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History of Nucleic Acid Chemistry

2024-09-25T16:52:18Z

Dragos: Added references to the new milestones.

== The History of Nucleic Acid Chemistry ==

=== Milestones ===

==== 1869 ⁠– Isolation of DNA ====
The person credited with being the first to isolate DNA was the Swiss physician Friedrich Miescher. He called the biochemical substance rich in phosphorus "nuclein". The initial work is dated as having occurred in early 1869.<ref>R. Dahm, Friedrich Miescher and the discovery of DNA. Devel. Biol. 2005, 278, 274-288. https://doi.org/10.1016/j.ydbio.2004.11.028</ref> Miescher worked at the University of Tübingen at the time, and did not know what the function of nuclein was.

==== 1944 – DNA carries genetic information====
Avery determines that DNA carries genetic information.<ref>Avery OT et al., Journal of Experimental Medicine 79 (1944) p137-158.</ref>

==== 1953 – Structure of the DNA double helix ====
The correct structure of the DNA double helix was published by Watson and Crick in two milestone papers in 1957.<ref>Watson, J. D.; Crick, F. H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. ''Nature'' '''1953''', ''171'', 737-738. https://doi.org/10.1038/171737a0</ref><ref>Watson, J. D.; Crick, F. H. Genetical implications of the structure of deoxyribonucleic acid. ''Nature'' '''1953''', ''171'', 964-967. https://doi.org/10.1038/171964b0
</ref> The diffraction data was not from their own work, and the G:C base pair was incorrectly assumed to have only two hydrogen bonds. Still, the structure was a major breakthrough, as it explained how genetic information is stored and passed on to the next generation.
<br><br>
Structure of base pairs:
<gallery heights=150 mode="packed">
File:Guanine Cytosine base pair red bond.png|Depiction of the G:C base pair with the hydrogen bond not yet identified in the 1957 paper highlighted in red.
File:Adenine Thymine base pair.png|Depiction of the A:T base pair.
</gallery>

==== 1956 – Phosphodiester chemistry ====
Khorana et al. establish phosphodiester chemistry for chain assembly in solution.<ref>Khorana HG et al. Chem. & Ind. London (1956), p. 1523.</ref>

==== 1965 – Phosphotriester chemistry ====
Letsinger and coworkers develop phosphotriester chemistry as improved method for solution-phase synthesis of DNA.<ref>Letsinger RL, Mahedevan V, J. Am. Chem. Soc. (1965), pp. 3526-3527.</ref>

==== 1970 – First synthesis of a gene ====
Khorana publishes the first synthesis of a gene (yeast alanine tRNA, 72mer via 19 fragments).<ref>Khorana HG, Nature 227 (1970), pp. 27-34.</ref>

==== 1977 – Solid phase DNA synthesis on polymeric support ====
Gait and Sheppard perform solid-phase DNA synthesis on a polymeric support.<ref>Gait MJ and Sheppard RC, NAR 4 (1977), pp. 1153 and 4391.</ref>

==== 1981 – Phosphoramidite approach ====
Building on the work of Letsinger, Beaucage and Caruthers demonstrate the superiority of the phosphoramidite approach.<ref>Beaucage SL and Caruthers MH, Tetrahedron Lett. 37 (1981), pp. 1859-1862.</ref>

==== 1984 – β-cyanoethyl phosphoramidite chemistry ====
Köster and Sinha patent ß-cyanoethyl phosphoramidite chemistry.<ref>Köster H & Sinha ND (1984), US Patent No. 4725677.</ref>

==== 1987 – 2'-o-TBDMS protection for RNA ====
Ogilvie reports 2´-O-TBDMS protection for RNA building blocks.<ref>Usman N et al., J. Am. Soc. Chem. (1957), pp. 7845-7854.</ref><ref>Ogilvie, K. K.; Sadana, K. L.;Thompson, E. A; Quilliam, M. A.; Westmore,. J. B. The use of silyl groups in protecting the hydroxyl functions of ribonucleosides. Tetrahedron Lett. 1974, 15, 2861-2863.</ref><ref>T. Wu; K. K. Ogilvie; R. T. Pon, Prevention of chain cleavage in the chemical synthesis of 2′-silylated oligoribonucleotides. Nucleic Acids Res. 1989, 17, 3501–3517.
</ref>

==== 1994 – Polymerase Chain Reaction ====
The polymerase chain reaction (PCR) was invented in the early 1980s by Kary B. Mullis while employed by Cetus Corporation. Mullis was awarded the Nobel Prize in Chemistry for his discovery in 1993.<ref>Mullis, K. B. The Polymerase Chain Reaction (Nobel Lecture). ''Angew. Chem. Int. Ed. Engl.'' '''1994''', ''33'', 1209-1213.</ref><ref>Process for amplifying nucleic acid sequences. US Patent US4683202A, filed on October 25, 1985.</ref>

== References ==
<references />

History of Nucleic Acid Chemistry

2024-09-25T16:39:30Z

Dragos: Added new milestones based on the presentation of Thomas Rupp in Herrenalb.

== The History of Nucleic Acid Chemistry ==

=== Milestones ===

==== 1869 ⁠– Isolation of DNA ====
The person credited with being the first to isolate DNA was the Swiss physician Friedrich Miescher. He called the biochemical substance rich in phosphorus "nuclein". The initial work is dated as having occurred in early 1869.<ref>R. Dahm, Friedrich Miescher and the discovery of DNA. Devel. Biol. 2005, 278, 274-288. https://doi.org/10.1016/j.ydbio.2004.11.028</ref> Miescher worked at the University of Tübingen at the time, and did not know what the function of nuclein was.

==== 1944 – DNA carries genetic information====
Avery determines that DNA carries genetic information.

==== 1953 – Structure of the DNA double helix ====
The correct structure of the DNA double helix was published by Watson and Crick in two milestone papers in 1957.<ref>Watson, J. D.; Crick, F. H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. ''Nature'' '''1953''', ''171'', 737-738. https://doi.org/10.1038/171737a0</ref><ref>Watson, J. D.; Crick, F. H. Genetical implications of the structure of deoxyribonucleic acid. ''Nature'' '''1953''', ''171'', 964-967. https://doi.org/10.1038/171964b0
</ref> The diffraction data was not from their own work, and the G:C base pair was incorrectly assumed to have only two hydrogen bonds. Still, the structure was a major breakthrough, as it explained how genetic information is stored and passed on to the next generation.
<br><br>
Structure of base pairs:
<gallery heights=150 mode="packed">
File:Guanine Cytosine base pair red bond.png|Depiction of the G:C base pair with the hydrogen bond not yet identified in the 1957 paper highlighted in red.
File:Adenine Thymine base pair.png|Depiction of the A:T base pair.
</gallery>

==== 1956 – Phosphodiester chemistry ====
Khorana et al. establish phosphodiester chemistry for chain assembly in solution.

==== 1965 – Phosphotriester chemistry ====
Letsinger and coworkers develop phosphotriester chemistry as improved method for solution-phase synthesis of DNA.

==== 1970 – First synthesis of a gene ====
Khorana publishes the first synthesis of a gene (yeast alanine tRNA, 72mer via 19 fragments).

==== 1977 – Solid phase DNA synthesis on polymeric support ====
Gait and Sheppard perform solid-phase DNA synthesis on a polymeric support.

==== 1981 – Phosphoramidite approach ====
Building on the work of Letsinger, Beaucage and Caruthers demonstrate the superiority of the phosphoramidite approach.

==== 1984 – β-cyanoethyl phosphoramidite chemistry ====
Köster and Sinha patent ß-cyanoethyl phosphoramidite chemistry.

==== 1987 – 2'-o-TBDMS protection for RNA ====
Ogilvie reports 2´-O-TBDMS protection for RNA building blocks.

==== 1994 – Polymerase Chain Reaction ====
The polymerase chain reaction (PCR) was invented in the early 1980s by Kary B. Mullis while employed by Cetus Corporation. Mullis was awarded the Nobel Prize in Chemistry for his discovery in 1993.<ref>Mullis, K. B. The Polymerase Chain Reaction (Nobel Lecture). ''Angew. Chem. Int. Ed. Engl.'' '''1994''', ''33'', 1209-1213.</ref><ref>Process for amplifying nucleic acid sequences. US Patent US4683202A, filed on October 25, 1985.</ref>

== References ==
<references />

History of Nucleic Acid Chemistry

2024-09-25T16:15:09Z

Dragos: Cleaned up the layout and grouped the two images into a gallery.

