Nucleowiki - User contributions [en]

Annealing

2026-01-26T17:06:38Z

Richert: Created page with " '''Annealing''' Annealing is a process leading to the formation of a folded nucleic acid structure by first heating the solution containing the nucleic acid strands to a temperature high enough to melt whatever partially folded structures may exist, and slowly cooling that solution to allow the strands to assemble into the desired, fully folded structure. The fully folded structure may be a duplex, triplex, quadruplex or higher structure, such as a DNA origami nanost..."

'''Annealing'''

Annealing is a process leading to the formation of a folded nucleic acid structure by first heating the solution containing the nucleic acid strands to a temperature high enough to melt whatever partially folded structures may exist, and slowly cooling that solution to allow the strands to assemble into the desired, fully folded structure. The fully folded structure may be a duplex, triplex, quadruplex or higher structure, such as a DNA origami nanostructure, but it may also be just a folded structure of a single strand, such as a ribozyme. This process is often the first step of an assay requiring functional assemblies of DNA or RNA strands. Leaving it out can give an incorrect result, as partially folded or unfolded structures do not have the same activity/function as fully folded ones. The heating ensures that the activation barrier for forming the fully folded structure is overcome. Slow cooling makes it easier for the molecules to reach the folded state of maximum base pairing and low energy. Annealing may be achieved by placing a vial in hot water and removing it again, or by more elaborate and controlled temperature programs, e.g. in a thermocycler. The term annealing is also used in other fields of research and development, for processes using other compounds than DNA or RNA.

'''Reference'''

Molecular biology techniques can be found in:

M. R. Green, J. Sambrook, Molecular Cloning: A Laboratory Manual (Fourth Edition), CSH Press, Cold Spring Harbor Laboratory Press, 2012.

<nowiki>http://www.molecularcloning.com/</nowiki>

DNG-Doktorandenseminar

2025-10-28T08:29:23Z

Richert:

The Graduate School Symposia of the DNG, with presentations by graduate students and invited experts, were formerly known as "DNG-Doktorandenseminare" and are now known as "DNG Graduate Schools". The following is a list of the meetings. The venue is Bad Herrenalb in Baden-Württemberg, in the Northern part of the Black Forest.

VIII. Doktorandenseminar Nucleinsäurechemie 17.-18.09.2026 (planned)

VII. Doktorandenseminar Nucleinsäurechemie 19.-20.09.2024

VI. Doktorandenseminar Nucleinsäurechemie 03. - 04.10.2022

V. Doktorandenseminar Nucleinsäurechemie 01. - 02.10.2020

IV. Doktorandenseminar Nucleinsäurechemie 20. - 21.09.2018

III. Doktorandenseminar Nucleinsäurechemie 22. - 23.09.2016

II. DNG-Doktorandeseminar 29.-30.09.2014

I. DNG Doktorandenseminar 01.-02.10.2012

Nucleinsäurechemietreffen

2025-10-28T08:27:44Z

Richert: updated

The symposia of the DNG with formal talks by PIs are called "Nucleinsäurechemietreffen".

The following Nucleinsäurechemietreffen have taken place so far.

XII. Nucleinsäurechemietreffen 2025 (Hamburg)

XI. Nucleinsäurechemietreffen 2023 (Würzburg)

X. Nucleinsäurechemietreffen 2021 (Bad Herrenalb)

IX. Nucleinsäurechemietreffen 2019 (Saarbrücken)

VIII. Nucleinsäurechemietreffen 2017 (Mainz)

VII. Nucleinsäurechemietreffen 2015 (Berlin)

VI. Nucleinsäurechemietreffen 2013 (Greifswald)

V. Nucleinsäurechemietreffen 2011 (Frankfurt)

IV. Nucleinsäurechemietreffen 2009 (Regensburg)

III. Nucleinsäurechemietreffen 2008 (Stuttgart)

II. Nucleinsäurechemietreffen 2006 (Göttingen)

I. Nucleinsäurechemietreffen 2004 (Karlsruhe)

Main Page

2025-01-13T18:16:21Z

Richert:

== 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>
=== Student Papers ===

*[[Media:Antisense_Oligonucleotides_FG_110125.pdf|Antisense Oligonucleotides (Felix Göbel)]]
</div>
<div style="padding-top: 10px; padding-right: 10px; padding-bottom: 10px; padding-left: 10px;">
<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]]

DNA Origami

2025-01-09T17:21:32Z

Richert: Created page with " '''DNA Origami''' The construction of nucleic acid-based structures was first proposed by Nadrian C. Seeman in 1982 [1]. This was a revolutionary idea that co-founded a new field of research known today as “structural DNA nanotechnology”. DNA origami is a nanotechnology technique that uses DNA molecules to create well defined nanoscale structures. It is based on the unique properties of DNA, in particular its ability to form complementary base pairs (A-T, C-G) an..."

'''DNA Origami'''

The construction of nucleic acid-based structures was first proposed by Nadrian C. Seeman in 1982 [1]. This was a revolutionary idea that co-founded a new field of research known today as “structural DNA nanotechnology”.

DNA origami is a nanotechnology technique that uses DNA molecules to create well defined nanoscale structures. It is based on the unique properties of DNA, in particular its ability to form complementary base pairs (A-T, C-G) and its double-stranded helical structure.

The DNA origami technique was developed by Paul Rothemund in 2006. It uses the self-organizing properties of DNA to create complex structures from a long, single-stranded DNA molecule (the “scaffold”) and shorter, synthetically produced DNA strands (the “staples” or staple strands) [2]. The scaffold-based DNA origami method has an entropic advantage over multi-strand methods, as the scaffold strand hybridizes less with itself and nucleates and templates hybridization events [3]. The DNA origami method is a bottom-up method in contrast to classic top-down nanostructuring methods, such as photolithography or dip-pen lithography [4].

Possible application are diverse and range from targeted drug delivery and nanomaterials to dynamic structures [5].

Nowadays, computer-aided simulations are mostly used to process and predict the enormous amounts of data from all possible basepairing interactions. Programs such as “CaDNAno” or “CanDo” help to find suitable designs.

