User talk:Hankwbass/Group 2

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DNA review

For the section Supercoiling I would go into more detail about the process of supercoiling and what its purpose is. For instance, I woudl include information found about DNA packing: At the primary level of compaction, the DNA is wrapped around a group of special proteins called histones. When DNA wraps around a group of histones, it forms a nucleosome. You can think of the system as DNA "thread" wound around a protein "spool".[1] and So the process of fitting all of that DNA into a tiny cell nucleus begins with wrapping the DNA around histones into a nucleosome. But it doesn't end there -- the chain of nucleosomes coils around a central axis to get even more compact. [2].

Sydharrington (talk) 21:18, 15 February 2017 (UTC)

HWBsay: that is good info -there is chromatin & nucleosomes further down the page - looked like you commented on DNA page, not G-quadruplex page, but that's OK - Hankwbass (talk) 03:35, 24 February 2017 (UTC)

G-quadruplex

Leave your notes and improvement ideas here

In this section, I would include (even if just one sentence) about the Hoogsteen hydrogen bonding and say why this bonding occurs (is it due to the elements involved or does it create a stronger bond?). I would mention the charges on the bonds in the center of the helix and further discuss why the cation stabilizes those charges. In addition, I would mention the history or discovery of G-quadruplexes, who discovered them and when, and why they are beneficial or not beneficial (with citations of course). --Akm14t (talk) 21:50, 21 February 2017 (UTC)

HWBsay: which citations would you recommend @Akm14t ? Hankwbass (talk) 04:12, 24 February 2017 (UTC)

@Hankwbass I recommend: and Akm14t (talk) 22:07, 23 March 2017 (UTC)

I feel like this page had many grammatical errors and could be more concise when it comes to getting across their ideas. — Preceding unsigned comment added by Joshteehee (talkLft15 (talk) 18:46, 24 February 2017 (UTC) • contribs) 23:47, 16 February 2017 (UTC)

HWBsay: which errors ? Hankwbass (talk) 04:15, 24 February 2017 (UTC)

Within the section Ligands which bind quadruplexes I believe it would be beneficial to insert a link to the ligand wikipedia to ensure that the reader understands what they are prior to reading further. --Kevinj7797 (talk) 01:35, 17 February 2017 (UTC)

HWBsay: good - did you do the tutorial on how to link to wiki pages? if so, can you drop in a draft edit w/ that addition? thanks Hankwbass (talk) 04:15, 24 February 2017 (UTC)

This page definitely needs to add a considerable amount of citations for the information it provides. In the Telomeric Quadruplexes section it does not give citations for any of the information save the first sentence. I researched myself and discovered a journal article supporting the majority of points made. This journal article gives details of studying quadruplexes using NMR. It also provides information on the RNA repeat sequences and telomerase activity in the presence of quadruplexes. Charliebuerk (talk) 02:40, 17 February 2017 (UTC)

HWBSay: @Charliebuerk, good citation - that's more about the telomeric RNA (not DNA), but G4-relevant.Hankwbass (talk) 04:25, 24 February 2017 (UTC)

The article "Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases" is a strong external source that could go in depth on non-B-form DNA, in which case it goes in depth on why it occurs, how it occurs and different examples of non-B-form DNA. The source is relevant because it has a direct connection to G-Quadruplex which is non-B-form. Kevinj7797 (talk) 02:48, 17 February 2017 (UTC)

HWBsay: @Sharma, that's a good publication - it's primarily on one class of enyzme thought to "unfold" G4 structures - a big question in the G4 field. Hankwbass (talk) 04:25, 24 February 2017 (UTC)

I recommend like a bigger emphasis of G-Quadruplex functions like its function as a regulator should be added Cubandrew (talk) 21:57, 23 February 2017 (UTC)Andrew Delgado

HWBsay: @Cubandrew, that's a good paper -also suggested by another user - i will try to get it added - 1st section citation re: biological functions Hankwbass (talk) 04:25, 24 February 2017 (UTC)

I think it would be important to discuss the G4 helicase prteins under the Telomeric quadruplexes section, since cancer is already discussed in the section, G4 helicase proteins do have a mutational history that could lead to cancer, and assist with with undwinding DNA and RNACubandrew (talk) 23:22, 2 March 2017 (UTC)Andrew Delgado

