Talk:Aptamer/GA2

GA Review

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Reviewer: Mertbiol (talk · contribs) 17:45, 18 December 2022 (UTC)

I will take on this review. I do have some knowledge of DNA- and RNA-based aptamers, although I have never worked with them personally. I look forward to working with the nominator on this article. Best wishes Mertbiol (talk) 17:45, 18 December 2022 (UTC)

General comment

• There appears to be no quantitative discussion of the affinity with which an aptamer binds to a ligand. I think that a K_D range should be given in both the lead section and in the "Properties" section. (The term "affinity" is only used once in the main text!!)

Lead section

• I suggest combining the second and third sentences of the first paragraph to give: "They can bind strongly, with little or no off-target binding,^[1] and are sometimes classified as chemical antibodies."
• I suggest replacing "tasks" with "applications" in the (current) fourth sentence of the first paragraph.

Etymology

• I suggest mentioning that the first aptamer publication was in 1990.
• Please link Jack W. Szostak in the main body of the text.
• Per MOS:FOREIGNITALIC, please render "aptus" in italics as aptus.
• Please delete the second period (full stop) after "to fit."
• I suggest rephrasing "Aptamers are occasionally referred to as "chemical antibodies" or "antibody mimics"" to "Aptamers are occasionally classified as "chemical antibodies" or "antibody mimics".
• I suggest deleting "and sensitive" from the final sentence of this section.

History

• I am not sure if the history of directed evolution before SELEX should be covered in so much detail. I suggest rewriting first paragraph to give: "Since its first application in 1967, directed evolution methodologies have been used to develop biomolecules with new properties and functions. Early examples include the modification of the bacteriophage Qbeta replication system and the generation of ribozymes with modified cleavage activity."
• Please expand the acronym SELEX in the second paragraph, as this is the first mention of this term in the main body of the text.
• Please link Evgeny Nudler.
• I suggest changing "comprehensive proofs of" to "definitive evidence for"
• Please rephrase the final sentence of this section to read "This discovery added support to the RNA world hypothesis, a postulated stage in time in the origin of life on Earth."
• The single quotation marks around "RNA world hypothesis" should be removed.

Industry and Research Community

• I suggest moving this section to the bottom of the article. It may be worth rewriting this paragraph as an "External links" section.
• Bare URLs should be removed from this section.

Properties

(Just a start on this section - more to come)

• It is not clear what is meant by a "peptide aptamer". Is this an aptamer with an amino acid backbone or a nucleic acid-based aptamer with nucleotides modified with the addition of amino acids?
• Please replace "Typically, nucleic acid aptamers" with "Typically, DNA- and RNA-based aptamers".

Stopping here for now. I will provide additional feedback in due course. Best wishes Mertbiol (talk) 17:45, 18 December 2022 (UTC)

Affinity

Hi Mertbiol, I wanted to check on your request for "quantitative discussion of the affinity with which an aptamer binds to a ligand." The article on antibodies, which has attained "good article" status, does not discuss the KD range for antibodies. Of course, a KD range would be easy to add, but it sounds like you're interested in a longer discussion of aptamer affinity. If so, can you give some more specific suggestions for what you'd like such a discussion to cover? Thank you for your feedback! AllAmericanBreakfast (talk) 19:30, 18 December 2022 (UTC)

Hi @AllAmericanBreakfast: I have just had a quick check on the antibody article. You are correct in saying that there is no K_D range given, although "affinity" is mentioned 20 times in total. I think it would be a good idea to provide a typical K_D range for "useful" aptamers. Is there any difference between DNA-, RNA-, XNA- and peptide-based aptamers? At the moment, I don't think a long discussion is required - a single sentence in each of the lead section and in the properties section may be enough. Best wishes Mertbiol (talk) 19:48, 18 December 2022 (UTC)

Hi Mertbiol. The "useful" Kd range depends entirely on the specific application. For example, an in vivo biosensor needing to detect physiologically relevant levels of a specific protein will have its useful Kd determined by what the physiological levels are in the specific site, and depend also on the disease condition, inflammation, etc. By contrast, an aptamer used for affinity chromatography might have an entirely different "useful" range, potentially requiring significant affinity but much lower than that required to detect physiological levels. Other times, it might be specificity rather than affinity that is the key determinant of what makes an aptamer useful. Because the dynamic range of the aptamer depends on affinity, having an excessively high affinity can actually be bad for some applications. We could, however, give a range of affinities that have been reported in literature, just to show what has been achieved so far. AllAmericanBreakfast (talk) 20:15, 18 December 2022 (UTC)

Thanks @AllAmericanBreakfast: Yes I think a range of affinities reported thus far would be good to include. And also a brief discussion of applications for which very high affinity binding is not appropriate. Best wishes Mertbiol (talk) 20:38, 18 December 2022 (UTC)

OK, I have implemented those changes in the first paragraph of the lead and in the applications section. Let me know what you think. AllAmericanBreakfast (talk) 22:49, 18 December 2022 (UTC)

Peptide aptamers

"It is not clear what is meant by a "peptide aptamer". Is this an aptamer with an amino acid backbone or a nucleic acid-based aptamer with nucleotides modified with the addition of amino acids?"