'''References'''

[1] Nadrian C. Seeman, Nucleic acid junctions and lattices, ''Journal of Theoretical Biology'', Volume 99, Issue 2, 1982, 237-247, ISSN 0022-5193, <nowiki>https://doi.org/10.1016/0022-5193(82)90002-9</nowiki>.

[2] Rothemund, P. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006). <nowiki>https://doi.org/10.1038/nature04586</nowiki>

[3] Saccà, B., & Niemeyer, C. M. (2012). DNA origami: the art of folding DNA. ''Angewandte Chemie International Edition'', ''51''(1), 58-66.

[4] a) P. W. K. Rothemund, "Design of DNA origami," ''ICCAD-2005. IEEE/ACM International Conference on Computer-Aided Design, 2005.'', San Jose, CA, USA, 2005, pp. 471-478, doi: 10.1109/ICCAD.2005.1560114. b) Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. ''Nature'' 2006, 440, 297-302.

[5] Jiang, Q., Shang, Y., Xie, Y., & Ding, B. (2024). DNA Origami: From Molecular Folding Art to Drug Delivery Technology. ''Advanced Materials,'' 36(22), 2301035.

DNA Sequencing

2025-01-06T16:01:04Z

Richert: formatted

'''DNA Sequencing'''

DNA sequencing is the process by which a nucleotide sequence in deoxyribonucleic acid (DNA) is determined. As such, it has applications in many fields of science, and is relevant for the development of gene therapy or the research into extinct species (Mathews, 2024).

History of DNA Sequencing
After the structure of the DNA double helix had been uncovered in 1953 (Watson & Crick, 1953), researchers turned their attention to determining the nucleotide sequence of DNA. Early efforts included the sequencing of yeast transfer ribonucleic acid (tRNA) and the analysis of single stranded ends of bacteriophage DNA (Booth, 2022, Mathews, 2024).
In 1977, the identification of longer sequences of DNA became practicable with the advent of two new methods: The chemical cleavage procedure, developed by Allan Maxam and Walter Gilbert (Maxam & Gilbert, 1977), and the chain termination procedure, developed by Frederick Sanger (Sanger et al., 1977). These two methods are often referred to as 'first-generation sequencing' methods.

'''First-Generation Sequencing'''

The Maxam-Gilbert procedure involves a set of four chemical reactions, each able to cleave the glycosidic bond of a specific nucleobase. Guanine can be methylated using dimethyl sulfate, followed by cleavage of the glycosidic bond under heating. Adenine can be methylated using dimethyl sulfate, followed by glycosidic bond cleavage under incubation with dilute acid. Thymine can be cleaved via treatment with hydrazine, whereas cytosine must be treated with hydrazine at high salt concentrations. Treatment of the abasic site in the backbone with piperidine as base will lead to strand cleavage at this site. The resulting DNA fragments are of unique length and can be separated via polyacrylamide gel electrophoresis (PAGE). The order of the bands in the gel corresponds to the nucleotide sequence (Booth, 2022).
In contrast, Sanger sequencing utilizes a DNA polymerase to form a complementary strand to the template region of interest. The polymerase is provided with all four 2’-deoxynucleotides (dNTPs), and one type of 2’,3’-dideoxynucleotide (ddNTP). This ddNTP is a chain terminator - upon incorporation of a ddNTP into the growing DNA strand, extension cannot continue (Mathews, 2024). Thus, DNA strands of different lengths are formed, each terminating at the position of the ddNTP incorporation. Separation via PAGE, with separate lanes for each ddNTP-containing solution, yields the order of nucleobases in the strand.
Over the following decade, two innovations further increased the efficiency of the Sanger procedure. First, by marking the ddNTPs with different fluorescent labels, electrophoresis of all four ddNTPs could be carried out in a single capillary. Second, so-called shotgun sequencing enabled analysis of long sequences. By breaking up DNA via sonication or endonucleases, multiple overlapping fragments are created, so-called 'reads'. Reads were sequenced separately, and the full sequence assembled via analysis of the overlaps (Booth, 2022, Heather & Chain, 2016).
This enabled sequencing of complete genomes, culminating in the deciphering of the human genome in 2001 (International Human Genome Sequencing Consortium, 2004).
As noted by Shendure et al. (2017), the increasing amount of genetic data also necessitated the development of algorithms and databases. Noteworthy innovations include the Smith-Waterman Algorithm (Smith & Waterman, 1981), BLAST (Altschul et al., 1990) and GenBank (Benson et al., 1993).

'''Second-Generation Sequencing'''

Over the course of the 1990s, multiple technologies further increased the throughput achievable. They are generally referred to as 'Second-Generation Sequencing Technologies' or 'Next Generation Sequencing Technologies' (Liu et al., 2012). Many of these were also commercialized as stand-alone platforms. Notable platforms include the pyrosequencing platform of 454 Life Sciences, the Illumina platform (initially Solexa), the SOLiD system from Applied Biosystems and the Ion Torrent technology of Life Technologies (Heather & Chain, 2016). The following is a brief description of each of the platforms, with an attempt to highlight advantages and disadvantages.
The pyrosequencing workflow begins by attaching single stranded (ss) DNA fragments to beads and amplifying them via emulsion PCR (emPCR) (Heather & Chain, 2016). Then, one type of dNTP at a time is washed over the beads, together with a DNA polymerase. If the dNTP is incorporated into the strand, pyrophosphate (PPi) is released. Pyrophosphate is used by ATP sulfurylase to produce ATP, which in turn is converted by the luciferase to produce light. Lastly, apyrase degrades ATP and dNTPs in between the addition of bases. Thus, if a flash of light can be detected, a dNTP has been incorporated into the sequence (Ahmadian et al., 2006).
Pyrosequencing can be used for de novo gene assembly, boasting long read lengths and high sequencing speeds. However, the length of homopolymeric regions, (that is, regions which contain repeats of just one nucleotide) is difficult to determine using pyrosequencing (Mathews, 2024). Also, the cost per base is comparatively high (Liu et al., 2012).
The acronym SOLiD is shorthand for 'Sequencing by Oligo Ligation Detection' (Heather & Chain, 2016). Again, ssDNA fragments are amplified in emPCR and attached to a solid support. Then, they are exposed to different degenerate DNA oligomers. Each oligomer carries a fluorophore, the colour of which corresponds to one base of the oligomer. The other bases are degenerate and can bind to any other base. A T4 DNA ligase ligates the oligomer to the primer, and via detection of the fluorescence, the identity of the ligated base can be determined (Shendure et al., 2005).
Accuracy of the SOLiD method is very high, making it useful for resequencing of genomes, for example to detect single nucleotide polymorphisms. However, read lengths are short, making assembly of longer sequences difficult (Liu et al., 2012).
The Ion Torrent procedure also begins by amplifying ssDNA fragments on a bead via emPCR. Beads are sequentially exposed to dNTPs, one type at a time, and a DNA polymerase extends the strands. Every time a triphosphate group is hydrolyzed, a proton is released, which changes the pH around the bead. This is detected and digitized by a sensor, indicating incorporation of a certain type of dNTP (Rothberg et al., 2011). While this method is fast, has low cost per base and is easy to scale, but accuracy in homopolymeric regions is low (Mathews, 2024).
In Illumina sequencing, DNA fragments are immobilized and amplified on a solid surface in a process called 'bridge amplification'. Then, fragments are exposed to dNTPs, each base marked by a different fluorescent molecule. The 3’-OH group of the dNTPs is protected by an azidomethyl group, leading to chain termination upon incorporation. So, only a single dNTP can be incorporated at a time. The type of dNTP can now be identified by four-colour imaging. Lastly, fluorescent groups and the 3’ protecting groups are cleaved, so that a new dNTP can be incorporated. This process can be repeated for read lengths of up to 300 bases (Booth, 2022).
The Illumina protocol allows for accurate, high throughput sequencing of DNA. Read lengths are short, compared to the other platforms (Liu et al., 2012). Still, as of September 2024, the Illumina method is the most common sequencing method in the world (Mathews, 2024).