I feel like this section needs to multiple sources. The page says that G-quadruplexes are secondary structures, but doesn't explain how G- quadruplex sites have provided compelling new data on the DNA secondary structure. This source explains how G-quadruplex DNA can modulate transcription, replication and also genome integrity. http://www.sciencedirect.com/science/article/pii/S0959437X13001494. 2:27, 28 March 2017 (UTC) Sushen Prashanth

G-Quadruplex

In the introduction section, the text states that G-Quadruplex are tertiary structures but gives no citation to back this up. Upon researching I found they are considered secondary structures I would suggest editing this and giving the citation. Brookemcfarland (talk) 01:43, 17 February 2017 (UTC)

Oddly enough this article supports the case that G-Quadruplex are secondary structures, and is cited. The article "DNA secondary structures: stability and function of G-quadruplex structures" also describes how G-Quadruplex are non-B-form which is mentioned in external articles but not in the text. The Wikipedia page may benefit from having this information incorporated as it displays the deviation from the canonical structure proposed by Watson and Crick.Kevinj7797 (talk) 02:40, 17 February 2017 (UTC)

A better visual for the structure of the g-quartet would be the one included in our powerpoint by Capra et. al. 2010, as it is much easier to understand.Brookemcfarland (talk) 02:24, 17 February 2017 (UTC)

I agree with both of your posts and believe they should be implemented in the draft Kevinj7797 (talk) 04:16, 17 February 2017 (UTC)

The section in the introduction that refers to "intra, bi, or tetramolecular" should be modified to add intermolecular as well. A source I found says the guanines that make up the G-quadruplex can come from many stands of nucleic acid, which is referred to as inter-molecular. Brookemcfarland (talk) 02:34, 17 February 2017 (UTC)

HWBsay: @Brookemvarland - yes, intermolecular should (and sort of is) included - "bi, or tetamolecular" are both intermolecular by definition. - but a better wording could be "intramolecular (single stranded) or intermolecular (2, 3, or 4 molecules/strands)" Code On! Hankwbass (talk) 14:27, 24 February 2017 (UTC)

In this section the text says that G-quadruplex are rich in guanine but makes no mention of hydrogen bonds and the amount in the structure. I believe this needs to be added emphasizing the importance of the rich guanine content. I believe saying there are a high amount of hydrogen bonds due to Guanine is key in understanding G-quadruplex. Sushenprashanth (talk) 23:47, 17 April 2017 (UTC) 7:47 17th April 2017 (UTC) Sushen Prashanth

This section also makes no mention of the damages to G-quadruplex, the section makes no mention of how the structure reacts to UV radiation. I wonder if the hydrogen bonds in G-quadruples would denature at 260nm as semiconservative DNA does? Or does G-quadruplex have a different wavelength were its hydrogen bonds break down? I would add a section on this to improve the quality of this page. 10:17 24th April 2017 (UTC) Sushen Prashanth — Preceding unsigned comment added by Sushenprashanth (talk • contribs)

G-Quadruplex Topology

This section needs more sources! I feel uneasy reading this source due to the fact that there is information listed but where does it come from? I would discuss why the folds take place and to what extent these folds contribute to the "success" of the G-quadruplex. I would also expand on the words parallel topology and anti parallel topology (these words need more clarification). Also, clarification is needed on dsDNA, not a common term someone will know with initially glancing at the page and no context to determine what that might be. Akm14t (talk) 22:02, 21 February 2017 (UTC)

The first paragraph of this section is very large but only includes one reference for all of the information. I suggest adding more sources to back up this information because getting all of that information from one source can be biased. Brookemcfarland (talk) 02:42, 17 February 2017 (UTC)

I agree that this section needs a bit more citation. I also think that a more informative introduction should be included regarding how sodium and potassium cations are responsible for the G-quadruplex structure variability due to the fact that they orient the G-quadruplex lengths in a linear fashion through the central core and along the exterior.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119469/ ReeceVesperman (talk) 05:17, 17 February 2017 (UTC)

This paragraph includes no links to definitions. It would be a better section if it included a link to a wikipedia page explaining what it is such as antiparallel, guanine, or intramolecular. Tfizzle96 (talk) 02:49, 18 February 2017 (UTC)

