplexes''' The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic..."

2024-07-06T18:16:54Z

Created page with " '''Isostable DNA Duplexes''' The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic..."

New page

'''Isostable DNA Duplexes'''

The stability of DNA duplexes depends strongly on the sequence. Because G:C base pairs are considerably more stable than A:T base pairs, the G:C content determines how high a temperature is required for dissociation of the strands forming a duplex. The higher the G:C content, the greater the thermal stability. The sequence dependence of the stability makes it difficult to detect A/T-rich sequences in a genomic context, e.g. in diagnostic or analytical tests. To overcome this problem, the concept of 'isostable DNA' was developed. In isostable DNA, the thermal stability of duplexes is independent of the G/C content. One way to accomplish this is to use non-canonical nucleobases. For example, guanine may be replaced by hypoxanthine to weaken the base pair with C, or thymine may be replaced by 6-ethynylpyridone as nucleobase surrogate to get a more stable base pair.

'''References'''

a) H.K. Nguyen, O. Fournier, U. Asseline, D. Dupret, N.T: Thuong, Smoothing of the thermal stability of DNA duplexes by using modified nucleosides and chaotropic agents. ''Nucleic Acids Res.'' '''1999''', ''27'', 1492-1498.

b) C. Ahlborn, K. Siegmund, C. Richert, Isostable DNA. ''J. Am. Chem. Soc.'' '''2007''', ''129'', 15218-15232.

c) M. Minuth, C. Richert, A nucleobase analog that pairs strongly with adenine. ''Angew. Chem. Int. Ed.'', '''2013''', ''52'', 10874-10877.