'''Third-Generation Sequencing'''

While second-generation sequencing methods are improved, as compared to first generation methods, in many ways, they still have some shortcomings.
Firstly, all second-generation platforms rely on DNA amplification. This not only adds a layer of complexity but can also introduce errors and biases (Pinard et al., 2006). Secondly, read lengths of all platforms are less than 1000 bp (Mathew, 2024). The human genome contains repeating regions of up to 104 bp, meaning these regions cannot be sequenced with second-generation methods (Li & Freudenberg, 2014).
Third-generation sequencing technologies try to address these problems. They rely on single molecule sequencing, meaning sequencing of long reads without previous amplification (Heather & Chain, 2016). Notable technologies include the single-molecule real-time sequencing (SMRT) method from Pacific Biosciences (PacBio) and nanopore sequencing from Oxford Nanopore Technologies (ONT) (Booth, 2022).
PacBio’s SMRT utilizes so-called zero-mode waveguides (ZMWs), which are essentially wells in a metal film with a diameter of less than 100 nm. Light with much longer wavelengths than 100 nm will decay exponentially in the well, so that fluorophore illumination in only a small part of the well can be detected (Heather & Chain, 2016). This is exploited by attaching a DNA polymerase to the bottom of the well and providing it with a single, long DNA fragment. Then, a mixture of dNTPs marked with different fluorophores is added. As a dNTP is incorporated into the strand, a fluorescence signal can be detected at the bottom of the well, before the fluorescent label is cleaved off and diffuses into the bulk of the solution (Booth, 2022). This not only provides information about the type of nucleotide added, but also gives real time data. The time-course data can contain additional information about modifications of DNA, like epigenetic methylations (Liu et al., 2012).
Overall, SMRT sequencing provides ultra-long reads of up to 105 bases, at accuracies of repeated reads similar to Illumina sequencing. However, raw error rates are still high (Mathews, 2024).
In ONT’s nanopore sequencing, a motor protein pulls ssDNA through a nanopore in a membrane. Applying a constant voltage drives an ionic current through the pore. Conductivity of the pore changes, depending on the nucleobases that pass through. Thus, the current changes over time, which can be measured. Different currents are characteristic for different DNA sequences (Deamer et al., 2019). Nucleobase sequences as well as epigenetic modifications may be detected.
Using ONTs nanopore sequencing, read lengths of up to 2.273⋅106 bp have been reported. ONTs smallest sequencers, the “MinIONs”, are portable, allowing for decentralized real-time sequencing. This has been utilized in real time surveillance of disease outbreaks around the world (Wang et al., 2021). However, output data analysis is complicated, and error rates are still comparatively high (Mathews, 2024).
Both PacBio’s SMRT and ONTs nanopore sequencing are still being optimized, and the introduction of new computational workflows and improved chemistry is to be expected, further reducing error rates and complexity. Probably, third-generation sequencing methods will replace second-generation sequencing in most applications (Athanasopoulou et al., 2022).

'''References'''

Ahmadian, A. et al. (2006). Pyrosequencing: history, biochemistry and future. Clin. Chim. Acta 363(1-2), 83-94. doi.org/10.1016/j.cccn.2005.04.038.

Altschul, S. F. et al. (1990). Basic local alignment search tool. J. Mol. Biol. 5;215(3):403-10. doi.org/10.1016/S0022-2836(05)80360-2.

Athanasopoulou, K. et al. (2022). Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics. Life 12(1), 30. doi.org/10.3390/life12010030.

Benson, D. et al. (1993). GenBank. Nucleic Acids Res. 21(13):2963-2965. doi.org/10.1093/nar/21.13.2963.

Booth, M. J. (2022). DNA and RNA sequencing. In: Blackburn, M. G. et al. (eds.) Nucleic Acids in Chemistry and Biology. 4th Edition, The Royal Society of Chemistry, London.

Deamer, D. et al. (2019). Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518-524. doi.org/10.1038/nbt.3424.

Heather, J. M., Chain, B. (2016). The sequence of sequencers: The history of sequencing DNA. Genomics 107(1), 1-8. doi.org/10.1016/j.ygeno.2015.11.003.

International Human Genome Sequencing Consortium (2004). Finishing the euchromatic sequence of the human genome. Nature 431, 931–945. doi.org/10.1038/nature03001.

Li, W., Freudenberg, J. (2014). Mappability and read length. Front. Genet. 5:381. doi.org/10.3389/fgene.2014.00381.

Liu, L. et al. (2012). Comparison of Next-Generation Sequencing Systems. J. Biomed. Biotechnol. 1, 251364. doi.org/ 10.1155/2012/251364.