I believe the section covers this in "While most aptamers are based on nucleic acids, peptide aptamers are artificial proteins selected or engineered to bind specific target molecules." Let me know if that isn't clear enough. Thanks! AllAmericanBreakfast (talk) 19:41, 18 December 2022 (UTC)

Thanks @AllAmericanBreakfast: I can see the explanation lower down in the section now - I had not looked ahead. I think the "Peptide aptamers" definition is in the wrong place - it needs to be higher up when the term is first introduced. Best wishes Mertbiol (talk) 19:48, 18 December 2022 (UTC)

I moved the definition to immediately under the heading, hopefully that is more clear. Thanks! AllAmericanBreakfast (talk) 20:16, 18 December 2022 (UTC)

Article organisation

Hi @AllAmericanBreakfast: Thanks for your replies so far. I think we need to take a look at the organisation of the article and think again about how different pieces of information are divided between different sections.

• Both the lead section and the "Etymology" section state that aptamers are nucleic acid-based ("Aptamers are short sequences of artificial DNA or RNA that bind a specific target molecule" and "the typical use is to describe a synthetically generated, nucleic acid-based ligand that is specific for a particular target molecule.") so the first reference to peptide-based and XNA-based aptamers is in the "Structure" subsection of the "Properties" section, where they are not properly defined.
  • I think we should leave the lead section for now and come back to it later in the review.
  • Please remove the final sentence of the "Etymology" section (starting "No formal definition exists...). The Joyce 1994 reference is now clearly out-of-date.
• Please create a new section entitled "Classification" or "Types of aptamer" or "Classes of aptamer" or similar, which I think should go above the "History" section. Please place any information that helps readers to understand the difference between DNA-, RNA-, XNA- and peptide-based aptamers, into this new section from the "Properties" section. Please bear in mind that not all of those reading this article will be specialists.
• Please move the final paragraph of the current "Structure" subsection (starting Unmodified aptamers are cleared rapidly from the bloodstream...) into a new section entitled "In vivo clearance and degredation" or similar. For now, this new section should be placed below the "Applications" section.
• Once you have done that, please look through the article again and make sure that all topics are grouped under appropriate headings.

When you are done, please ping me and I will take another look. Best wishes Mertbiol (talk) 19:34, 19 December 2022 (UTC)

Hi Mertbiol. I think some discussion is in order about classification of aptamers before making further changes. There is no definitive source offering a consensus definition of "aptamer," but a representative example of such a definition is:

"Aptamers are single-stranded oligonucleotides that fold into well-defined three-dimensional shapes, allowing them to bind their targets with high affinity and specificity."

However, the peptide aptamer community defines "peptide aptamer" as follows:

"Peptide aptamers are small combinatorial proteins that are selected to bind to specific sites on their target molecules. Peptide aptamers consist of short, 5-20 amino acid residues long sequences, typically embedded as a loop within a stable protein scaffold... a short amino acid sequence embedded (“double constrained”) within the context of a small and very stable protein backbone (“scaffold”). Conformational constraint is important, since it stabilizes the insert loop and makes it more likely to fold and recognize cognate surfaces"

If we accept the first definition, then "peptide aptamers" aren't aptamers at all, because they are not oligonucleotides. I may be wrong, but I suspect there is no source offering a comprehensive, single definition for "aptamer" that covers all use cases.

My view is that by far the most common use of the term "aptamer" is to refer to an oligonucleotide with high affinity for a specific target. However, the latin-derived name simply means "to fit," and so it would make some sense to define the term more broadly as any small polymer that binds a specific target, or set of targets, with high affinity. But I don't have a source giving that definition - in fact, it seems to me that few if any authors in the aptamer research community are taking pains to classify aptamers with that level of precision. It is a term of convenience. Since this is Wikipedia, I don't want to impose my own definition on the article, and yet I also don't expect I'll be able to find a single definition that encompasses all use cases. My best compromise would be to offer several sets of definitions and let the reader make sense of them all. What do you think? AllAmericanBreakfast (talk) 20:25, 19 December 2022 (UTC)

Hi @AllAmericanBreakfast: Thanks for your message. Before reading this article, I hadn't come across "peptide aptamers", but it does seem (from a bit of reading today) that this term has been in use for around 20+ years, so I don't think that this Wikipedia article can ignore it. My preference would be to offer as broad a definition as possible for "aptamer" and then to state that there are broadly four different types (DNA-, RNA-, XNA- and peptide-based). I think this would be the best way of dealing with the "definition problem". I think if you tried to present multiple definitions side-by-side, you would just end up confusing the reader. Best wishes Mertbiol (talk) 21:03, 19 December 2022 (UTC)