Telomeric Quadruplexes

There needs to be background knowledge on what a telomeric repeats are and why they are so important. More information needs to be included for how this is involved in cancer and the information the wiki page does have needs to cite the information! I think that the types of cancers involved (with a citation) could be included because there is probably research on what kind of cancers G-quadruplexes are involved in. This section has information that definitely comes from some place and not common knowledge so it should be cited. Akm14t (talk) 23:11, 21 February 2017 (UTC)

The formation of these quadruplexes in telomeres has been shown to decrease the activity of the enzyme telomerase, which is responsible for maintaining length of telomeres and is involved in around 85% of all cancers. (This was missing a reference. The following source was the only source I found to support the information.) Jomagiles (talk) 03:53, 17 February 2017 (UTC)

Links to "Human telomeric" and "X-ray crystal structure" are bad links. There are no Wikipedia pages for either of those phrases, only pages for the individual words. Jomagiles (talk) 04:18, 17 February 2017 (UTC)

The link for "chicken β-globin gene" is also a bad link only having connections to pages for each individual word rather than the phrase.Mmz15 (talk) 05:43, 17 February 2017 (UTC)

Here is a second source that I found regarding quadruplexes and cancer research, but I agree some editing should be done in regards to this lapse in citation and these ideas should be expanded on. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119469/ReeceVesperman (talk) 05:56, 17 February 2017 (UTC)

Referring to the bad links you mentioned, I agree that the entire phrase needs to linked rather each single word and I have included some links explaining the entire phrases that I believe should replace the ones found on the current live article. In addition, "X-ray crystal structure" does not make sense in the sentence and should be replaced with "X-ray crystallography" which does have a wiki page that I have also included. X-ray crystallography

http://www.jbc.org/content/271/9/5208.long http://www.jbc.org/content/269/34/21858.abstractReeceVesperman (talk) 00:18, 18 February 2017 (UTC)

I found a source regarding parallel quadruplexes crystal structure and human telomeric DNA. The article was published in the science journal, Nature. Here is some interesting information we can incorporate into the wiki page. The DNA sequence of Telomeric ends creates four parallel strands of quadruplexes structures. These quadruplexes obtain their crystallized form due to repeats in the human telomeric DNA and factors such as potassium concentration. Telomeric ends of the chromosome are essential in preventing degradation and recombination within the cell. A mutation or change that affects the DNA sequence of the telomeres can lead to cell death. Scientists are exploring this phenomenon as a future treatment method for cancer. Jessica nelson12 (talk) 08:25, 17 February 2017 (UTC)

Non-telomeric quadruplexes

When the page says recently, how recently does this mean? When was this posted to the page? Recently is all relative. Also, it says the G-quadruplexes are found in many things and keep increasing but how? Who is discovering these and how? I think there needs to be more explanation regarding the promoters. Akm14t (talk) 03:01, 22 February 2017 (UTC)

The terms upregulation and down regulation should be described in more depth because there is not any context to what these are and no citations so readers can find more information. Many thoughts and ideas regarding telomeric and non telomeric G-quadruplexes can be found here: https://academic.oup.com/nar/article/33/14/4649/1021366/Not-so-crystal-clear-the-structure-of-the-human which is a reliable primary source that can be used. Akm14t (talk) 20:18, 22 February 2017 (UTC)

The sentence at the start of this section, "Recently, there has been increasing interest in quadruplexes in locations other than at the telomere." is pure opinion and should be reworded. I suggest the following edits and references:

"Quadruplexes are present in locations other than at the telomere. The proto-oncogene c-myc forms a quadruplex in a nuclease hypersensitive region critical for gene activity.[9][10] Other genes shown to form G-quadruplexes in their promoter regions include the chicken β-globin gene, human ubiquitin-ligase RFP2, and the proto-oncogenes c-kit, bcl-2, VEGF, H-ras and N-ras."

The last sentence in the paragraph, "This list is ever-increasing.", should be deleted. Aab05 (talk) 04:29, 17 February 2017 (UTC)

Quadruplex Function

The last part of this section where it states the "positive and negative roles" of quadruplexes in telomere replication and function are controversial does not seem to agree with the next sentence stating that they are among one of the DNA structures that protect and regulate telomere ends. Is this implying that the impact of replication and protection of telomere ends is controversial? This just seems like a confusing and vague way to end this section. Mmz15 (talk) 05:28, 17 February 2017 (UTC)

I am putting it in this section because it doesn't exist on this page for some reason, but under "Quadruplex prediction techniques" it only gives one very vague way to predict. It could give a lot more detail and more ways for quadruplex prediction. Tfizzle96 (talk) 02:26, 18 February 2017 (UTC)

Ligands which bind quadruplexes

This section is certainly in need of citations and detail. This section does not have any citations at all which is pretty concerning regarding its legitimacy.

