User talk:Cantusn/sandbox

→Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling. There are two classes of cruciform DNA, folded and unfolded. The folded cruciform structure has two arms that cross and form two acute angles at the intersection while the folded structure has 4 equal 90˚ angles and is square planar (ref 46). Cruciform DNA is found in both prokaryotes and eukaryotes and has a role in the transcription of DNA(ref 110, 38), double strand repair (ref 53), and recombination (ref 79) (see Holliday junction), without regulations that occur due to cruciform formations there is genome instability, DNA translocation, and formation of various diseases (ref 72, 55,6). Cruciform DNA is nonrandom in its formation is often found at break point junctions, promoter regions, and sites of replication initiation. (Cantusn (talk) 13:42, 8 November 2017 (UTC))

Cruciform DNA-main paragraph
-‘Cruciform DNA’ should be bold in first paragraph. (look at other wiki pages, this is a standard theme)

-Use wikilinks to link to other Wikipedia pages when mentioned (eg. Nucleotide, transcription, DNA repair).

-Remove: ‘Cruciform DNA is nonrandom in its formation and is often found at break point junctions, promoter regions, and sites of replication initiation’.

-Replace “there are two classes of cruciform DNA” with “Two classes of cruciform DNA have been described”

“regulation of genomic instability” should be replaced. Genomic instability is not a good thing that is regulated. You can say: “formation of cruciform DNA may increase genomic instability” --MichaelChiorazzo (talk) 21:32, 11 November 2017 (UTC)

-Maybe add detail to what "various diseases" cruciform might cause and how they occur, such as through DNA translocation. --Fordl (talk) 4:21, 12 November 2017 (UTC)

-I feel like most of this paragraph belongs elsewhere. The beginning paragraph is supposed to be a short pitch for later sections. This is why the structure section is repetitive and the biological significance section seems so short. I would state that there are two forms of cruciform DNA in this section and then explain the structures of these forms in the Structure section. --Fordl (talk) 4:21, 12 November 2017 (UTC)

- Make sure to link to other wiki pages: "supercoiling" "Holiday junction" "translocation" etc - Maybe add a visual representation of what a cruciform looks like to help better understand this page. - A lot of this paragraph can be moved or combined with structure. Rodrigu7 (talk) 00:18, 13 November 2017 (UTC)

-In describing the two forms of cruciform, it would be very useful to include a image that compares/contrasts the two. It would also be extremely beneficial to the general audience if you could also label the stem, branch point and loop in these pictures as well, as mentioned in the first sentence. Maurogarcia21 (talk) 02:39, 13 November 2017 (UTC)

Cruciform DNA-Structure
This seems repetitive after main paragraph. Maybe remove this and put all structure in main paragraph. --MichaelChiorazzo (talk) 21:33, 11 November 2017 (UTC)

I agree that this section sounds repetitive to the main paragraph, but I would remove from the main paragraph and add to this instead. --Fordl (talk) 4:23, 12 November 2017 (UTC)

A visual representation of cruciform structure would really help here. Maybe you could make one in Pymol. --Fordl (talk) 10:58, 12 November 2017 (UTC)

Don't forget to add wiki links. As already stated, this section should be removed and added to the main paragraph because of the repetition. Rodrigu7 (talk) 00:20, 13 November 2017 (UTC)

You mentioned it can adopt two forms (folded and unfolded), in which you described the geometry of the two. I think it would be super beneficial to include why it may adopt one form over the other in certain conditions (salt concentrations, pH, sequencing, etc.). Maurogarcia21 (talk) 02:30, 13 November 2017 (UTC)

Cruciform DNA-Biological Significance
-“Cruciform extrusion alleviates superhelical stress, therefore it is the stable conformation at high negative superhelical densities” This should be reworded. Cruciform DNA structures are stabilized through supercoiling and their formation alleviates stress generated from DNA supercoiling.

-“ Cruciform structures circumvent the  recognition of the promoter by RNA polymerase or disrupt a kinetic pathway step which lead to the regulation of  transcription initiation”. This sentence is very confusing. Which promoter? What does ‘kinetic pathway step’ mean?

-“ RuvA / RuvB Repair” : what does this have to do with cruciform DNA? Need to describe in a bit more detail. --MichaelChiorazzo (talk) 21:34, 11 November 2017 (UTC)

-"RuvA / RuvB" explain what these are (proteins) in the context of DNA, otherwise the section feels out of place with an awkward lack of detail on what these proteins do biologically. --Fordl (talk) 4:22, 12 November 2017 (UTC)

This section needs more depth: what are RuvA, RuvB and p53? Why are the important and relevant to this wiki page? I agree that "Cruciform structures circumvent the  recognition of the promoter by RNA polymerase or disrupt a kinetic pathway step which lead to the regulation of  transcription initiation” is confusing. Break this sentence down and explain better. Rodrigu7 (talk) 00:23, 13 November 2017 (UTC)

-RuvA, RuvB, and p53 were randomly introduced at the end of this paragraph. To really incorporate their biological significance, it would be ideal to transition from the main paragraph into each of these subsections. Also, it is very important to state that p53 is a protein. RuvA, RuvB, and p53 are lacking important details, which would bridge the knowledge gap in how these play important roles in biological systems. Maurogarcia21 (talk) 02:49, 13 November 2017 (UTC)