Talk:G-quadruplex

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Introduction edit

The placement and bonding to form G-quadruplexes are not random and serve very unique functional purposes. The quadruplex structure is further stabilized by the presence of a cation, especially potassium, which sits in a central channel between each pair of tetrads.[2] They can be formed of DNA, RNA, LNA, and PNA, and may be intramolecular, bimolecular, or tetramolecular. Since there was no page for tetramolecular I decided to take out the function of navigating to a link that wasn't there. Crh15j (talk) 15:33, 24 February 2017 (UTC)Crh15jCrh15j (talk) 15:33, 24 February 2017 (UTC)[reply]

sequence

d(GGTTAG) - is there a reason for this form of noting the sequence? a) as a sidenote d(sequence) probably means that it is the deoxy form of the sequence - will this be understood by the casual reader? b) why GGTTAG and not e.g. TTAGGG - it will be the Gs that form the quadruplex, so if the sequence repeats anyways, why split up the Gs? Iridos 01:40, 11 May 2007 (UTC)[reply]

a) It's the standard nomenclature, and I don't see how it could be massively improved b) There is - the enzyme telomerase, which elongates telomeres, contains an inbuilt RNA template, that adds the repeat d(GGTTAG) many times. Hence there is a starting point for the sequence. Jlh29 16:15, 7 June 2007 (UTC)[reply]

Sorry for the "drive-by-commenting" back then. As to a) I know it is standard for denoting "deoxy" and would not have objected in a scientific publication. For readers of an article in Wikipedia, I would not presume the same level of proficiency, though. To improve on it, one could either remove it altogether — and include a word that teleomeric repeats are found in DNA, which would imply the d(), or possibly link the d( to ... perhaps deoxynucleotide — well, actually somewhere that explains what it means. Such a link might violate linking conventions, so I would prefer the first solution.

b) fair enough. Then it is inconsistent, though, that the introduction to Telomerase starts with: "Telomerase is an enzyme that adds DNA sequence repeats ("TTAGGG" in all vertebrates)" (the image next to it even shows a different sequence).

Iridos (talk) 17:46, 5 July 2011 (UTC)[reply]

repeat edits/reversion

Could 202.46.222.112 and 121.247.190.198 please cease reinserting papers - wikipedia is not pubmed, and does not need multiple listings of all papers published by their group! If they would like to suggest a change, can they discuss it here first.

Potential functions

Could anyone write a few lines on what these structures might actually do? At least hypothetical ideas. --David Munch (talk) 12:38, 22 September 2011 (UTC)[reply]

I've added a (very) brief starting point, which I intend to improve upon over the next few weeks/months Sarahburge (talk) 17:40, 30 November 2011 (UTC)[reply]

Monovalent cations

I removed the word "monovalent" from the introductory paragraph; quadruplexes can happily form with divalent cations; calcium and strontium cations have both been seen in quadruplexes.^[1] Sarahburge (talk) 17:31, 7 November 2011 (UTC)[reply]

References

^ Lee, M. P.; Parkinson, G. N.; Hazel, P; Neidle, S (2007). "Observation of the coexistence of sodium and calcium ions in a DNA G-quadruplex ion channel". Journal of the American Chemical Society. 129 (33): 10106–7. doi:10.1021/ja0740869. PMID 17661470.

Possible source

Amos, Jonathan (20 January 2013). "'Quadruple helix' DNA seen in human cells". BBC. Retrieved 21 January 2013.

Chris857 (talk) 01:19, 21 January 2013 (UTC)[reply]

Hoogsteen Hydrogen Bonding

I think this should be more detailed. There is an excerpt that I found from a research article that states the following: "The building blocks of G-quadruplexes are G-quartets that are formed through a cyclic Hoogsten hydrogen-bonding arrangement of four guanines with each other. The planar G-quartets stack on top of one another forming four-stranded helical structures. G-quadruplex formation is driven by monovalent cations such as Na+ and K+, and hence physiological buffer conditions favour their formation" [1] Sydharrington (talk) 21:58, 16 February 2017 (UTC)[reply]

External Links

After reading the a majority of the article "G-quadruplexes and their regulatory roles in biology" from Daniela Rhodes and Hans J. Lipps published in Nucleic Acids Research, I found that it would make a great external link for people to go. It provides clear and concise examples that was very helpful in understanding the structure, function and formation of the G-quadruplex. ^[1] Sydharrington (talk) 22:14, 16 February 2017 (UTC)[reply]

One of the weaker sections within the G-quadruplex wikipedia was on the Quadruplex prediction techniques, a review which may assist in offering more information on the techniques used is "Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes" by Julian Leon Huppert. Offering further details on the tools utilized to perform the predictions and how they function may benefit the page. ^[2]Kevinj7797 (talk) 02:06, 17 February 2017 (UTC)[reply]

References

^ Daniela Rhodes, Hans J. Lipps; G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res 2015; 43 (18): 8627-8637. doi: 10.1093/nar/gkv862
^ Huppert, Julian Leon (23 June 2008). "Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes". Chemical Society Reviews. doi:10.1039/B702491F.

References

The reference's <ref>Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2006). "Quadruplex DNA: sequence, topology and structure". Nucleic Acids Research. 34 (19): 5402–5415. doi:10.1093/nar/gkl655. PMC 1636468Freely accessible. PMID 17012276. <ref>Neidle & Balasubramanian, ed. (2006). Quadruplex Nucleic Acids. ISBN 0-85404-374-8.Cite error: The opening <ref> tag is malformed or has a bad name (see the help page). are out of date and if clicked on will not bring up any article. azilberfarb (talk) 16 February 2017 (UTC)

g-quadruplex location

These structures are four stranded and occur naturally in nature. They are normally located near the ends of the chromosomes or the better known as the telomeric regions and in transcriptional regulatory regions of multiple oncogenes.

Han, Haiyong (2000). "G-quadruplex DNA: a potential target for anti-cancer drug design". TiPS. 21: 136–142 – via Google Scholar.

-Joshua Tijerino, Peter Turner, Logan Turner, Nicolas Guevara

[Lee2007-1] Lee, M. P.; Parkinson, G. N.; Hazel, P; Neidle, S (2007). "Observation of the coexistence of sodium and calcium ions in a DNA G-quadruplex ion channel". Journal of the American Chemical Society. 129 (33): 10106–7. doi:10.1021/ja0740869. PMID 17661470.

[2] Daniela Rhodes, Hans J. Lipps; G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res 2015; 43 (18): 8627-8637. doi: 10.1093/nar/gkv862

[3] Huppert, Julian Leon (23 June 2008). "Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes". Chemical Society Reviews. doi:10.1039/B702491F.

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