== The History of Nucleic Acid Chemistry ==

=== Milestones ===

==== Isolation of DNA ====
The person credited with being the first to isolate DNA was the Swiss physician Friedrich Miescher. He called the biochemical substance rich in phosphorus "nuclein". The initial work is dated as having occurred in early 1869.<ref>R. Dahm, Friedrich Miescher and the discovery of DNA. Devel. Biol. 2005, 278, 274-288. https://doi.org/10.1016/j.ydbio.2004.11.028</ref> Miescher worked at the University of Tübingen at the time, and did not know what the function of nuclein was.

==== Structure of the DNA double helix ====
The correct structure of the DNA double helix was published by Watson and Crick in two milestone papers in 1957.<ref>Watson, J. D.; Crick, F. H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. ''Nature'' '''1953''', ''171'', 737-738. https://doi.org/10.1038/171737a0</ref><ref>Watson, J. D.; Crick, F. H. Genetical implications of the structure of deoxyribonucleic acid. ''Nature'' '''1953''', ''171'', 964-967. https://doi.org/10.1038/171964b0
</ref> The diffraction data was not from their own work, and the G:C base pair was incorrectly assumed to have only two hydrogen bonds. Still, the structure was a major breakthrough, as it explained how genetic information is stored and passed on to the next generation.
<br><br>
Structure of base pairs:
<gallery heights=150 mode="packed">
File:Guanine Cytosine base pair red bond.png|Depiction of the G:C base pair with the hydrogen bond not yet identified in the 1957 paper highlighted in red.
File:Adenine Thymine base pair.png|Depiction of the A:T base pair.
</gallery>
==== Polymerase Chain Reaction ====
The polymerase chain reaction (PCR) was invented in the early 1980s by Kary B. Mullis while employed by Cetus Corporation. Mullis was awarded the Nobel Prize in Chemistry for his discovery in 1993.<ref>Mullis, K. B. The Polymerase Chain Reaction (Nobel Lecture). ''Angew. Chem. Int. Ed. Engl.'' '''1994''', ''33'', 1209-1213.</ref><ref>Process for amplifying nucleic acid sequences. US Patent US4683202A, filed on October 25, 1985.</ref>

== References ==
<references />

Isostable DNA Duplexes

2024-09-06T07:36:27Z

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

== Isostable DNA Duplexes ==

[[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.]]
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

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

[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

File:6-Ethynylpyridone Adenine base pair.png

2024-09-06T07:30:15Z

Dragos: Dragos uploaded a new version of File:6-Ethynylpyridone Adenine base pair.png

== Summary ==
Depicition of the non-canonincal base pair between 6-ethynylpyridone and adenine featuring the pi-pi stacking interaction of the ethynyl substituent.

DNG

2024-09-03T16:32:04Z

Dragos: Changed the format that the DNG logo is displayed in.

[[File:DNG_logo.png|right|thumb|Logo of the DNG.]]
Deutsche Nucleinsäurechemiegemeinschaft e.V. ('''DNG''') is a scientific society focused on nucleic acid chemistry.

The URL of the DNG homepage is: https://dnarna.de

C-Nucleosides

2024-09-03T14:00:38Z

Dragos: Added a depiction of the general structure of a C-nucleoside.

== ''C''-Nucleosides ==

[[File:General structure c-nucleoside.png|thumb|right|General structure of a C-nucleoside featuring D-ribose as the sugar unit. Note the C-C bond that links the nucleobase to the sugar.]]
In ''C''-nucleosides, a carbon-carbon bond links the nucleobase (or nucleobase analog) to the sugar. This is in contrast to canonical nucleosides, where a nitrogen atom links the base to the ribose or 2'-deoxyribose. The best-known natural ''C''-nucleoside is pseudouridine. Several therapeutic nucleosides (or their prodrug forms used as active pharmaceutical ingredients) are known that are ''C''-nucleosides.

== References ==

=== Review ===
[1] M. Hocek, ''C''-Nucleosides: synthetic strategies and biological applications. ''Chem. Rev''. '''2009''', ''109'', 6729–6764. https://doi.org/10.1021/cr9002165

=== Synthetic Papers ===
[2] H.-J. Kim, N. A. Leal, S. Hoshika, S. A. Benner, Ribonucleosides for an artificially expanded genetic information system. ''J. Org. Chem''. '''2014''', ''79'', 3194−3199. https://doi.org/10.1021/jo402665d

[3] T. Gniech, C. Richert, Diastereoselective synthesis of pyridone ''ribo''-''C''-nucleosides via Heck reaction and oxidation. ''Eur. J. Org. Chem.'' '''2024''', e202400342. https://doi.org/10.1002/ejoc.202400342

File:General structure c-nucleoside.png

2024-09-03T13:58:26Z

Dragos: General structure of a C-nucleoside featuring D-ribose.

== Summary ==
General structure of a C-nucleoside featuring D-ribose.

History of Nucleic Acid Chemistry

2024-09-03T13:52:37Z

Dragos: Added structures of the G:C and A:T base pairs. Hydrogen bond not yet identified in 1957 in the G:C base pair is highlighted in red.

== The History of Nucleic Acid Chemistry ==

=== Milestones ===
[[File:Guanine Cytosine base pair red bond.png|right|thumb|Depiction of the G:C base pair with the hydrogen bond not yet identified in the 1957 paper highlighted in red.]]
[[File:Adenine Thymine base pair.png|right|thumb|Depiction of the A:T base pair.]]
==== Isolation of DNA ====
The person credited with being the first to isolate DNA was the Swiss physician Friedrich Miescher. He called the biochemical substance rich in phosphorus "nuclein". The initial work is dated as having occurred in early 1869.<ref>R. Dahm, Friedrich Miescher and the discovery of DNA. Devel. Biol. 2005, 278, 274-288. https://doi.org/10.1016/j.ydbio.2004.11.028</ref> Miescher worked at the University of Tübingen at the time, and did not know what the function of nuclein was.

'''Structure of the DNA double helix'''
The correct structure of the DNA double helix was published by Watson and Crick in two milestone papers in 1957.<ref>Watson, J. D.; Crick, F. H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. ''Nature'' '''1953''', ''171'', 737-738. https://doi.org/10.1038/171737a0</ref><ref>Watson, J. D.; Crick, F. H. Genetical implications of the structure of deoxyribonucleic acid. ''Nature'' '''1953''', ''171'', 964-967. https://doi.org/10.1038/171964b0
</ref> The diffraction data was not from their own work, and the G:C base pair was incorrectly assumed to have only two hydrogen bonds. Still, the structure was a major breakthrough, as it explained how genetic information is stored and passed on to the next generation.

== References ==
<references />

File:Guanine Cytosine base pair red bond.png

2024-09-03T13:49:10Z

Dragos: Depiction of the base pair between guanine and cytosine with the hydrogen bond that wasn't yet identified in the 1957 paper highlighted in red.

== Summary ==
Depiction of the base pair between guanine and cytosine with the hydrogen bond that wasn't yet identified in the 1957 paper highlighted in red.

Isostable DNA Duplexes

2024-09-03T13:44:15Z

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

== Isostable DNA Duplexes ==

[[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 ==
[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

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

[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

File:Hypoxanthine Cytosine base pair new.png

2024-09-03T13:37:29Z

Dragos: A depiction of the non-canonical base pair between hypoxanthine and cytosine.

== Summary ==
A depiction of the non-canonical base pair between hypoxanthine and cytosine.

File:6-Ethynylpyridone Adenine base pair.png

2024-09-03T13:35:06Z

Dragos: Dragos uploaded a new version of File:6-Ethynylpyridone Adenine base pair.png

== Summary ==
Depicition of the non-canonincal base pair between 6-ethynylpyridone and adenine featuring the pi-pi stacking interaction of the ethynyl substituent.

Quinolone DNA complexes

2024-09-03T13:17:28Z

Dragos: Added an image of the structure of levofloxacin.

