Talk:DNA polymerase

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Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 12 May 2020 and 22 June 2020. Further details are available on the course page. Student editor(s): Cstaheli. Peer reviewers: Mkalarobinson, Km86867. 20:55, 19 January 2022 (UTC)[reply]

DNA Polymerase α

In the article it says that it acts both as the Primase enzyme and the Polymerase. According to pg567, World of the Cell (Becker et al, 2006, Benjamin Cummings) although the Primase and the Pol α are closely asssociated they are separate proteins. I've looked through some other literature but its mostly older stuff so is fairly ambiguous.GiollaUidir 08:18, 20 October 2006 (UTC)[reply]

Infact, I've found another source that says they are separate: Figure 4-36, pg136, Molecular Cell Biology, Lodish et al., 2004, W.H. Freeman and Company. I'll edit when I get a chance. (Guess who's in the middle of an essay!? :P)GiollaUidir 09:03, 20 October 2006 (UTC)[reply]

Made the edit. Primase actually combines with the PriS and PriL subunits, with the subunits active in creating the RNA primer, and Pol alpha extending the RNA primer with DNA for 20-30 nt. This is a source from 2006 and is what I was taught this year so it should be fairly recent. Jimhsu77479 (talk) 08:29, 25 February 2009 (UTC)[reply]

Confusing sentence

"Nuclease is a great advocate for DNA replication." ... maybe it's just today, but I have no idea what that is actually trying to say. Nuclease CLEAVES DNA strands so I don't think you want too much of it around during replication. Jimhsu77479 (talk) 06:50, 6 March 2009 (UTC)[reply]

Agreed this makes no sense. Get rid of it or replace with meaningful sentence.

Primer removal

Any idea what actually removes the RNA primer from the DNA strand? Pol I in prokaryotes as far as I can see but I can't find what removes it from eukaryotes.GiollaUidir 08:37, 20 October 2006 (UTC)[reply]

Yes, I'm talking to myself. 'tis Proliferating Cell Nuclear Antigen-Replication Factor C-DNA Polymerase δ (PCNA-Rfc-DNA Pol δ-a complex formed to stabilise Pol ’s binding to the template) from: Figure 4-36, pg136, Molecular Cell Biology, Lodish et al., 2004, W.H. Freeman and Company.GiollaUidir 09:47, 20 October 2006 (UTC)[reply]

http://nar.oxfordjournals.org/cgi/content/abstract/34/6/1772

As far as I know, DNA pol delta displaces the primer, which creates a flap removed by flap endonuclease. Ligase seals the resulting nick. (I don't have a particular reference in mind). Jimhsu77479 (talk) 08:13, 25 February 2009 (UTC)[reply]

Introduction

You introduced what the enzyme does, but should have also mentioned the different types in prokaryotes vs eukaryotes. There should be a reference to the possibilities of mutation and what could happen if that takes place. Referring to its importance in lab procedures is not important to the wider audience that may be trying to understand holistically what a DNA polymerase protein is and does. Arjbajarj (talk) 05:29, 4 February 2014 (UTC)[reply]

Strand nomenclature?

I've always thought that "leading" and "lagging" refer to newly synthesized strands, not the template strands. As such, it would seem to me that pol δ and ε are mislabeled.--Estelahe 20:24, 8 October 2007 (UTC)[reply]

I thought that technically it doesn't matter: the leading strand is simply the one that can replicate continuously in a 5'->3' fashion without stopping. But yes, the title of that reference for Dna pol epsilon directly conflicts with the statement in the article. Maybe more references are needed, or it should be labeled "ambiguous"? Jimhsu77479 (talk) 08:36, 25 February 2009 (UTC)[reply]

Nomenclature

There seem to be lots of different ways to link to pages about individual polymerases used in this article. What is the standard nomenclature / page list? --Dan|^(talk) 14:03, 17 December 2010 (UTC)[reply]

Catalytic mechanism?