Mathews, A. (2024). DNA Sequencing: A Brief History. In: Abdurakhmonov, I. Y. (eds.). DNA Sequencing – History, Present and Future. Intech Open, Rijeka. doi.org/10.5772/intechopen.1007844.

Maxam, A. M., Gilbert, W. (1977). A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA 74(2):560-4. doi.org/10.1073/pnas.74.2.560.

Pinard, R. et al. (2006). Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics 7, 216. doi.org/10.1186/1471-2164-7-216.

Rothberg, J. M. et al. (2011). An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348-52. doi.org/10.1038/nature10242.

Sanger, F. et al. (1977). DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74(12):5463-7. doi.org/10.1073/pnas.74.12.5463.

Shendure, J. et al. (2005). Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome. Science 309(5741), 1728-1732.

Shendure, J. et al. (2017). DNA sequencing at 40: past, present and future. Nature 550, 345-353. doi.org/10.1038/nature24286.

Smith, T. F., Waterman, M. S. (1981). Identification of common molecular subsequences. J. Mol. Biol. 25;147(1):195-7. doi.org/10.1016/0022-2836(81)90087-5.

Wang, Y. et al. (2022). Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348-1365. doi.org/10.1038/s41587-021-01108-x.

Watson, J., Crick, F. (1953). Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature 171, 737–738. doi.org/10.1038/171737a0.

DNA Sequencing

2025-01-06T15:56:59Z

Richert: Created page with "DNA Sequencing DNA sequencing is the process by which a nucleotide sequence in deoxyribonucleic acid (DNA) is determined. As such, it has applications in many fields of science, and is relevant for the development of gene therapy or the research into extinct species (Mathews, 2024). History of DNA Sequencing After the structure of the DNA double helix had been uncovered in 1953 (Watson & Crick, 1953), researchers turned their attention to determining the nucleotide seq..."

DNA Sequencing

DNA sequencing is the process by which a nucleotide sequence in deoxyribonucleic acid (DNA) is determined. As such, it has applications in many fields of science, and is relevant for the development of gene therapy or the research into extinct species (Mathews, 2024).

History of DNA Sequencing
After the structure of the DNA double helix had been uncovered in 1953 (Watson & Crick, 1953), researchers turned their attention to determining the nucleotide sequence of DNA. Early efforts included the sequencing of yeast transfer ribonucleic acid (tRNA) and the analysis of single stranded ends of bacteriophage DNA (Booth, 2022, Mathews, 2024).
In 1977, the identification of longer sequences of DNA became practicable with the advent of two new methods: The chemical cleavage procedure, developed by Allan Maxam and Walter Gilbert (Maxam & Gilbert, 1977), and the chain termination procedure, developed by Frederick Sanger (Sanger et al., 1977). These two methods are often referred to as 'first-generation sequencing' methods.

First-Generation Sequencing
The Maxam-Gilbert procedure involves a set of four chemical reactions, each able to cleave the glycosidic bond of a specific nucleobase. Guanine can be methylated using dimethyl sulfate, followed by cleavage of the glycosidic bond under heating. Adenine can be methylated using dimethyl sulfate, followed by glycosidic bond cleavage under incubation with dilute acid. Thymine can be cleaved via treatment with hydrazine, whereas cytosine must be treated with hydrazine at high salt concentrations. Treatment of the abasic site in the backbone with piperidine as base will lead to strand cleavage at this site. The resulting DNA fragments are of unique length and can be separated via polyacrylamide gel electrophoresis (PAGE). The order of the bands in the gel corresponds to the nucleotide sequence (Booth, 2022).
In contrast, Sanger sequencing utilizes a DNA polymerase to form a complementary strand to the template region of interest. The polymerase is provided with all four 2’-deoxynucleotides (dNTPs), and one type of 2’,3’-dideoxynucleotide (ddNTP). This ddNTP is a chain terminator - upon incorporation of a ddNTP into the growing DNA strand, extension cannot continue (Mathews, 2024). Thus, DNA strands of different lengths are formed, each terminating at the position of the ddNTP incorporation. Separation via PAGE, with separate lanes for each ddNTP-containing solution, yields the order of nucleobases in the strand.
Over the following decade, two innovations further increased the efficiency of the Sanger procedure. First, by marking the ddNTPs with different fluorescent labels, electrophoresis of all four ddNTPs could be carried out in a single capillary. Second, so-called shotgun sequencing enabled analysis of long sequences. By breaking up DNA via sonication or endonucleases, multiple overlapping fragments are created, so-called 'reads'. Reads were sequenced separately, and the full sequence assembled via analysis of the overlaps (Booth, 2022, Heather & Chain, 2016).
This enabled sequencing of complete genomes, culminating in the deciphering of the human genome in 2001 (International Human Genome Sequencing Consortium, 2004).
As noted by Shendure et al. (2017), the increasing amount of genetic data also necessitated the development of algorithms and databases. Noteworthy innovations include the Smith-Waterman Algorithm (Smith & Waterman, 1981), BLAST (Altschul et al., 1990) and GenBank (Benson et al., 1993).