== Complexes of Quinolone Antibiotics and DNA ==

[[File:Levofloxacin structure.png|right|thumb|Structure of levofloxacin, a prototypical quinolone antibiotic.]]Quinolone antibiotics are widely used in the clinic. They inhibit the re-sealing of the DNA after cleavage by a gyrase, thus turning a topoisomerase into a nuclease. Three-dimensional structures of covalent quinolone-DNA complexes have been elucidated by NMR and restrained molecular dynamics.<br><br><br><br><br><br><br>

== References ==
[1] J. Tuma, W. H. Connors, D. H. Stitelman, C. Richert, On the Effect of Covalently Appended Quinolones on Termini of DNA-Duplexes. ''J. Am. Chem. Soc.'' '''2002''', ''124,'' 4236-4246. https://doi.org/10.1021/ja0125117

[2] K. Siegmund, S. Maheshwary, S. Narayanan, W. Connors, M. Riedrich, M. Printz, C. Richert, Molecular details of quinolone-DNA interactions: Solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids Res.'', '''2005''', ''33'', 4838-4848. https://doi.org/10.1093%2Fnar%2Fgki795

File:Levofloxacin structure.png

2024-09-03T13:10:47Z

Dragos: Structure of levofloxacin, a quinolone antibiotic.

== Summary ==
Structure of levofloxacin, a quinolone antibiotic.

File:Hypoxanthine Cytosine base pair.png

2024-09-03T13:10:10Z

Dragos: Depiction of the non-canonical base pair between hypoxanthine and cytosine.

== Summary ==
Depiction of the non-canonical base pair between hypoxanthine and cytosine.

File:Guanine Cytosine base pair original.png

2024-09-03T13:09:36Z

Dragos: Depicition of the base pair between guanine and cytosine as originally proposed in 1957.

== Summary ==
Depicition of the base pair between guanine and cytosine as originally proposed in 1957.

File:Guanine Cytosine base pair modern.png

2024-09-03T13:08:46Z

Dragos: Modern depiction of the base pair between guanine and cytosine.

== Summary ==
Modern depiction of the base pair between guanine and cytosine.

File:Adenine Thymine base pair.png

2024-09-03T13:08:09Z

Dragos: Depiction of the base pair between adenine and thymine.

== Summary ==
Depiction of the base pair between adenine and thymine.

File:6-Ethynylpyridone Thymine base pair.png

2024-09-03T13:07:03Z

Dragos:

== Summary ==
Delete when possible. The name is wrong.

File:6-Ethynylpyridone Adenine base pair.png

2024-09-03T13:05:57Z

Dragos: Depicition of the non-canonincal base pair between 6-ethynylpyridone and adenine featuring the pi-pi stacking interaction of the ethynyl substituent.

== Summary ==
Depicition of the non-canonincal base pair between 6-ethynylpyridone and adenine featuring the pi-pi stacking interaction of the ethynyl substituent.

File:6-Ethynylpyridone Thymine base pair.png

2024-09-03T13:02:52Z

Dragos: Depicition of the non-canonincal base pair between 6-ethynylpyridone and thymine featuring the pi-pi stacking interaction of the ethynyl substituent.

== Summary ==
Depicition of the non-canonincal base pair between 6-ethynylpyridone and thymine featuring the pi-pi stacking interaction of the ethynyl substituent.

Main Page

2024-08-15T13:31:51Z

Dragos: Fixed a typo.

== Welcome to Nucleowiki ==

Nucleowiki is an encyclopedia for nucleic acid chemistry-related topics, maintained by members of the [[DNG|"Deutsche Nucleinsäurechemie-Gemeinschaft" (DNG)]]. The site is still under construction. A list of currently available articles can be found below.

{| class="center" style="list-style-position: inside; text-align: left;"
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== The DNG & Related Events ===

*[[DNG]]
*[[Nucleinsäurechemietreffen]]
*[[DNG-Doktorandenseminar]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Research Fields ===

*[[Prebiotic Chemistry]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Compound Classes ===

*[[Antisense Oligonucleotides]]
*[[Aptamers]]
*[[Branched Oligonucleotide Hybrids]]
*[[C-Nucleosides]]
*[[Quinolone DNA complexes]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Chemical Processes & Principles ===

*[[Chemical Primer Extension]]
*[[Organocapture]]
*[[Neighbor Exclusion Principle]]
*[[Triplex]]
*[[Isostable DNA Duplexes]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Analytical Methods ===

*[[Quantitative MALDI-TOF MS of Oligonucleotides]]
*[[UV-Melting Curves]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Synthetic Methods ===

*[[Solution-Phase Oligonucleotide Synthesis]]
*[[Vorbrüggen Base Introduction Reaction]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== History ===

*[[History of Nucleic Acid Chemistry]]
</div>

|}
<br>
Aditionally, '''a list of all available entries''' can be found [[Special:AllPages|here]].
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Main Page

2024-08-15T12:38:41Z

Dragos: Fixed a spelling mistake.

== Welcome to Nucleowiki ==

Nucleowiki is an encyclopedia for nucleic acid chemistry-related topics, maintained by members of the [[DNG|"Deutsche Nucleinsäurechemie-Gemeinschaft" (DNG)]]. The site is still under construction. A list of currently available articles can be found below.

{| class="center" style="list-style-position: inside; text-align: left;"
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== The DNG & Related Events ===

*[[DNG]]
*[[Nucleinsäurechemietreffen]]
*[[DNG-Doktorandenseminar]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Research fields ===

*[[Prebiotic Chemistry]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Compound Classes ===

*[[Antisense Oligonucleotides]]
*[[Aptamers]]
*[[Branched Oligonucleotide Hybrids]]
*[[C-Nucleosides]]
*[[Quinolone DNA complexes]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Chemical Processes & Principles ===

*[[Chemical Primer Extension]]
*[[Organocapture]]
*[[Neighbor Exclusion Principle]]
*[[Triplex]]
*[[Isostable DNA Duplexes]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Analytical Methods ===

*[[Quantitative MALDI-TOF MS of Oligonucleotides]]
*[[UV-Melting Curves]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Synthetic Methods ===

*[[Solution-Phase Oligonucleotide Synthesis]]
*[[Vorbrüggen Base Introduction Reaction]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== History ===

*[[History of Nucleic Acid Chemistry]]
</div>

|}
<br>
Aditionally, '''a list of all available entries''' can be found [[Special:AllPages|here]].
<br><hr>
=== New to this site? ===

* Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.
* For your first steps in writing Wiki code you can ouse the [[Sandbox]].
* Here is help for [[mediawikiwiki:Help:Editing_pages|editing pages]]
* Here is help to [[mediawikiwiki:Help:Navigation|navigate]]
* Here are some [[metawikimedia:Help:Wikitext_examples|Wikitext examples]]
* Here are some infos about the [[mediawikiwiki:MediaWiki|Mediawiki]] platform
* And here is a [[wikipedia:Help:Introduction|general introduction to Wikipedia]]

Main Page

2024-08-15T12:38:01Z

Dragos: Moved the links to the user guide and the sandbox to the "New to this site?" section and added a separatory line.

== Welcome to Nucleowiki ==

Nucleowiki is an encyclopedia for nucleic acid chemistry-related topics, maintained by members of the [[DNG|"Deutsche Nucleinsäurechemie-Gemeinschaft" (DNG)]]. The site is still under construction. A list of currently available articles can be found below.