Can someone point me at good references describing the active site / catalytic mechanism of the polymerase? Is it a single domain, or do several domains need to work in concert in order to catalyse the addition of a base? Structural differences between the (presumably conserved) catalytic domains of the different enzyme types must be fascinating, so I'd like to start a section on that topic. --Dan|^(talk) 14:03, 17 December 2010 (UTC)[reply]

Proposal for updates/edits

Below is a justification of why our group for our Molecular Biology course chose to update this article: We have chosen to edit and update the DNA Polymerase Wikipedia article due to the “High Importance” placed on this article by the MCB WikiProject. Currently, the status of the article is rated as “Start Class” meaning that it has an overall grade below a C on the quality scale. The DNA Polymerase page has more information than a stub article but it lacks flow, clarity and numerous references. Finding and adding references should be a quick fix that will greatly enhance the article and the article’s credibility.

A good starting point will be to investigate further the suggestions from the talk page and implement those changes where appropriate. At first glance, we have also identified that the article lacks information on the functionality of the various DNA Polymerase subunits. In addition, there is significant information and research that can be added about the holoenzyme complex. We have also just learned about processivity of DNA Polymerase when interacting with clamp proteins and this vital information is missing from the article. The sections outlining the DNA Polymerase families lacks references, flow and connectivity. Additionally, these sections can be expanded to elaborate on the similarities, differences and research performed on the different families. While we do not want to duplicate the sections referencing Prokaryotic DNA polymerase and Eukaryotic DNA polymerase on other Wikipedia pages, we feel that sections could be included that outline any similarities and differences between the two types of polymerases.

We think that the DNA Polymerase page will allow us as a group to not only expand our knowledge on a very important subject in molecular biology, but the different needs of the page allow us to work on various functions within Wikipedia that will expand our overall knowledge of Wikipedia.

Below is our suggested new outline for this article with the possiblity of merging Prokaryotic DNA polymerase and Eukaryotic DNA polymerase pages with this main page as they are short pages:

1. History

1.1 purification

2. Function/Action

2.1 Catalytic Mechanism 2.2 Processivity

3. Variations among species

3.1 Prokaryotic Polymerases

3.1.1 pol I

3.1.2 pol II

3.1.3 pol III

3.1.4 pol IV

3.1.5 pol V

3.2 Eukaryotic polymerases

3.2.1 Polymerase beta and lambda

3.2.2 Polymerases alpha, delta and epsilon

3.2.3 Polymerase eta, iota and kappa

3.2.4 Polymerase Rev1 and polymerase zeta

3.2.5 Polymerase sigma

3.2.6 Telomerase

3.2.7 Polymerase gamma

3.2.8 Polymerase mu

3.2.9 Polymerase theta

Does anyone have any suggestions, concerns, or any feedback on our ideas? We would greatly appreciate any feedback that anyone has to offer. Thanks! Abenson9 (talk) 03:15, 12 November 2012 (UTC)[reply]

This article would greatly benefit from some sustained attention, and I'm excited about the work that Johns Hopkins University is doing with WikiProject MCB. The proposed article restructuring sounds reasonable to me. Here are a few suggestions:

I would add an "Evolution" section to specifically discuss the evolutionary origins of DNA polymerase and its variations, and a "Technological applications" section to discuss, e.g., the subject's use in PCR and DNA sequencing.
Keep in mind that accessibility is important. When introducing technical jargon, a small amount of context goes a long way.

I'll be available to give feedback if wanted -- just leave a note here or on my talk page. Best, Emw (talk) 15:10, 12 November 2012 (UTC)[reply]

Thank you so much for your feedback. We will keep you posted on our updates! Abenson9 (talk) 00:31, 13 November 2012 (UTC)[reply]

I'm from group 83D and I like the work you are doing on this article. When you say History do you intend to speak to how and where the first DNA polymerase was discovered? I think the article could benefit from more information on the active site of DNA polymerase. What metal ions, interactions, and residues are important for the reaction to occur. Katesee (talk) 23:20, 27 November 2012 (UTC)[reply]

Yes, Kate we do intend to speak to how and where the first DNA polymerase was discovered. I have added a section on that just now. I also like your other suggestions and will work to incorporate that. I was thinking it might potentially fit in the function section following the newly added structure description. Let us know what you think as we progress. Thank you for your input.Aehall47 (talk) 14:29, 1 December 2012 (UTC)[reply]