Second-Generation Sequencing
Over the course of the 1990s, multiple technologies further increased the throughput achievable. They are generally referred to as 'Second-Generation Sequencing Technologies' or 'Next Generation Sequencing Technologies' (Liu et al., 2012). Many of these were also commercialized as stand-alone platforms. Notable platforms include the pyrosequencing platform of 454 Life Sciences, the Illumina platform (initially Solexa), the SOLiD system from Applied Biosystems and the Ion Torrent technology of Life Technologies (Heather & Chain, 2016). The following is a brief description of each of the platforms, with an attempt to highlight advantages and disadvantages.
The pyrosequencing workflow begins by attaching single stranded (ss) DNA fragments to beads and amplifying them via emulsion PCR (emPCR) (Heather & Chain, 2016). Then, one type of dNTP at a time is washed over the beads, together with a DNA polymerase. If the dNTP is incorporated into the strand, pyrophosphate (PPi) is released. Pyrophosphate is used by ATP sulfurylase to produce ATP, which in turn is converted by the luciferase to produce light. Lastly, apyrase degrades ATP and dNTPs in between the addition of bases. Thus, if a flash of light can be detected, a dNTP has been incorporated into the sequence (Ahmadian et al., 2006).
Pyrosequencing can be used for de novo gene assembly, boasting long read lengths and high sequencing speeds. However, the length of homopolymeric regions, (that is, regions which contain repeats of just one nucleotide) is difficult to determine using pyrosequencing (Mathews, 2024). Also, the cost per base is comparatively high (Liu et al., 2012).
The acronym SOLiD is shorthand for 'Sequencing by Oligo Ligation Detection' (Heather & Chain, 2016). Again, ssDNA fragments are amplified in emPCR and attached to a solid support. Then, they are exposed to different degenerate DNA oligomers. Each oligomer carries a fluorophore, the colour of which corresponds to one base of the oligomer. The other bases are degenerate and can bind to any other base. A T4 DNA ligase ligates the oligomer to the primer, and via detection of the fluorescence, the identity of the ligated base can be determined (Shendure et al., 2005).
Accuracy of the SOLiD method is very high, making it useful for resequencing of genomes, for example to detect single nucleotide polymorphisms. However, read lengths are short, making assembly of longer sequences difficult (Liu et al., 2012).
The Ion Torrent procedure also begins by amplifying ssDNA fragments on a bead via emPCR. Beads are sequentially exposed to dNTPs, one type at a time, and a DNA polymerase extends the strands. Every time a triphosphate group is hydrolyzed, a proton is released, which changes the pH around the bead. This is detected and digitized by a sensor, indicating incorporation of a certain type of dNTP (Rothberg et al., 2011). While this method is fast, has low cost per base and is easy to scale, but accuracy in homopolymeric regions is low (Mathews, 2024).
In Illumina sequencing, DNA fragments are immobilized and amplified on a solid surface in a process called 'bridge amplification'. Then, fragments are exposed to dNTPs, each base marked by a different fluorescent molecule. The 3’-OH group of the dNTPs is protected by an azidomethyl group, leading to chain termination upon incorporation. So, only a single dNTP can be incorporated at a time. The type of dNTP can now be identified by four-colour imaging. Lastly, fluorescent groups and the 3’ protecting groups are cleaved, so that a new dNTP can be incorporated. This process can be repeated for read lengths of up to 300 bases (Booth, 2022).
The Illumina protocol allows for accurate, high throughput sequencing of DNA. Read lengths are short, compared to the other platforms (Liu et al., 2012). Still, as of September 2024, the Illumina method is the most common sequencing method in the world (Mathews, 2024).

Third-Generation Sequencing
While second-generation sequencing methods are improved, as compared to first generation methods, in many ways, they still have some shortcomings.
Firstly, all second-generation platforms rely on DNA amplification. This not only adds a layer of complexity but can also introduce errors and biases (Pinard et al., 2006). Secondly, read lengths of all platforms are less than 1000 bp (Mathew, 2024). The human genome contains repeating regions of up to 104 bp, meaning these regions cannot be sequenced with second-generation methods (Li & Freudenberg, 2014).
Third-generation sequencing technologies try to address these problems. They rely on single molecule sequencing, meaning sequencing of long reads without previous amplification (Heather & Chain, 2016). Notable technologies include the single-molecule real-time sequencing (SMRT) method from Pacific Biosciences (PacBio) and nanopore sequencing from Oxford Nanopore Technologies (ONT) (Booth, 2022).
PacBio’s SMRT utilizes so-called zero-mode waveguides (ZMWs), which are essentially wells in a metal film with a diameter of less than 100 nm. Light with much longer wavelengths than 100 nm will decay exponentially in the well, so that fluorophore illumination in only a small part of the well can be detected (Heather & Chain, 2016). This is exploited by attaching a DNA polymerase to the bottom of the well and providing it with a single, long DNA fragment. Then, a mixture of dNTPs marked with different fluorophores is added. As a dNTP is incorporated into the strand, a fluorescence signal can be detected at the bottom of the well, before the fluorescent label is cleaved off and diffuses into the bulk of the solution (Booth, 2022). This not only provides information about the type of nucleotide added, but also gives real time data. The time-course data can contain additional information about modifications of DNA, like epigenetic methylations (Liu et al., 2012).
Overall, SMRT sequencing provides ultra-long reads of up to 105 bases, at accuracies of repeated reads similar to Illumina sequencing. However, raw error rates are still high (Mathews, 2024).
In ONT’s nanopore sequencing, a motor protein pulls ssDNA through a nanopore in a membrane. Applying a constant voltage drives an ionic current through the pore. Conductivity of the pore changes, depending on the nucleobases that pass through. Thus, the current changes over time, which can be measured. Different currents are characteristic for different DNA sequences (Deamer et al., 2019). Nucleobase sequences as well as epigenetic modifications may be detected.
Using ONTs nanopore sequencing, read lengths of up to 2.273⋅106 bp have been reported. ONTs smallest sequencers, the “MinIONs”, are portable, allowing for decentralized real-time sequencing. This has been utilized in real time surveillance of disease outbreaks around the world (Wang et al., 2021). However, output data analysis is complicated, and error rates are still comparatively high (Mathews, 2024).
Both PacBio’s SMRT and ONTs nanopore sequencing are still being optimized, and the introduction of new computational workflows and improved chemistry is to be expected, further reducing error rates and complexity. Probably, third-generation sequencing methods will replace second-generation sequencing in most applications (Athanasopoulou et al., 2022).