{| class="center" style="list-style-position: inside; text-align: left;"
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== The DNG & Related Events ===

*[[DNG]]
*[[Nucleinsäurechemietreffen]]
*[[DNG-Doktorandenseminar]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Research fields ===

*[[Prebiotic Chemistry]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Compound Classes ===

*[[Antisense Oligonucleotides]]
*[[Aptamers]]
*[[Branched Oligonucleotide Hybrids]]
*[[C-Nucleosides]]
*[[Quinolone DNA complexes]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Chemical Processes & Principles ===

*[[Chemical Primer Extension]]
*[[Organocapture]]
*[[Neighbor Exclusion Principle]]
*[[Triplex]]
*[[Isostable DNA Duplexes]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Analytical Methods ===

*[[Quantitative MALDI-TOF MS of Oligonucleotides]]
*[[UV-Melting Curves]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Synthetic Methods ===

*[[Solution-Phase Oligonucleotide Synthesis]]
*[[Vorbrüggen Base Introduction Reaction]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== History ===

*[[History of Nucleic Acid Chemistry]]
</div>

|}
<br>
Aditionally, '''list of all available entries''' can be found [[Special:AllPages|here]].
<br><hr>
=== New to this site? ===

* Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.
* For your first steps in writing Wiki code you can ouse the [[Sandbox]].
* Here is help for [[mediawikiwiki:Help:Editing_pages|editing pages]]
* Here is help to [[mediawikiwiki:Help:Navigation|navigate]]
* Here are some [[metawikimedia:Help:Wikitext_examples|Wikitext examples]]
* Here are some infos about the [[mediawikiwiki:MediaWiki|Mediawiki]] platform
* And here is a [[wikipedia:Help:Introduction|general introduction to Wikipedia]]

Main Page

2024-08-15T12:33:31Z

Dragos:

== Welcome to Nucleowiki ==

Nucleowiki is an encyclopedia for nucleic acid chemistry-related topics, maintained by members of the [[DNG|"Deutsche Nucleinsäurechemie-Gemeinschaft" (DNG)]]. The site is still under construction. A list of currently available articles can be found on this page.

{| class="center" style="list-style-position: inside; text-align: left;"
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== The DNG & Related Events ===

*[[DNG]]
*[[Nucleinsäurechemietreffen]]
*[[DNG-Doktorandenseminar]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Research fields ===

*[[Prebiotic Chemistry]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Compound Classes ===

*[[Antisense Oligonucleotides]]
*[[Aptamers]]
*[[Branched Oligonucleotide Hybrids]]
*[[C-Nucleosides]]
*[[Quinolone DNA complexes]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Chemical Processes & Principles ===

*[[Chemical Primer Extension]]
*[[Organocapture]]
*[[Neighbor Exclusion Principle]]
*[[Triplex]]
*[[Isostable DNA Duplexes]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Analytical Methods ===

*[[Quantitative MALDI-TOF MS of Oligonucleotides]]
*[[UV-Melting Curves]]
</div>

|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== Synthetic Methods ===

*[[Solution-Phase Oligonucleotide Synthesis]]
*[[Vorbrüggen Base Introduction Reaction]]
</div>

|-
|
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
=== History ===

*[[History of Nucleic Acid Chemistry]]
</div>

|}
A '''list of available entries''' can be found [[Special:AllPages|here]].

Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.

For your first steps in writing Wiki code you can ouse the [[Sandbox]].

=== New to this site? ===

* Here is help for [[mediawikiwiki:Help:Editing_pages|editing pages]]
* Here is help to [[mediawikiwiki:Help:Navigation|navigate]]
* Here are some [[metawikimedia:Help:Wikitext_examples|Wikitext examples]]
* Here are some infos about the [[mediawikiwiki:MediaWiki|Mediawiki]] platform
* And here is a [[wikipedia:Help:Introduction|general introduction to Wikipedia]]

Main Page

2024-08-15T12:18:38Z

Dragos: Added a list of the currently available articles sorted into categories.

== Welcome to Nucleowiki ==

Nucleowiki is an encyclopedia for nucleic acid chemistry-related topics, maintained by members of the [[DNG|"Deutsche Nucleinsäurechemie-Gemeinschaft" (DNG)]]. The site is still under construction. A list of currently available articles can be found on this page.

{|
|
=== The DNG & Related Events ===

<div>
*[[DNG]]
*[[Nucleinsäurechemietreffen]]
*[[DNG-Doktorandenseminar]]
</div>

|
=== Research fields ===

<div>
*[[Prebiotic Chemistry]]
</div>

|-
|
=== Compound Classes ===

<div>
*[[Antisense Oligonucleotides]]
*[[Aptamers]]
*[[Branched Oligonucleotide Hybrids]]
*[[C-Nucleosides]]
*[[Quinolone DNA complexes]]
</div>

|
=== Chemical Processes & Principles ===

<div>
*[[Chemical Primer Extension]]
*[[Organocapture]]
*[[Neighbor Exclusion Principle]]
*[[Triplex]]
*[[Isostable DNA Duplexes]]
</div>

|-
|
=== Analytical Methods ===

<div>
*[[Quantitative MALDI-TOF MS of Oligonucleotides]]
*[[UV-Melting Curves]]
</div>

|
=== Synthetic Methods ===

<div>
*[[Solution-Phase Oligonucleotide Synthesis]]
*[[Vorbrüggen Base Introduction Reaction]]
</div>

|-
|
=== History ===

<div>
*[[History of Nucleic Acid Chemistry]]
</div>

|}
A '''list of available entries''' can be found [[Special:AllPages|here]].

Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.

For your first steps in writing Wiki code you can ouse the [[Sandbox]].

=== New to this site? ===

* Here is help for [[mediawikiwiki:Help:Editing_pages|editing pages]]
* Here is help to [[mediawikiwiki:Help:Navigation|navigate]]
* Here are some [[metawikimedia:Help:Wikitext_examples|Wikitext examples]]
* Here are some infos about the [[mediawikiwiki:MediaWiki|Mediawiki]] platform
* And here is a [[wikipedia:Help:Introduction|general introduction to Wikipedia]]

History of Nucleic Acid Chemistry

2024-08-15T09:06:21Z

Dragos:

Sandbox

2024-08-09T08:54:18Z

Dragos: Undo revision 77 by Dragos (talk)

'''Test message'''.
LX was here.
And so was CR.

This is a line I made with <u>visual editor.</u>

* This is really visual

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Sandbox

2024-08-09T08:53:54Z

Dragos:

'''Test message'''.
LX was here.
And so was CR.

This is a line I made with <u>visual editor.</u>
The Sun is pretty big.<ref>E. Miller, ''The Sun'', (New York: Academic Press, 2005), 23–25.</ref> The Moon, however, is not so big.<ref>R. Smith, "Size of the Moon", ''Scientific American'', 46 (April 1978): 44–46.</ref>

* This is really visual
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==Notes==
<references />

History of Nucleic Acid Chemistry

2024-08-08T19:51:18Z

Dragos: Changed the reference to superscript, separated reference [2] into two different entries and added DOI links to them.

Vorbrüggen Base Introduction Reaction

2024-08-05T11:52:25Z

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

== Vorbrüggen Base Introduction Reaction ==
The Vorbrüggen method is perhaps the most important method for linking the base to the sugar in the synthesis of nucleosides. It is named after Helmut Vorbrüggen, an industrial chemist at Schering, Berlin, who worked meticulously on optimizing the reaction conditions, building on a substantial body of work in the earlier literature. The method uses a peracylated glycosyl donor, a silylated base, and a mild Lewis acid, typically in the form of a trimethylsilyl cation as active species.

== References ==
[1] H. Vorbrüggen, K. Krolikiewicz, B. Bennua, Nucleoside synthesis with trimethylsilyl triflate and perchlorate as catalysts. ''Chem. Ber''. '''1981''', ''114'', 1234-1255. https://doi.org/10.1002/cber.19811140404

[2] H. Vorbrüggen, B. Bennua, A new simplified nucleoside synthesis. ''Chem. Ber.'' '''1981''', ''114'', 1279-1286. https://doi.org/10.1002/cber.19811140407

[3] B. Bennua-Skalmowski, K. Krolikiewicz, H. Vorbrüggen, A new simple nucleoside synthesis. ''Tetrahedron Lett.'' '''1995''', ''36'', 7845-7848. https://doi.org/10.1016/0040-4039(95)01667-7

UV-Melting Curves

2024-08-05T11:50:27Z

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

== UV-Melting Points ==
One traditional method to determine the stability of DNA or RNA duplexes is to heat an aqueous solution of the duplex in question and observing the change in the UV absorption of the solution as the temperature increases. Upon dissociation of the duplex, the base stacking is lost, so that the UV absorption increases. Plotting the UV absorption against the temperature then yields a so-called melting curve. The temperature at which half of the duplex is dissociated is called the 'melting point'. The more stable the duplex, the higher the UV-melting point. Standard settings are a heating rate of 1 °C/min and UV monitoring at 260 nm. From the UV melting curves, enthalpy and entropy of duplex formation/dissociation can be derived.