Proposed merger of subsections into this article

Please post any suggestions surrounding the merger of Prokaryotic DNA polymerase‎ and Eukaryotic DNA polymerase to the main page of DNA polymerase Abenson9 (talk) 03:21, 13 November 2012 (UTC)[reply]

Hi, I think, what you meant was, that you want discussion to take place right here. Klortho (talk) 03:24, 13 November 2012 (UTC)[reply]

I favor the merger. It seems logical for this article to discuss general features of DNA pols and provide an overview of the different individual polymerases (pol alpha, pol I, etc), and then link to pages specific to the individual pols. I don't see the point of maintaining separate articles for eukaryotic and prokaryotic pols, since each of those enzymes (e.g. prokaryotic pol I, II and III) are as different from one another as they are from the eukaryotic enzymes. And then there are further complications, such as (1) whether the mitochondrial and chloroplast DNA polymerases are actually eukaryotic or prokaryotic, (2) where to put the archaeal enzymes, and (3) where to put viral and bacteriophage polymerases. --John Mackenzie Burke (talk) 03:47, 13 November 2012 (UTC)[reply]

Consolidation/Movement of Information

I moved the information below and categorized it by Prokaryotic vs. Eukaryotic polymerases like mentioned above. I am going to delete the sections below but wanted to preserve the information below somewhere so that if someone disagrees we have a point of reference. Abenson9 (talk) 18:33, 19 November 2012 (UTC)[reply]

deleted material

Family AFamily A polymerases function as repair and replication polymerases[3]. Replicative members from this family include T7 DNA polymerase, T3 DNA polymerase and T5 DNA polymerase. Additional polymerases associated with replication are the eukaryotic mitochondrial DNA polymerase γ and DNA polymerase θ. The repair polymerases are DNA polymerase υ, Escherichia coli DNA pol I, Thermus aquaticus pol I, and Bacillus stearothermophilus pol I. These repair polymerases are involved in excision repair and processing of Okazaki fragments generated during lagging strand synthesis.

[edit] Family BB family polymerases are involved in nuclear DNA replication. These include; Pol II (bacterial), Pol B (archaebacterial), and Pol α, δ, ε, ζ (eukaryotic). Pol α consists of four subunits, two α and two-subunit primase. Once primase has crated the RNA primer, Pol α starts replication. Pol δ takes over the lagging strand synthesis and Pol ε takes over leading strand synthesis from Pol α.[4] Pol ζ another B family polymerase, is made of two subunits Rev3 and Rev7 and is involved in translesion synthesis. Pol ζ is unique in that it can extend primers with terminal mismatches.

[edit] Family CPolymerases in Family C are the primary bacterial chromosomal replicative enzymes with no eukaryotic equivalents. DNA polymerase III holoenzyme is the primary enzyme invoved in DNA replication in E. coli. It consists of three assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The core consists of three subunits - α, the polymerase activity hub, ɛ, exonucleolytic proofreader, and θ, which may act as a stabilizer for ɛ. The holoenzyme contains two cores, one for each strand, the lagging and leading. [5] The beta sliding clamp processivity factor is also present in duplicate, one for each core, to create a clamp that encloses DNA allowing for high processivity. [6] The third assembly is a seven-subunit (τ2γδδ′χψ) clamp loader complex. [7] Recent research has classified Family C polymerases as a subcategory of Family X. [8]

[edit] Family DPolymerases are still not very well characterized. All known examples are found in the Euryarchaeota subdomain of Archaea and are thought to be replicative polymerases.

[edit] Family XContains the well-known eukaryotic polymerase pol β, as well as other eukaryotic polymerases such as pol σ, pol λ, pol μ, and terminal deoxynucleotidyl transferase (TdT). Pol β is required for short-patch base excision repair, a DNA repair pathway that is essential for repairing alkylated or oxidised bases as well as abasic sites. Pol λ and Pol μ are involved in non-homologous end-joining, a mechanism for rejoining DNA double-strand breaks. TdT is expressed only in lymphoid tissue, and adds "n nucleotides" to double-strand breaks formed during V(D)J recombination to promote immunological diversity. The yeast Saccharomyces cerevisiae has only one Pol X polymerase, Pol IV, which is involved in non-homologous end-joining.