References
Ahmadian, A. et al. (2006). Pyrosequencing: history, biochemistry and future. Clin. Chim. Acta 363(1-2), 83-94. doi.org/10.1016/j.cccn.2005.04.038.
Altschul, S. F. et al. (1990). Basic local alignment search tool. J. Mol. Biol. 5;215(3):403-10. doi.org/10.1016/S0022-2836(05)80360-2.
Athanasopoulou, K. et al. (2022). Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics. Life 12(1), 30. doi.org/10.3390/life12010030.
Benson, D. et al. (1993). GenBank. Nucleic Acids Res. 21(13):2963-2965. doi.org/10.1093/nar/21.13.2963.
Booth, M. J. (2022). DNA and RNA sequencing. In: Blackburn, M. G. et al. (eds.) Nucleic Acids in Chemistry and Biology. 4th Edition, The Royal Society of Chemistry, London.
Deamer, D. et al. (2019). Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518-524. doi.org/10.1038/nbt.3424.
Heather, J. M., Chain, B. (2016). The sequence of sequencers: The history of sequencing DNA. Genomics 107(1), 1-8. doi.org/10.1016/j.ygeno.2015.11.003.
International Human Genome Sequencing Consortium (2004). Finishing the euchromatic sequence of the human genome. Nature 431, 931–945. doi.org/10.1038/nature03001.
Li, W., Freudenberg, J. (2014). Mappability and read length. Front. Genet. 5:381. doi.org/10.3389/fgene.2014.00381.
Liu, L. et al. (2012). Comparison of Next-Generation Sequencing Systems. J. Biomed. Biotechnol. 1, 251364. doi.org/ 10.1155/2012/251364.
Mathews, A. (2024). DNA Sequencing: A Brief History. In: Abdurakhmonov, I. Y. (eds.). DNA Sequencing – History, Present and Future. Intech Open, Rijeka. doi.org/10.5772/intechopen.1007844.
Maxam, A. M., Gilbert, W. (1977). A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA 74(2):560-4. doi.org/10.1073/pnas.74.2.560.
Pinard, R. et al. (2006). Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics 7, 216. doi.org/10.1186/1471-2164-7-216.
Rothberg, J. M. et al. (2011). An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348-52. doi.org/10.1038/nature10242.
Sanger, F. et al. (1977). DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74(12):5463-7. doi.org/10.1073/pnas.74.12.5463.
Shendure, J. et al. (2005). Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome. Science 309(5741), 1728-1732.
Shendure, J. et al. (2017). DNA sequencing at 40: past, present and future. Nature 550, 345-353. doi.org/10.1038/nature24286.
Smith, T. F., Waterman, M. S. (1981). Identification of common molecular subsequences. J. Mol. Biol. 25;147(1):195-7. doi.org/10.1016/0022-2836(81)90087-5.
Wang, Y. et al. (2022). Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348-1365. doi.org/10.1038/s41587-021-01108-x.
Watson, J., Crick, F. (1953). Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature 171, 737–738. doi.org/10.1038/171737a0.

History of Nucleic Acid Chemistry

2024-09-10T09:26:34Z

Richert:

== 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:
[[File:Guanine Cytosine base pair red bond.png|center|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|center|thumb|Depiction of the A:T base pair.]]
<br><br>
'''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

2024-08-08T16:48:20Z

Richert:

Organocapture

2024-07-31T09:33:03Z

Richert: Created page with " '''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..."

'''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'''

B. List, R. A. Lerner, C. F.Barbas III. Proline-catalyzed direct asymmetric aldol reactions. ''J. Am. Chem. Soc.'' '''2000''', ''122'', 2395–2396.

D. W. C. MacMillan, The advent and development of organocatalysis. ''Nature'' '''2008''', ''455'', 304–308.

'''Reference Organocapture'''

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.

Aptamers

2024-07-30T08:11:30Z

Richert: Created page with " '''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''' A. D. Ellington, J. W. Szostak, In vitro selection of RNA molecules that bind specific ligands. ''Nature'' '''1990''', ''346'', 818-822. D. Irvine, C. Tuerk, L. Gold, Selexion - Systematic evolution..."

'''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'''

A. D. Ellington, J. W. Szostak, In vitro selection of RNA molecules that bind specific ligands. ''Nature'' '''1990''', ''346'', 818-822.

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.

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.

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

Prebiotic Chemistry

2024-07-26T11:51:33Z

Richert: Created page with " '''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''' R. Lohrmann, L.E.Orgel, Prebiotic activation processes. ''Nature''. '''1973''', ''244'', 418-420. S.A. B..."

'''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'''

R. Lohrmann, L.E.Orgel, Prebiotic activation processes. ''Nature''. '''1973''', ''244'', 418-420.

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.

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

C. De Duve, The onset of selection. ''Nature'' '''2005''', ''433'', 581–582.

J.W. Szostak, The eightfold path to non-enzymatic RNA replication. ''J. Systems Chem.'' '''2012''', ''3'', 2.

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.

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.

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

Solution-Phase Oligonucleotide Synthesis

2024-07-23T08:44:10Z

Richert: Created page with " '''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. Rec..."

'''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.

'''Classical Papers'''

a) 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.

b) 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.

'''Recent Papers'''

a) 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.

b) 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.

c) 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. link

d) V. Damakoudi, T. Feldner, E. Dilji, A. Belkin, C. Richert, Hybridization networks of mRNA and branched RNA hybrids. ''ChemBioChem'' '''2020''', ''22'', 924-930.

UV-Melting Curves

2024-07-09T12:19:29Z

Richert:

'''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''

Breslauer, K.J. Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. ''Methods Enzymol.'' '''1995''', ''259'', 221-242.

''Paper mentioning the Meltwin software for extracting enthalpy and entropy from melting curves''

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.

''Application of melting curves for DNA duplexes''

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

Neighbor Exclusion Principle

2024-07-09T11:45:53Z

Richert: Created page with " '''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''' C. Robledo-Luiggi, W.D. Wilson, E. Pares, M. Vera, C.S. Martinez, D. Santiago, Partial intercalation with DNA of pept..."

'''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'''

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.

DOI: 10.1039/C5SC03740A (Edge Article)

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.

Main Page

2024-07-08T14:56:59Z

Richert: Formatting change

== Welcome ==

'''Nucleowiki is an encyclopedia for nucleic acid chemistry-related topics, maintained by members of the [[DNG|"Deutsche Nucleinsäurechemie-Gemeinschaft" (DNG)]].'''

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]]

Isostable DNA Duplexes

2024-07-06T18:16:54Z

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..."

'''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.

Branched Oligonucleotide Hybrids

2024-07-04T11:26:35Z

Richert: Created page with " '''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 s..."

'''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''

a) P. W. K. Rothemund, Folding DNA to create nanoscale shapes and patterns. ''Nature'' '''2006''', ''440'', 297-302.

b) Jones, M. R.; Seeman, N. C.; Mirkin, C. A. Programmable materials and the nature of the DNA bond. ''Science'' '''2015''', ''347'', 840.