Typically, the point of inflection of the first derivative of the (often smoothed) experimental curve is being interpreted as the UV melting point. To avoid misinterpretation of experimental data, it is recommended to measure melting curves at extinction values of between 0.1 and 1.2. Further, only sigmoidal transitions should be interpreted, and hyperchromicities accompanying the melting transition should be in the range of 8-35% of the initial extinction reading. Also, it is important to establish proper baselines in the low and high temperature region of the curve. Finally, evaporation effects should be avoided, e.g. by ensuring a properly filled and sealed cuvette for the acquisition of UV-melting curves.

== References ==

=== Overview Papers ===
[1] Breslauer, K.J. Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. ''Methods Enzymol.'' '''1995''', ''259'', 221-242. https://doi.org/10.1016/0076-6879(95)59046-3

=== Paper mentioning the Meltwin software for extracting enthalpy and entropy from melting curves ===
[2] McDowell, J.A.; Turner, D.H. Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)<sub>2</sub> by two-dimensional NMR and simulated annealing. ''Biochemistry'' '''1996''', ''35'', 14077-14089. https://doi.org/10.1021/bi9615710

=== Application of melting curves for DNA duplexes ===
[3] C. Ahlborn, K. Siegmund, C. Richert, Isostable DNA. ''J. Am. Chem. Soc.'' '''2007''', ''129'', 15218-15232. https://doi.org/10.1021/ja074209p

Triplex

2024-08-05T11:42:24Z

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

'''Triple Helices''' or '''Triplexes''' are formed when a third strand binds to a duplex.

Triplex formation is known for DNA and RNA. The third strand may bind via Hoogsteen or reverse Hoogsteen base pairing.

== References ==

=== Classical Paper ===
[1] Felsenfeld, G.; Rich, A. Studies on the formation of two- and three-stranded polyribonucleotides. ''Biochim. Biophys. Acta.'' '''1957''', ''26'', 457-68. https://doi.org/10.1016/0006-3002(57)90091-4

=== Review ===
[2] Thuong, N.T.; Hélène, C. Sequence-specific recognition and modification of double-helical DNA by oligonucleotides. ''Angew. Chem. Int. Ed. Engl.'' '''1993''', ''32'', 666-690. https://doi.org/10.1002/anie.199306661

=== Selected Papers on Applications ===
[3] C. Kröner, M. Röthlingshöfer, C. Richert, Designed nucleotide binding motifs. ''J. Org. Chem.'' '''2011''', ''76'', 2933-2936. https://doi.org/10.1021/jo2003067

[4] C. Kröner, M. Thunemann, S. Vollmer, M. Kinzer, R. Feil, C. Richert, Endless: A purine-binding motif that can be expressed in cells. ''Angew. Chem. Int. Ed.'' '''2014''', ''53'', 9198-9202. https://doi.org/10.1002/anie.201403579

[4] S. Vollmer, C. Richert, DNA triplexes that bind several cofactor molecules. ''Chem. Eur. J.'' '''2015''', ''21'', 18613-18622. https://doi.org/10.1002/chem.201503220

[5] A. Göckel, C. Richert, Synthesis of an oligonucleotide with a nicotinamide mononucleotide residue and its molecular recognition in DNA helices. ''Org. Biomol. Chem.'' '''2015''', ''13'', 10303-10309. https://doi.org/10.1039/C5OB01714A

Solution-Phase Oligonucleotide Synthesis

2024-08-05T11:37:30Z

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

== Solution-Phase Oligonucleotide Synthesis ==
By far the most common way of synthesizing oligonucleotides is solid-phase synthesis. Solution-phase synthesis methods do exist, however. For example, before solid supports for the immobilization of the first nucleoside (and subsequent nucleotides during chain assembly) became available, oligonucleotides were prepared in solution. Perhaps the best-known example of this early work is Khorana's synthesis of tRNA genes. Recently, synthetic methods that utilize the phosphoramidite building blocks of solid-phase synthesis as inexpensive and readily available starting materials have been developed.

== References ==

=== Classical Papers ===
[1] Agarwal, K. L. et al. & Khorana, H. G. Total synthesis of the gene for an alanine transfer ribonucleic acid from yeast. ''Nature'' '''1970''', ''227'', 27-34. https://doi.org/10.1038/227027a0

[2] Brown, E.L.; Belagaje, R.; Ryan, M.J.; Khorana, H.G. Chemical synthesis and cloning of a tyrosine tRNA gene. ''Methods Enzymol.'' '''1979''', ''68'', 109-151. https://doi.org/10.1016/0076-6879(79)68010-2

=== Recent Papers ===
[3] H. Griesser, M. Tolev, A. Singh, T. Sabirov, C. Gerlach, C. Richert, Solution-phase synthesis of branched DNA hybrids based on dimer phosphoramidites and phenolic or nucleosidic cores. ''J. Org. Chem.'' '''2012''', ''77'', 2703-2717. https://doi.org/10.1021/jo202505h

[4] A. Singh, M. Tolev, C. Schilling, S. Bräse, H. Griesser, C. Richert, Solution-phase synthesis of branched DNA hybrids via H-phosphonate dimers. ''J. Org. Chem.'' '''2012''', ''77'', 2718-2728. https://doi.org/10.1021/jo202508n

[5] R. Suchsland, B. Appel, S. Müller. Synthesis of trinucleotide building blocks in solution and on solid phase. ''Curr. Protoc. Nucleic Acid Chem.'' '''2018''', ''75'', 1, e60. https://doi.org/10.1002/cpnc.60

[6] V. Damakoudi, T. Feldner, E. Dilji, A. Belkin, C. Richert, Hybridization networks of mRNA and branched RNA hybrids. ''ChemBioChem'' '''2020''', ''22'', 924-930. https://doi.org/10.1002/cbic.202000678

Quinolone DNA complexes

2024-08-05T11:31:30Z

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

== Complexes of Quinolone Antibiotics and DNA ==
Quinolone antibiotics are widely used in the clinic. They inhibit the re-sealing of the DNA after cleavage by a gyrase, thus turning a topoisomerase into a nuclease. Three-dimensional structures of covalent quinolone-DNA complexes have been elucidated by NMR and restrained molecular dynamics.

== References ==
[1] J. Tuma, W. H. Connors, D. H. Stitelman, C. Richert, On the Effect of Covalently Appended Quinolones on Termini of DNA-Duplexes. ''J. Am. Chem. Soc.'' '''2002''', ''124,'' 4236-4246. https://doi.org/10.1021/ja0125117

[2] K. Siegmund, S. Maheshwary, S. Narayanan, W. Connors, M. Riedrich, M. Printz, C. Richert, Molecular details of quinolone-DNA interactions: Solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it. ''Nucleic Acids Res.'', '''2005''', ''33'', 4838-4848. https://doi.org/10.1093%2Fnar%2Fgki795

Quantitative MALDI-TOF MS of Oligonucleotides

2024-08-05T11:23:19Z

Dragos: Fixed formatting for "Papers on quantitative MALDI-TOF" sub-heading.

== Quantitative MALDI-TOF Mass Spectrometry of Oligonucleotides ==
The acronym MALDI-TOF MS stands for Matrix-Assisted Laser-Desorption-Ionization Time-of-Flight Mass Spectrometry. This type of mass spectrometry was invented by Franz Hillenkamp and Michael Karas at the University of Münster.

The advantage of MALDI MS is that it gives a sharp, predictable signal for a biomacromolecule, with great sensitivity and robustness to assay components like buffers. One disadvantage is the difficult to quantify. One approach to overcome this weakness is to use an internal standard or relative signal intensity, proper acquisition conditions, calibration plots and correction factors. Acquisition conditions that have been found to be successful include using moderately increased laser power and at least 100 laser shots to achieve near-exhaustive ablation of a given region of the matrix, acquiring several spectra and averaging over the relative signal (analyte versus internal standard) to obtain reliable data on concentration. Some matrices give more reproducible spectra than others. For example, trihydroxyacetophenone with diammonium citrate as co-matrix fulfills these criteria and has been used to monitor selection, genotyping or footprinting assays.