[edit] Family YY Polymerases differ from others in having a low fidelity on undamaged templates and in their ability to replicate through damaged DNA, known as translesion synthesis (TLS). Members of this family are hence called translesion synthesis polymerases. Depending on the lesion, TLS polymerases can bypass the damage in an error-free or error-prone fashion, the latter resulting in elevated mutagenesis. Xeroderma pigmentosum variant (XPV) patients for instance have mutations in the gene encoding Pol η (eta), which is error-free for UV-lesions. In XPV patients, alternative error-prone polymerases, e.g., Pol ζ (zeta) (polymerase ζ is a B Family polymerase a complex of the catalytic subunit REV3L with Rev7, which associates with Rev1[9]), are thought to be involved in mistakes that result in the cancer predisposition of these patients. Other members in humans are Pol ι (iota), Pol κ (kappa), and Rev1 (terminal deoxycytidyl transferase). In E. coli, two TLS polymerases, Pol IV (DINB) and Pol V (UmuD'2C), are known.

[edit] Family RTSome viruses also encode special DNA polymerases, such as Hepatitis B virus DNA polymerase. These may selectively replicate viral DNA through a variety of mechanisms. Retroviruses encode an unusual DNA polymerase called reverse transcriptase, which is an RNA-dependent DNA polymerase (RdDp). It polymerizes DNA from a template of RNA. The reverse transcriptase family contains examples from both retroviruses and eukaryotic polymerases. The eukaryotic polymerases are usually restricted to telomerases. These polymerases use an RNA template to synthesize the DNA strand.

[edit] Prokaryotic DNA polymerasesMain article: Prokaryotic DNA polymerase Bacteria have 5 known DNA polymerases.

[edit] Eukaryotic DNA polymerasesMain article: Eukaryotic DNA polymerase Eukaryotes have at least 15 DNA Polymerases.[10]

Hi, Amy. It is a good sentiment, to want to preserve this text, but completely unnecessary! The way the wiki software works is that all the prior page revisions are all preserved. It's actually much better and more robust to rely on the wiki software, than copying text here into the talk page, because no one could ever really know, without a lot of work, which version of the page this text that you pasted belonged to. Just click "View history" on the page, to see what I mean. Klortho (talk) 22:48, 19 November 2012 (UTC)[reply]

Citation suggestion

If you haven't seen this yet, please check out User:Diberri's Wikipedia template filling tool (instructions). Given a PubMed ID, one can quickly produce a full citation that can be copied and pasted into a Wikipedia article. This tool can save you a lot of work and ensure that the citations are displayed in a consistent manner. Cheers. Boghog (talk) 11:04, 2 December 2012 (UTC)[reply]

Thanks for fixing the reference. You were correct in assuming that it was the confusion between the two ids. The paper that is referenced now is correct. Thanks again! Abenson9 (talk) 02:12, 3 December 2012 (UTC)[reply]

Final week mini-review

Hi, guys. Here's a final-week mini-review of your page. It is just a few random notes, that I jotted down while skimming the page, and is not intended as a comprehensive review.

In the introduction, you have "generation of antibody diversity", which links to the page Terminal deoxynucleotidyl transferase. I can't figure out whether this is correct, or what it's supposed to mean.
Under "Function", in the second paragraph, you make mention of the fact that one of the two strands is synthesized in a directionality opposite to that of DNA Polymerase, but you never discuss how this problem is resolved. A little more explanation there might be in order.
I am a little bit confused by "processivity". You say, "DNA polymerase’s rapid catalysis is due to its processive nature." But then it seems as if you are defining processivity to be the number of nucleotides added per second. This is circular.
Again under "processivity", the second paragraph could use a little work. Try to introduce new terms, like "sliding clamp loader", for example, before you use them. Also, those terms might be able to be linked to relevant wikipedia articles. For example, "sliding clamp loader" could link to Replication factor C.
Under "Structure", you could improve this a bit, I think, by explaining and/or linking the terms associated with the chemical reactions as you go. For example (this is just one example) what is the "phosphoryl transfer reaction"? That hasn't been described anywhere in this article prior to that point, and it should be introduced. You could break this "structure" section up into separate paragraphs for each domain.
Why is "structure" under "Variation across species"?
Starting with "Conserved structures usually indicate ...", this text doesn't seem to have anything to do with structure anymore. A little reorganizing of this content would help, I think.
I was confused by the concept of "family", and then I realized that this line, "Based on sequence homology, DNA polymerases can be further subdivided into seven different families: A, B, C, D, X, Y, and RT." explains it. But I think it is not good enough. Throughout the article, you refer to families, and it is not easy to see how they correspond to Euk. Pol I, II, III, and the various prokaryotic polymerases. I see that the version of the article when you started had the categorization broken down by family, and that you reorganized it. Nevertheless, I'd suggest that maybe a table summarizing the families would help the reader understand what is going on.