The last sentence mentioning cationic porphyrins needs to have supporting detail. This random fact kind of stands alone not relating much to the other information. Perhaps an explanation of what cationic porphyrins are and what kind of role or function they play when binding with G-quadruplexes would be appropriate here. And, once again, this bit of information needs to be cited.Mmz15 (talk) 05:35, 17 February 2017 (UTC)

Quadruplex Function

This section needs to expand on several of the points that it makes regarding the mechanisms behind how quadruplexes function. The information was rather vague in regards to quadruplex structure and its role in transcription and translation for gene regulation. I found several sources discussing these topics and I think it is worth noting that G-quadrupluxes have been found to play a role in the recruitment of specific transcription promoting factors. In addition, it should be included that 5'-UTR G-quadruplexes alter RNA stability by inhibiting and promoting cap-dependent and cap-independent translation initiation, thereby regulating gene expression. Furthermore, it has been suggested that quadruplex's play a role in gene regulation due to their prevalence in a number gene regulating elements including CpG islands, enhancers, insulators, and so on. ReeceVesperman (talk) 06:02, 17 February 2017 (UTC)

G-Quadraplex

I personally feel that the first paragraph needs some help. First, I am pretty sure that G-quadraplexes are secondary structures not tertiary. Also I feel that towards the end of the first paragraph it is kind of awkward to leave the reader hanging with quickly mentioning parallel and antiparallel without explaining what that means. Ayap213 (talk) 14:33, 17 February 2017 (UTC)

I agree that the first paragraph needs more information and should be better fact checked. I believe it should be noted in the second sentence that the G-tetrads and resulting G-quadruplex structure are held together by non-covalent attractive pi interactions which I found have included a source for. I also think a hyperlink to the wiki page for pi interactions should be added which I have also included. Pi interaction *Note- the source is provided through fsu library so off campus access is required. ReeceVesperman (talk) 00:27, 18 February 2017 (UTC)

Quadruplex prediction techniques

This section needs to be more specific in describing prediction techniques (whether there is lots of information on the topic or not, it should be stated). The simple pattern needs to be explained more in depth on what that technique shows us if it is a G-quadruplex or not and to what extent it is correct. There should also be something stated of why it is used versus other techniques or methods. Akm14t (talk) 20:24, 22 February 2017 (UTC)

I feel that this section is quite undeveloped and could use some background information to support the prediction and understanding of when G-quadruplexes can occur. Q-quadruplex sequences are dispersed throughout the human genome in eons, introns, untranslated regions, promoter sequences, and within gene desert regions. Due to their frequency, this section could discuss how to understand which signs and traits within the human genome can give us a red flag for a possible G-quadruplexes, rather than just giving a simple pattern match to determine if a G-quadruplex is present. Identifying G-quadruplexes is not new and finding peer reviewed sources that discuss information about identification techniques is not necessarily difficult to come across.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1636468/

In order to edit this section they could also give more ways on how to predict the quadruplexes if they want to explain that way.Tfizzle96 (talk) 02:28, 18 February 2017 (UTC)

Damage

In my opinion the Damage section focuses too much on individual examples of damage to DNA. I believe the section should be more broad and focus on all kinds of damages to DNA. For example, the section addresses ultra-violet rays but doesn't explain how ultra-violet rays damage DNA. In my opinion, this needs to be addressed. I would add the amount of ultra-violet rays would be considered dangerous for humans. I would also address what happens to the DNA when the ultra-violet light denatures the DNA. I would address how this would affect transcription and translation. Sushenprashanth (talk) 18:29, 22 February 2017 (UTC)Sushenprashanth 1:29, 22 February 2017 (UTC).

DNA: Genetic Engineering

For the Genetic Engineering section I recommend certain gene editing techniques like the CRISPR/Cas9 technique should be at least be mentioned, which has been shown to affect both medical science and agricultural science.

Cubandrew (talk) 21:43, 23 February 2017 (UTC) Cubandrew (talk) 21:45, 23 February 2017 (UTC)Andrew Delgado