== References ==

=== MALDI Papers ===
[1] M. Karas, F. Hillenkamp, Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. ''Anal. Chem.'' '''1988''', ''60'', 2299–2301. https://doi.org/10.1021/ac00171a028

[2] Berkenkamp, S.; Kirpekar, F.; Hillenkamp, F. Infrared MALDI mass spectrometry of large nucleic acids. ''Science'' '''1998''', ''281'', 260-262. https://doi.org/10.1126/science.281.5374.260

[3] Kirpekar, F.; Nordhoff, E.; Larsen, L. K.; Kristiansen, K.; Roepstorff, P.; Hillenkamp, F. DNA sequence analysis by MALDI mass spectrometry. ''Nucleic Acids Res.'' '''1998''', ''26'', 2554-2559. https://doi.org/10.1093%2Fnar%2F26.11.2554

[4] MALDI MS. A Practical Guide to Instrumentation, Methods and Applications. Edited by Franz Hillenkamp and Jasna Peter-Katalinic, Wiley-VCH Verlag, Weinheim, 2007. ISBN: 978-3-527-31440-9

=== Papers on quantitative MALDI-TOF MS of oligonucleotides (cited by later papers on the topic) ===
[5] D. Sarracino, C. Richert, Quantitative MALDI-TOF Spectrometry of Oligonucleotides and a Nuclease Assay. ''Bioorg. Med. Chem. Lett.,'' '''1996''', ''6'', 2543-2548. https://doi.org/10.1016/0960-894X(96)00465-9

[6] K. Berlin, R. K. Jain, C. Tetzlaff, C. Steinbeck, C. Richert, Spectrometrically monitored selection experiments: quantitative laser desorption mass spectrometry of small chemical libraries. ''Chem. Biol.'' '''1997''', ''4'', 63-77. https://doi.org/10.1016/s1074-5521(97)90237-4

[7] J. Störker, J. Mayo, C. N. Tetzlaff, D. A. Sarracino, I. Schwope, C. Richert, Rapid genotyping via MALDI-monitored nuclease selection from probe libraries, ''Nature Biotechn.'' '''2000''', ''18'', 1213-1216. https://doi.org/10.1038/81226

Quantitative MALDI-TOF MS of Oligonucleotides

2024-08-05T11:22:27Z

Dragos: Fixed the reference numbering.

== Quantitative MALDI-TOF Mass Spectrometry of Oligonucleotides ==
The acronym MALDI-TOF MS stands for Matrix-Assisted Laser-Desorption-Ionization Time-of-Flight Mass Spectrometry. This type of mass spectrometry was invented by Franz Hillenkamp and Michael Karas at the University of Münster.

The advantage of MALDI MS is that it gives a sharp, predictable signal for a biomacromolecule, with great sensitivity and robustness to assay components like buffers. One disadvantage is the difficult to quantify. One approach to overcome this weakness is to use an internal standard or relative signal intensity, proper acquisition conditions, calibration plots and correction factors. Acquisition conditions that have been found to be successful include using moderately increased laser power and at least 100 laser shots to achieve near-exhaustive ablation of a given region of the matrix, acquiring several spectra and averaging over the relative signal (analyte versus internal standard) to obtain reliable data on concentration. Some matrices give more reproducible spectra than others. For example, trihydroxyacetophenone with diammonium citrate as co-matrix fulfills these criteria and has been used to monitor selection, genotyping or footprinting assays.

== References ==

=== MALDI Papers ===
[1] M. Karas, F. Hillenkamp, Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. ''Anal. Chem.'' '''1988''', ''60'', 2299–2301. https://doi.org/10.1021/ac00171a028

[2] Berkenkamp, S.; Kirpekar, F.; Hillenkamp, F. Infrared MALDI mass spectrometry of large nucleic acids. ''Science'' '''1998''', ''281'', 260-262. https://doi.org/10.1126/science.281.5374.260

[3] Kirpekar, F.; Nordhoff, E.; Larsen, L. K.; Kristiansen, K.; Roepstorff, P.; Hillenkamp, F. DNA sequence analysis by MALDI mass spectrometry. ''Nucleic Acids Res.'' '''1998''', ''26'', 2554-2559. https://doi.org/10.1093%2Fnar%2F26.11.2554

[4] MALDI MS. A Practical Guide to Instrumentation, Methods and Applications. Edited by Franz Hillenkamp and Jasna Peter-Katalinic, Wiley-VCH Verlag, Weinheim, 2007. ISBN: 978-3-527-31440-9

==== Papers on quantitative MALDI-TOF MS of oligonucleotides (cited by later papers on the topic) ====
[5] D. Sarracino, C. Richert, Quantitative MALDI-TOF Spectrometry of Oligonucleotides and a Nuclease Assay. ''Bioorg. Med. Chem. Lett.,'' '''1996''', ''6'', 2543-2548. https://doi.org/10.1016/0960-894X(96)00465-9

[6] K. Berlin, R. K. Jain, C. Tetzlaff, C. Steinbeck, C. Richert, Spectrometrically monitored selection experiments: quantitative laser desorption mass spectrometry of small chemical libraries. ''Chem. Biol.'' '''1997''', ''4'', 63-77. https://doi.org/10.1016/s1074-5521(97)90237-4

[7] J. Störker, J. Mayo, C. N. Tetzlaff, D. A. Sarracino, I. Schwope, C. Richert, Rapid genotyping via MALDI-monitored nuclease selection from probe libraries, ''Nature Biotechn.'' '''2000''', ''18'', 1213-1216. https://doi.org/10.1038/81226

Quantitative MALDI-TOF MS of Oligonucleotides

2024-08-05T10:52:14Z

Dragos: Fixed a typo, cleaned up the page formatting, redid the numbering of the references and added links to the cited papers.

== Quantitative MALDI-TOF Mass Spectrometry of Oligonucleotides ==
The acronym MALDI-TOF MS stands for Matrix-Assisted Laser-Desorption-Ionization Time-of-Flight Mass Spectrometry. This type of mass spectrometry was invented by Franz Hillenkamp and Michael Karas at the University of Münster.

The advantage of MALDI MS is that it gives a sharp, predictable signal for a biomacromolecule, with great sensitivity and robustness to assay components like buffers. One disadvantage is the difficult to quantify. One approach to overcome this weakness is to use an internal standard or relative signal intensity, proper acquisition conditions, calibration plots and correction factors. Acquisition conditions that have been found to be successful include using moderately increased laser power and at least 100 laser shots to achieve near-exhaustive ablation of a given region of the matrix, acquiring several spectra and averaging over the relative signal (analyte versus internal standard) to obtain reliable data on concentration. Some matrices give more reproducible spectra than others. For example, trihydroxyacetophenone with diammonium citrate as co-matrix fulfills these criteria and has been used to monitor selection, genotyping or footprinting assays.

== References ==

=== MALDI Papers ===
[1] M. Karas, F. Hillenkamp, Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. ''Anal. Chem.'' '''1988''', ''60'', 2299–2301. https://doi.org/10.1021/ac00171a028

[2] Berkenkamp, S.; Kirpekar, F.; Hillenkamp, F. Infrared MALDI mass spectrometry of large nucleic acids. ''Science'' '''1998''', ''281'', 260-262. https://doi.org/10.1126/science.281.5374.260

[3] Kirpekar, F.; Nordhoff, E.; Larsen, L. K.; Kristiansen, K.; Roepstorff, P.; Hillenkamp, F. DNA sequence analysis by MALDI mass spectrometry. ''Nucleic Acids Res.'' '''1998''', ''26'', 2554-2559. https://doi.org/10.1093%2Fnar%2F26.11.2554

[4] MALDI MS. A Practical Guide to Instrumentation, Methods and Applications. Edited by Franz Hillenkamp and Jasna Peter-Katalinic, Wiley-VCH Verlag, Weinheim, 2007. ISBN: 978-3-527-31440-9

==== Papers on quantitative MALDI-TOF MS of oligonucleotides (cited by later papers on the topic) ====
[1] D. Sarracino, C. Richert, Quantitative MALDI-TOF Spectrometry of Oligonucleotides and a Nuclease Assay. ''Bioorg. Med. Chem. Lett.,'' '''1996''', ''6'', 2543-2548. https://doi.org/10.1016/0960-894X(96)00465-9

[2] K. Berlin, R. K. Jain, C. Tetzlaff, C. Steinbeck, C. Richert, Spectrometrically monitored selection experiments: quantitative laser desorption mass spectrometry of small chemical libraries. ''Chem. Biol.'' '''1997''', ''4'', 63-77. https://doi.org/10.1016/s1074-5521(97)90237-4

[3] J. Störker, J. Mayo, C. N. Tetzlaff, D. A. Sarracino, I. Schwope, C. Richert, Rapid genotyping via MALDI-monitored nuclease selection from probe libraries, ''Nature Biotechn.'' '''2000''', ''18'', 1213-1216. https://doi.org/10.1038/81226

Prebiotic Chemistry

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== Prebiotic Chemistry ==
The field of prebiotic chemistry studies chemical processes that may have contributed to the molecular origin of life on planet Earth. The focus is on processes that may have occurred prior to the beginning of biological evolution. A number of hypotheses exist on how molecular evolution may have occurred.