Klortho (talk) 01:12, 10 December 2012 (UTC)[reply]

Hi Chris! Thank you for your review and feedback. I think it helped a lot in shaping the article and organizing it better.To address your points in order:

I made reference to the page terminal deoxynucleotidyl transferase as the polymerase used for generation of antibody diversity.
I added some clarification to second paragraph of function, mentioning how DNA polymerase requires a free 3’ OH group to initiate synthesis.
I think I may have addressed the third point by clarifying the definition of processivity.
Following your suggestion, I referenced the replication factor C page, and clarified the role of the clamp loader.
We will discuss how to address the structure section to improve and expand it.
I also think it is more appropriate for the structure section to be either under function or as a new header. I moved it under function for now until we discuss its location.
Moving the structures section addressed this point.
I provided a table summarizing the different families. Please let us know whether the information is sufficient for readers to understand.

I hope I addressed everything you mentioned. Your feedback is of great help and is appreciated. Thank you. Aahmed25 (talk) 05:26, 10 December 2012 (UTC)[reply]

Okay, I'm glad you addressed these points. I probably won't have time to look at this article again this week, though, since I have my own class final exam to worry about, but keep in mind what I wrote at the top, that my review wasn't intended to be comprehensive. I'd urge you to go through the entire article, as much as you can until Saturday (which is the last day of the semester, right?) and critique it yourself using the same "eye" that I used, and see where you can make further improvements. Cheers! Klortho (talk) 13:35, 10 December 2012 (UTC)[reply]

Suggestions

Please Wikilink POLH, POLI, POLK, POLG, POLQ and Pol ε (epsilon) to POLE (enzyme) .

crated fedility insterter look like typos

Please wikilink Xeroderma Pigmentosum Variant (XPS) to Xeroderma pigmentosum#Types, perhaps reference with {{OMIM|278750|Xeroderma Pigmentosum, Variant Type; XPV}}. The two sentences referencing XPS could probably be consolidated.

The section Polymerase Rev1 and zeta section is lacking refs
The PubMed search review[pt Polymerase zeta] gives 42 review articles

From a quick look at the abstracts maybe (guessing)
Cell Res. 2008 Jan;18(1):174-83. DNA polymerase zeta (pol zeta) in higher eukaryotes. PMID: 18157155

Cell Cycle. 2010 Feb 15;9(4):729-35. Epub 2010 Feb 23. Multiple two-polymerase mechanisms in mammalian translesion DNA synthesis. PMID: 20139724

http://diberri.crabdance.com/cgi-bin/templatefiller/index.cgi?ddb=&type=pubmed_id&id=&add_text_url=1 will format refs based on PMID
http://diberri.crabdance.com/cgi-bin/templatefiller/index.cgi?ddb=&type=pubmedcentral_id&id=&add_text_url=1 and on PMC RDBrown (talk) 12:43, 11 December 2012 (UTC)[reply]

Thanks for the suggestions. I thought I had linked back to XPS, but I will definitely do that. I am currently working on updating the families section and I haven't made it to Rev1 and zeta yet. What is there currently is what was there originally. Thanks for the article suggestions as that should make my life a little easier! I will also link back to the genes of interest as well. Thanks again for the feedback and hope you think everything is starting to take shape. Abenson9 (talk) 00:40, 12 December 2012 (UTC)[reply]