''Branched oligonucleotide hybrids''

a) 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.

b) 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.

c) 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.

d) 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.

e) A. Schwenger, T.P. Jurkowski, C. Richert, Capturing and stabilizing folded proteins in lattices formed with branched oligonucleotide hybrids. ''ChemBioChem'' '''2018''', ''19'', 1523-1530.

f) V. Damakoudi, T. Feldner, E. Dilji, A. Belkin, C. Richert, Hybridization networks of mRNA and branched RNA hybrids. ''ChemBioChem'' '''2020''', ''22'', 924-930.

Chemical Primer Extension

2024-07-04T10:01:42Z

Richert:

'''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''

K. B. Mullis, The polymerase chain reaction (Nobel Lecture). ''Angew. Chem. Int. Ed. Engl.'' '''1994''', ''33'', 1209-1213.

''Chemical Primer Extension''

a) 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.

b) J. A. Rojas Stütz, E. Kervio, C. Deck, C. Richert, Chemical primer extension - individual steps of spontaneous replication. ''Chem. Biodiv.'' '''2007''', ''4'', 784-802.

c) 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.

Chemical Primer Extension

2024-07-04T10:01:17Z

Richert: Created page with " '''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 in..."

UV-Melting Curves

2024-07-02T06:17:50Z

Richert:

'''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 01. 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''

Breslauer, K.J. Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. ''Methods Enzymol.'' '''1995''', ''259'', 221-242.

''Paper mentioning the Meltwin software for extracting enthalpy and entropy from melting curves''

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.

''Application of melting curves for DNA duplexes''

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

UV-Melting Curves

2024-07-02T06:16:54Z

Richert:

'''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 01. 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 acquistion of UV-melting curves.

'''References'''

''Overview''

Breslauer, K.J. Extracting thermodynamic data from equilibrium melting curves for oligonucleotide order-disorder transitions. ''Methods Enzymol.'' '''1995''', ''259'', 221-242.

''Paper mentioning the Meltwin software for extracting enthalpy and entropy from melting curves''

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.

''Application of melting curves for DNA duplexes''

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

UV-Melting Curves

2024-06-30T14:28:35Z

Richert: Created page with " '''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 d..."

Quantitative MALDI-TOF MS of Oligonucleotides

2024-06-29T16:42:01Z

Richert:

'''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''

a) M. Karas, F. Hillenkamp, Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. ''Anal. Chem.'' '''1988''', ''60'', 2299–2301.

b) Berkenkamp, S.; Kirpekar, F.; Hillenkamp, F. Infrared MALDI mass spectrometry of large nucleic acids. ''Science'' '''1998''', ''281'', 260-262.

c) 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.

d) 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

''<br />
''Paper on quantitative MALDI-TOF MS of oligonucleotides (cited by later papers on the topic)''

a) D. Sarracino, C. Richert, Quantitative MALDI-TOF Spectrometry of Oligonucleotides and a Nuclease Assay. ''Bioorg. Med. Chem. Lett.,'' '''1996''', ''6'', 2543-2548.

b) 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.

c) 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.

Quantitative MALDI-TOF MS of Oligonucleotides

2024-06-25T09:08:26Z

Richert:

Quantitative MALDI-TOF MS of Oligonucleotides

2024-06-25T09:07:38Z

Richert:

History of Nucleic Acid Chemistry

2024-06-25T05:58:48Z

Richert: Created page with " '''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.<sup>[1]</sup> Miescher worked at the University of Tübingen at the time, and did not know what the function of nuclein was. '''References''' [1] R. Dah..."

'''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.<sup>[1]</sup> Miescher worked at the University of Tübingen at the time, and did not know what the function of nuclein was.

'''References'''

[1] R. Dahm, Friedrich Miescher and the discovery of DNA. ''Devel. Biol.'' '''2005''', ''278'', 274-288. DOI:10.1016/j.ydbio.2004.11.028

Vorbrüggen Base Introduction Reaction

2024-06-24T08:14:13Z

Richert: Created page with " '''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, ty..."

'''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'''

a) H. Vorbrüggen, K. Krolikiewicz, B. Bennua, Nucleoside synthesis with trimethylsilyl triflate and perchlorate as catalysts. ''Chem. Ber''. '''1981''', ''114'', 1234-1255.

b) H. Vorbrüggen, B. Bennua, A new simplified nucleoside synthesis. ''Chem. Ber.'' '''1981''', ''114'', 1279-1286.

c) B. Bennua-Skalmowski, K. Krolikiewicz, H. Vorbrüggen, A new simple nucleoside synthesis. ''Tetrahedron Lett.'' '''1995''', ''36'', 7845-7848.

Quinolone DNA complexes

2024-06-23T06:10:45Z

Richert: Created page with " '''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''' a) J. Tuma, W. H. Connors, D. H. Stitelman, C. Richert, On the Effect of Covalently Appended Quinolones on..."

'''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'''

a) 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.

b) 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.

Quantitative MALDI-TOF MS of Oligonucleotides

2024-06-23T06:03:54Z

Richert: Created page with "'''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 disad..."

Antisense Oligonucleotides

2024-06-19T14:46:01Z

Richert: Created page with " '''Antisense Oligonucleotides''' Oligodeoxynucleotides that block translation of specific mRNAs by hybridizing to complementary sequences are called antisense oligonucleotides. They are one class of therapeutic oligonucleotides. '''Seminal Papers''' (a) 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. (b) Ste..."

'''Antisense Oligonucleotides'''

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

'''Seminal Papers'''

(a) 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.

(b) 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

'''Homepage of the Oligonucleotide Therapeutics Society (OTS)'''

www.oligotherapeutics.org

C-Nucleosides

2024-06-16T13:54:01Z

Richert: Created page with "'''''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. Review M. Hocek, ''C''-Nucleoside..."

'''''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.

Review

M. Hocek, ''C''-Nucleosides: synthetic strategies and biological applications. ''Chem. Rev''. '''2009''', ''109'', 6729–6764.

Synthetic Papers

1. 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.

2. T. Gniech, C. Richert, Diastereoselective synthesis of pyridone ''ribo''-''C''-nucleosides via Heck reaction and oxidation. ''Eur. J. Org. Chem.'' '''2024''', e202400342.