== Selected References ==
[1] R. Lohrmann, L.E.Orgel, Prebiotic activation processes. ''Nature''. '''1973''', ''244'', 418-420. https://doi.org/10.1038/244418a0

[2] S.A. Benner, A.D. Ellington, A. Tauer, Modern metabolism as a palimpsest of the RNA world. ''Proc. Natl. Acad. Sci. U.S.A.'' '''1989''', ''86'', 7054-7058. https://doi.org/10.1073/pnas.86.18.7054

[3] Gesteland, R.F.; Atkins, J.F. (eds.) ''The RNA World''. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1993.

[4] C. De Duve, The onset of selection. ''Nature'' '''2005''', ''433'', 581–582. https://doi.org/10.1038/433581a

[5] J.W. Szostak, The eightfold path to non-enzymatic RNA replication. ''J. Systems Chem.'' '''2012''', ''3'', 2. https://doi.org/10.1186/1759-2208-3-2

[6] K. Ruiz-Mirazo, C. Briones, A. de la Escosura, Prebiotic systems chemistry: New perspectives for the origins of life. ''Chem. Rev.'' '''2014''', ''114'', 285-366.

[7] M. Frenkel-Pinter, M. Samanta, G. Ashkenasy, L. J. Leman, Prebiotic Peptides: Molecular Hubs in the Origin of Life. ''Chem. Rev.'' '''2020''', ''120'', 4707–4765. https://doi.org/10.1021/cr2004844

[8] W.F. Martin, K. Kleinermanns, ''The Geochemical Origin of Microbes''. CRC Press, Boca Raton, 2024.

Neighbor Exclusion Principle

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== Neighbor Exclusion Principle ==

The neighbor exclusion principle of classical intercalation says that between intercalation sites in a duplex one site must remain free. In other words, only every other intercalation site is occupied when classical intercalators bind to duplexes. There are numerous exceptions to this principle.

== References ==

[1] C. Robledo-Luiggi, W.D. Wilson, E. Pares, M. Vera, C.S. Martinez, D. Santiago, Partial intercalation with DNA of peptides containing two aromatic amino acids. ''Biopolymers'' '''1991''', ''31'', 907-917. https://doi.org/10.1002/bip.360310710

[2] M. Yousuf, I. S. Youn, J. Yun, L. Rasheed, R. Valero, G. Shi, K. S. Kim, Violation of DNA neighbor exclusion principle in RNA recognition. ''Chem. Sci''. '''2016''', ''7'', 3581-3588. https://doi.org/10.1039/C5SC03740A (Edge article)

Isostable DNA Duplexes

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== 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 ==
[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

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

[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

History of Nucleic Acid Chemistry

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Branched Oligonucleotide Hybrids

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== Branched Oligonucleotide Hybrids ==
One of the non-biological applications for DNA is nanostructuring. Because oligo- and polynucleotides engage in predictable base pairing interactions, designed three-dimensional structures can be generated, based on the hybridization and folding of such strands. A wide array of structures on the scale of nanometers have been created using unmodified DNA. For applications in material sciences, branched oligonucleotides are being synthesized that consist of an organic molecule as branching element and oligonucleotides appended to it through covalent bonds. Because these synthetic species are constructed from two different classes of compounds, they are called 'hybrids'.

== References ==

=== DNA nanostructuring ===
[1] P. W. K. Rothemund, Folding DNA to create nanoscale shapes and patterns. ''Nature'' '''2006''', ''440'', 297-302. https://doi.org/10.1038/nature04586

[2] Jones, M. R.; Seeman, N. C.; Mirkin, C. A. Programmable materials and the nature of the DNA bond. ''Science'' '''2015''', ''347'', 840. https://doi.org/10.1126/science.1260901

=== Branched oligonucleotide hybrids ===
[3] M. Meng, C. Ahlborn, M. Bauer, O. Plietzsch, S. A. Soomro, A. Singh, T. Muller, W. Wenzel, S. Bräse, C. Richert, Two base pair duplexes suffice to build a novel material. ''ChemBioChem'' '''2009''', ''10'' , 1335-1339. https://doi.org/10.1002/cbic.200900162

[4] A. Singh, M. Tolev, M. Meng, K. Klenin, O. Plietzsch, C. I. Schilling, T. Muller, M. Nieger, S. Bräse, W. Wenzel, C. Richert, Branched DNA that forms a solid at 95 °C. ''Angew. Chem. Int. Ed.'' '''2011''', ''50'', 3227-3231. https://doi.org/10.1002/anie.201006992

[5] H. Griesser, M. Tolev, A. Singh, T. Sabirov, C. Gerlach, C. Richert, Solution-phase synthesis of branched DNA hybrids based on dimer phosphoramidites and phenolic or nucleosidic cores. ''J. Org. Chem.'' '''2012''', ''77'', 2703-2717. https://doi.org/10.1021/jo202505h

[6] A. Singh, M. Tolev, C. Schilling, S. Bräse, H. Griesser, C. Richert, Solution-phase synthesis of branched DNA hybrids via H-phosphonate dimers. ''J. Org. Chem.'' '''2012''', ''77'', 2718-2728. https://doi.org/10.1021/jo202508n

[7] A. Schwenger, T.P. Jurkowski, C. Richert, Capturing and stabilizing folded proteins in lattices formed with branched oligonucleotide hybrids. ''ChemBioChem'' '''2018''', ''19'', 1523-1530. https://doi.org/10.1002/cbic.201800145

[8] V. Damakoudi, T. Feldner, E. Dilji, A. Belkin, C. Richert, Hybridization networks of mRNA and branched RNA hybrids. ''ChemBioChem'' '''2020''', ''22'', 924-930. https://doi.org/10.1002/cbic.202000678

Chemical Primer Extension

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== Chemical Primer Extension ==

The copying of genetic information usually occurs via enzymatically catalyzed elongation of a short oligonucleotide, dubbed 'primer' that binds to the template. The enzymes that catalyze primer extension are called 'polymerases', and their substrates are usually nucleoside triphosphates (NTPs or dNTPs). The best-known application that utilizes enzymatically catalyzed primer extension is the polymerase chain reaction (PCR), which was invented by Mullis. It is less well known that primer extension can also be induced in the absence of enzymes, solely based on molecular recognition of activated nucleotides and the template-primer duplex. This version of the reaction is called enzyme-free or 'chemical primer reaction'. It is relevant for the origin of life and can be used for SNP genotyping.