Polymerase Family C

In the table summarizing DNA polymerase families, it says family C is only found in eukaryotic species. Yet it (correctly) lists Pol III as an example, which is a prokaryotic enzyme. Shouldn't the Species column be changed from 'eukaryotic' to include prokaryotic, or even to just prokaryotic? — Preceding unsigned comment added by 50.55.140.186 (talk) 03:57, 7 January 2013 (UTC)[reply]

When I read in the article that "recent research" had indicated that Family C DNA polymerase was really a subfamily of Family X DNA polymerase, I decided to check out the cite to get a sense of when that "recent" research occurred. The current reference [Footnote 11] is to a source that does not cite research but rather cites this Wikipedia article as its source of information. Thus, currently, the citation is completely circular. I assume that at some point someone had in mind some actual research supporting that claim. If that research could be ascertained and substituted as the authority for the claim it would be very helpful. In the meantime, I suggest the "citation" be deleted as misleading, since in its current form it merely reiterates this article. That would produce the result that the article contains an important claim without citation of authority. That often happens and when it does occur, the problem is flagged and people are invited to find some authority to support the statment. In my view, that is the current state of affairs and it would be best to make it explicit by deleting the citation.120.192.27.83 (talk) 15:33, 26 April 2014 (UTC)Ray Glock-Grueneich[reply]

Please update with: "Polθ reverse transcribes RNA and promotes RNA-templated DNA repair"

Please update the article with info on this paper's findings. It may also be relevant to other articles (I'm only adding some info to the article POLQ).

It's featured in 2021 in science like so:

Biologists report that DNA polymerases, long thought to only transcribe DNA into DNA or RNA, can also write RNA segments into DNA. Polθ was found to promote RNA-templated DNA repair, with large implications for many fields of biology.^[1]^[2]

--Prototyperspective (talk) 10:51, 20 July 2021 (UTC)[reply]

References

^ "New discovery shows human cells can write RNA sequences into DNA". phys.org. Retrieved 10 July 2021.
^ Chandramouly, Gurushankar; Zhao, Jiemin; McDevitt, Shane; Rusanov, Timur; Hoang, Trung; Borisonnik, Nikita; Treddinick, Taylor; Lopezcolorado, Felicia Wednesday; Kent, Tatiana; Siddique, Labiba A.; Mallon, Joseph; Huhn, Jacklyn; Shoda, Zainab; Kashkina, Ekaterina; Brambati, Alessandra; Stark, Jeremy M.; Chen, Xiaojiang S.; Pomerantz, Richard T. (1 June 2021). "Polθ reverse transcribes RNA and promotes RNA-templated DNA repair". Science Advances. 7 (24): eabf1771. doi:10.1126/sciadv.abf1771. ISSN 2375-2548. PMC 8195485. PMID 34117057.

Wiki Education assignment: Adv Molecular Bio Bass-FSU-Fa23

This article was the subject of a Wiki Education Foundation-supported course assignment, between 28 August 2023 and 15 December 2023. Further details are available on the course page. Student editor(s): Hafiza Sara Akram (article contribs). Peer reviewers: Hcs22e.

— Assignment last updated by Hcs22e (talk) 22:41, 5 November 2023 (UTC)[reply]

[1] "New discovery shows human cells can write RNA sequences into DNA". phys.org. Retrieved 10 July 2021.

[10.1126/sciadv.abf1771-2] Chandramouly, Gurushankar; Zhao, Jiemin; McDevitt, Shane; Rusanov, Timur; Hoang, Trung; Borisonnik, Nikita; Treddinick, Taylor; Lopezcolorado, Felicia Wednesday; Kent, Tatiana; Siddique, Labiba A.; Mallon, Joseph; Huhn, Jacklyn; Shoda, Zainab; Kashkina, Ekaterina; Brambati, Alessandra; Stark, Jeremy M.; Chen, Xiaojiang S.; Pomerantz, Richard T. (1 June 2021). "Polθ reverse transcribes RNA and promotes RNA-templated DNA repair". Science Advances. 7 (24): eabf1771. doi:10.1126/sciadv.abf1771. ISSN 2375-2548. PMC 8195485. PMID 34117057.

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