Triplex

2024-06-16T12:57:07Z

Richert: Created page with "'''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. Classical Paper Felsenfeld, G.; Rich, A. Studies on the formation of two- and three-stranded polyribonucleotides. ''Biochim. Biophys. Acta.'' '''1957''', ''26'', 457-68. Review Thuong, N.T.; Hélène, C. Sequence-specific recognition and modification of dou..."

'''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.

Classical Paper

Felsenfeld, G.; Rich, A. Studies on the formation of two- and three-stranded polyribonucleotides. ''Biochim. Biophys. Acta.'' '''1957''', ''26'', 457-68.

Review

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

Selected Papers on Applications

1. C. Kröner, M. Röthlingshöfer, C. Richert, Designed nucleotide binding motifs. ''J. Org. Chem.'' '''2011''', ''76'', 2933-2936.

2. 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.

3. S. Vollmer, C. Richert, DNA triplexes that bind several cofactor molecules. ''Chem. Eur. J.'' '''2015''', ''21'', 18613-18622.

4. 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.

DNG

2024-06-14T16:13:54Z

Richert:

Deutsche Nucleinsäurechemiegemeinschaft e.V. ('''DNG''') is a scientific society focused on nucleic acid chemistry.

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

DNG-Doktorandenseminar

2024-06-14T12:36:13Z

Richert: Created page with " The Graduate School Symposia of the DNG, with presentations by graduate students and invited experts, were formerly known as "DNG-Doktorandenseminare" and are now known as "DNG Graduate Schools". The following is a list of the meetings. The venue is Bad Herrenalb in Baden-Württemberg, in the Northern part of the Black Forest. VII. Doktorandenseminar Nucleinsäurechemie 19.-20.09.2024 VI. Doktorandenseminar Nucleinsäurechemie 03. - 04.10.2022 V. Doktorandenseminar..."

The Graduate School Symposia of the DNG, with presentations by graduate students and invited experts, were formerly known as "DNG-Doktorandenseminare" and are now known as "DNG Graduate Schools". The following is a list of the meetings. The venue is Bad Herrenalb in Baden-Württemberg, in the Northern part of the Black Forest.

VII. Doktorandenseminar Nucleinsäurechemie 19.-20.09.2024

VI. Doktorandenseminar Nucleinsäurechemie 03. - 04.10.2022

V. Doktorandenseminar Nucleinsäurechemie 01. - 02.10.2020

IV. Doktorandenseminar Nucleinsäurechemie 20. - 21.09.2018

III. Doktorandenseminar Nucleinsäurechemie 22. - 23.09.2016

II. DNG-Doktorandeseminar 29.-30.09.2014

I. DNG Doktorandenseminar 01.-02.10.2012

Nucleinsäurechemietreffen

2024-06-14T12:30:01Z

Richert:

The symposia of the DNG with formal talks by PIs are called "Nucleinsäurechemietreffen".

The following Nucleinsäurechemietreffen have taken place so far.

XI. Nucleinsäurechemietreffen 2023 (Würzburg)

X. Nucleinsäurechemietreffen 2021 (Bad Herrenalb)

IX. Nucleinsäurechemietreffen 2019 (Saarbrücken)

VIII. Nucleinsäurechemietreffen 2017 (Mainz)

VII. Nucleinsäurechemietreffen 2015 (Berlin)

VI. Nucleinsäurechemietreffen 2013 (Greifswald)

V. Nucleinsäurechemietreffen 2011 (Frankfurt)

IV. Nucleinsäurechemietreffen 2009 (Regensburg)

III. Nucleinsäurechemietreffen 2008 (Stuttgart)

II. Nucleinsäurechemietreffen 2006 (Göttingen)

I. Nucleinsäurechemietreffen 2004 (Karlsruhe)

Nucleinsäurechemietreffen

2024-06-14T12:28:50Z

Richert: Created page with " The symposia of the DNG with formal talks by PIs are called Nucleinsäurechemietreffen. The following Nucleinsäurechemietreffen have taken place so far. XI. Nucleinsäurechemietreffen 2023 (Würzburg) X. Nucleinsäurechemietreffen 2021 (Bad Herrenalb) IX. Nucleinsäurechemietreffen 2019 (Saarbrücken) VIII. Nucleinsäurechemietreffen 2017 (Mainz) VII. Nucleinsäurechemietreffen 2015 (Berlin) VI. Nucleinsäurechemietreffen 2013 (Greifswald) V. Nucleinsäureche..."

The symposia of the DNG with formal talks by PIs are called Nucleinsäurechemietreffen.

The following Nucleinsäurechemietreffen have taken place so far.

XI. Nucleinsäurechemietreffen 2023 (Würzburg)

X. Nucleinsäurechemietreffen 2021 (Bad Herrenalb)

IX. Nucleinsäurechemietreffen 2019 (Saarbrücken)

VIII. Nucleinsäurechemietreffen 2017 (Mainz)

VII. Nucleinsäurechemietreffen 2015 (Berlin)

VI. Nucleinsäurechemietreffen 2013 (Greifswald)

V. Nucleinsäurechemietreffen 2011 (Frankfurt)

IV. Nucleinsäurechemietreffen 2009 (Regensburg)

III. Nucleinsäurechemietreffen 2008 (Stuttgart)

II. Nucleinsäurechemietreffen 2006 (Göttingen)

I. Nucleinsäurechemietreffen 2004 (Karlsruhe)

DNG

2024-06-14T12:23:20Z

Richert:

Deutsche Nucleinsäurechemiegemeinschaft e.V. ('''DNG''') is a scientific society focused on nucleic acid chemistry.

The URL of its homepage is: https://dnarna.de

DNG

2024-06-14T12:00:16Z

Richert: Created page with " Deutsche Nucleinsäurechemiegemeinschaft e.V. (DNG) is a scientific society focused on nucleic acid chemistry. The URL of its homepage is: https://dnarna.de"

Deutsche Nucleinsäurechemiegemeinschaft e.V. (DNG) is a scientific society focused on nucleic acid chemistry.
The URL of its homepage is: https://dnarna.de

Sandbox

2024-06-14T11:53:44Z

Richert:

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

Sandbox

2024-06-14T11:51:55Z

Richert:

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

Sandbox

2024-06-14T11:51:08Z

Richert: Created page with " Test message."

Test message.