== References ==

=== PCR ===
[1] K. B. Mullis, The polymerase chain reaction (Nobel Lecture). ''Angew. Chem. Int. Ed. Engl.'' '''1994''', ''33'', 1209-1213. https://doi.org/10.1002/anie.199412091

=== Chemical Primer Extension ===
[2] M. Zielinski, I. A. Kozlov, L. E. Orgel, A comparison of RNA with DNA in template-directed synthesis. ''Helv. Chim. Acta'' '''2000''', ''83'', 1678-1684. https://doi.org/10.1002/1522-2675(20000809)83:8%3C1678::AID-HLCA1678%3E3.0.CO;2-P

[3] J. A. Rojas Stütz, E. Kervio, C. Deck, C. Richert, Chemical primer extension - individual steps of spontaneous replication. ''Chem. Biodiv.'' '''2007''', ''4'', 784-802. https://doi.org/10.1002/cbdv.200790064

[4] N. Griesang, K. Giessler, T. Lommel, C. Richert, Four color, enzyme-free interrogation of DNA sequences with chemically activated, 3'-fluorophore-labeled nucleotides. ''Angew. Chem. Int. Ed.'' '''2006''', ''45'' , 6144-6148. https://doi.org/10.1002/anie.200600804

C-Nucleosides

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== ''C''-Nucleosides ==

In ''C''-nucleosides, a carbon-carbon bond links the nucleobase (or nucleobase analog) to the sugar. This is in contrast to canonical nucleosides, where a nitrogen atom links the base to the ribose or 2'-deoxyribose. The best-known natural ''C''-nucleoside is pseudouridine. Several therapeutic nucleosides (or their prodrug forms used as active pharmaceutical ingredients) are known that are ''C''-nucleosides.

== References ==

=== Review ===
[1] M. Hocek, ''C''-Nucleosides: synthetic strategies and biological applications. ''Chem. Rev''. '''2009''', ''109'', 6729–6764. https://doi.org/10.1021/cr9002165

=== Synthetic Papers ===
[2] H.-J. Kim, N. A. Leal, S. Hoshika, S. A. Benner, Ribonucleosides for an artificially expanded genetic information system. ''J. Org. Chem''. '''2014''', ''79'', 3194−3199. https://doi.org/10.1021/jo402665d

[3] T. Gniech, C. Richert, Diastereoselective synthesis of pyridone ''ribo''-''C''-nucleosides via Heck reaction and oxidation. ''Eur. J. Org. Chem.'' '''2024''', e202400342. https://doi.org/10.1002/ejoc.202400342

Branched Oligonucleotide Hybrids

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== Branched Oligonucleotide Hybrids ==
One of the non-biological applications for DNA is nanostructuring. Because oligo- and polynucleotides engage in predictable base pairing interactions, designed three-dimensional structures can be generated, based on the hybridization and folding of such strands. A wide array of structures on the scale of nanometers have been created using unmodified DNA. For applications in material sciences, branched oligonucleotides are being synthesized that consist of an organic molecule as branching element and oligonucleotides appended to it through covalent bonds. Because these synthetic species are constructed from two different classes of compounds, they are called 'hybrids'.

== References ==

=== '''''DNA nanostructuring''''' ===
[1] P. W. K. Rothemund, Folding DNA to create nanoscale shapes and patterns. ''Nature'' '''2006''', ''440'', 297-302. https://doi.org/10.1038/nature04586

[2] Jones, M. R.; Seeman, N. C.; Mirkin, C. A. Programmable materials and the nature of the DNA bond. ''Science'' '''2015''', ''347'', 840. https://doi.org/10.1126/science.1260901

=== '''''Branched oligonucleotide hybrids''''' ===
[3] M. Meng, C. Ahlborn, M. Bauer, O. Plietzsch, S. A. Soomro, A. Singh, T. Muller, W. Wenzel, S. Bräse, C. Richert, Two base pair duplexes suffice to build a novel material. ''ChemBioChem'' '''2009''', ''10'' , 1335-1339. https://doi.org/10.1002/cbic.200900162

[4] A. Singh, M. Tolev, M. Meng, K. Klenin, O. Plietzsch, C. I. Schilling, T. Muller, M. Nieger, S. Bräse, W. Wenzel, C. Richert, Branched DNA that forms a solid at 95 °C. ''Angew. Chem. Int. Ed.'' '''2011''', ''50'', 3227-3231. https://doi.org/10.1002/anie.201006992

[5] H. Griesser, M. Tolev, A. Singh, T. Sabirov, C. Gerlach, C. Richert, Solution-phase synthesis of branched DNA hybrids based on dimer phosphoramidites and phenolic or nucleosidic cores. ''J. Org. Chem.'' '''2012''', ''77'', 2703-2717. https://doi.org/10.1021/jo202505h

[6] A. Singh, M. Tolev, C. Schilling, S. Bräse, H. Griesser, C. Richert, Solution-phase synthesis of branched DNA hybrids via H-phosphonate dimers. ''J. Org. Chem.'' '''2012''', ''77'', 2718-2728. https://doi.org/10.1021/jo202508n

[7] A. Schwenger, T.P. Jurkowski, C. Richert, Capturing and stabilizing folded proteins in lattices formed with branched oligonucleotide hybrids. ''ChemBioChem'' '''2018''', ''19'', 1523-1530. https://doi.org/10.1002/cbic.201800145

[8] V. Damakoudi, T. Feldner, E. Dilji, A. Belkin, C. Richert, Hybridization networks of mRNA and branched RNA hybrids. ''ChemBioChem'' '''2020''', ''22'', 924-930. https://doi.org/10.1002/cbic.202000678

Aptamers

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== Aptamers ==

Aptamers are single-stranded RNA or DNA molecules that can fold and bind target structures with high affinity and a specificity comparable to that of antibodies. They are identified by selection from libraries of sequences.

== Selected References ==

[1] A. D. Ellington, J. W. Szostak, In vitro selection of RNA molecules that bind specific ligands. ''Nature'' '''1990''', ''346'', 818-822. https://doi.org/10.1038/346818a0

[2] D. Irvine, C. Tuerk, L. Gold, Selexion - Systematic evolution of ligands by exponential enrichment with integrated optimization by nonlinear-analysis. ''J. Mol. Biol.'' '''1991''', ''222'', 739-761. https://doi.org/10.1016/0022-2836(91)90509-5<nowiki/>☃☃

[3] M. Egli, In vitro selected receptors rationalized: the first 3D structures of RNA aptamer/substrate complexes. ''Angew. Chem. Int. Ed. Engl.'' '''1997''', ''36'', 480-482. https://doi.org/10.1002/anie.199704801

[4] S. Müller (ed.), Nucleic acids from A to Z - A concise encyclopedia. Wiley-VCH, Weinheim: 2008, ISBN: 978-3-527-31211-5.

Antisense Oligonucleotides

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== Antisense Oligonucleotides ==
Oligodeoxynucleotides that block the translation of specific mRNAs by hybridizing to complementary sequences are called antisense oligonucleotides. They are one class of therapeutic oligonucleotides.

== Seminal Papers ==
[1] Zamecnik, P. C.; Stephenson, M. L., Inhibition of Rous sarcoma virus replication and cell transformation by a specific oligodeoxynucleotide. ''Proc. Natl. Acad. Sci. U.S.A.'' '''1978''', ''75'', 280-284. https://doi.org/10.1073/pnas.75.1.280

[2] Stephenson, M. L.; Zamecnik, P. C., Inhibition of Rous sarcoma viral RNA translation by a specific oligodeoxyribonucleotide. ''Proc. Natl. Acad. Sci. U.S.A.'' '''1978''', ''75'', 285-288. https://doi.org/10.1073%2Fpnas.75.1.285

== Homepage of the Oligonucleotide Therapeutics Society (OTS) ==
https://www.oligotherapeutics.org

Organocapture

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== Organocapture ==
When small organic molecules, rather than transition metal complexes, enzymes or mere acids/bases, catalyze a reaction, the term "organocatalysis" is used. Sometimes the "catalyst" increases the yield of a reaction without accelerating the reaction leading to the desired product by reducing the rate of competing reactions more than that of the desired reaction. When this happens and a covalent intermediate is involved, the term "organocapture" may be used.

== References ==

=== Organocatalysis ===

[1] B. List, R. A. Lerner, C. F. Barbas III. Proline-catalyzed direct asymmetric aldol reactions. ''J. Am. Chem. Soc.'' '''2000''', ''122'', 2395–2396. https://doi.org/10.1021/ja994280y

[2] D. W. C. MacMillan, The advent and development of organocatalysis. ''Nature'' '''2008''', ''455'', 304–308. https://doi.org/10.1038/nature07367

=== Reference Organocapture ===

[3] P. Tremmel, H. Griesser, U. E. Steiner, C. Richert, How small heterocycles make a reaction network of amino acids and nucleotides efficient in water. ''Angew. Chem. Int. Ed.'' '''2019''', ''58'', 13087-13092. https://doi.org/10.1002/anie.201905427