Hi @AllAmericanBreakfast: Can you let me know please if you are happy to continue working on the "Properties" section on your own or if you would like some input from me? Best wishes, Mertbiol (talk) 21:10, 22 December 2022 (UTC)

Yes, if you could give me your further thoughts on improvements to the properties section, that would be helpful. Thanks. AllAmericanBreakfast (talk) 02:18, 23 December 2022 (UTC)

Picking the review up again

Hi @AllAmericanBreakfast: I have been thinking about this article over the Christmas break. I’ve also been rereading the antibody article to give a bit of a guide as to structure. As you say, our main problem is that there isn’t a good unifying definition for "aptamer", which means that defining the scope is challenging. Peptide aptamers appear to have only a limited connection to the nucleic acid-based aptamers and so integrating them into a cohesive single article is very difficult.
At this stage, I am tempted to propose a split into two separate articles – Nucleic acid-based aptamers and Peptide aptamers or similar. (The current article would remain either as a disambiguation page or as a redirect to the Nucleic acid-based aptamers article.) I note that aptamers, nucleotide and aptamers, peptide already exist as redirects. Splitting would, of course, need to take place outside of the review process and would require consultation with other editors. Once the peptide aptamers were removed, the nucleic acid-based material could easily be polished up and resubmitted for GA review.
Alternatively, we could continue with the article as it currently stands. My feeling is that it would need a major reorganisation to satisfy Criteria 1a and 3b.
Please let me know your thoughts. Best wishes, Mertbiol (talk) 10:49, 28 December 2022 (UTC)

Hi @AllAmericanBreakfast: Hope you've had a good break over the festive season. Could you let me know your thoughts on the above please? Thanks Mertbiol (talk) 21:00, 5 January 2023 (UTC)

Sorry, got halfway through a response and then had to step on an airplane.

Before committing to any article split, let's consider the argument for keeping them together.

"Aptamer" doesn't have a rigid definition, but that's not a prerequisite for a topic having a wikipedia article. Art has a wikipedia page, for example, as does pornography, even though it's a cliche that the difference is that "we know it when we see it." To me, what groups peptide and nucleic acid-based aptamers together is a combination of size, function as an affinity ligand, and a basis for that affinity in the chemistry of combinatorial polymers. If some third chemistry allowing for combinatorial polymers proved fertile for generating affinity ligands against a wide range of specific targets, then we could have aptamers based on that chemistry as well. It's only because we have just two examples (nucleic acid-based and protein-based) and the lack of effort on the part of the field to achieve definitional clarity that the specific chemistry stands out as a differentiator and the abstract unity of the term is disguised. Splitting the article and redirecting "aptamer" to "nucleic acid-based aptamer" disguises that unity further. It's not that this is a slam-dunk argument, it's just that we'd then have to defend this decision to other editors with a proclivity toward lumping rather than splitting, and I don't think there's going to be a consensus official source to point to any time in the near future.

Given that lack of a valid expert consensus, I think it's best to just leave both "nucleic acid aptamer" and "peptide aptamer" in the "aptamer" article as two examples of what an aptamer can be. Perhaps I just need to look harder - it would be surprising if the number of sources giving a unified definition of "aptamer" that incorporates both nucleic acid and peptide aptamers was zero. 2601:400:C100:5510:2F0F:8D85:FA47:CB4D (talk) 21:28, 5 January 2023 (UTC)

Thanks @AllAmericanBreakfast: Then it that case, we'll continue without splitting. For me, the main problem with the article as it stands is that is primarily about nucleic acid aptamers, with a (short) stand-alone subsection on peptide aptamers about half-way down the page, after which the story reverts back to the DNA/RNA versions. The challenge now will be to integrate the peptide aptamer material into the rest of the article, so that it looks less like an afterthought. I will think about this further over the next couple of days and will give you some more input at the weekend. Best wishes Mertbiol (talk) 21:41, 5 January 2023 (UTC)

I think the problem we're hitting is that the term "aptamer" does get used as a shorthand for "nucleic acid aptamer," because this is where the thrust of the research is and because, on a practical level, proteins and nucleic acids have distinct engineering applications. We see this in the sentence "Aptamers and antibodies can be used in many of the same applications, but the nucleic acid-based structure of aptamers, which are mostly oligonucleotides, is very different from the amino acid-based structure of antibodies, which are proteins. This difference can make aptamers a better choice than antibodies for some purposes (see antibody replacement)."

I suspect this is the cause of the tension. Within aptamer research, it's understood that "aptamer" means "nucleic acid aptamer" unless specified otherwise, but we can also recognize that in the abstract, "aptamer" has a more broad definition that includes peptide aptamers and possibly other chemistries. Most people who encounter the idea of aptamers (i.e. in a biochemistry class) will have the term applied specifically to nucleic acid aptamers without getting into this much detail.

In writing the article as I submitted it, I aimed to make it reflect the way the language is typically used (at least in my experience), and what I think users are expecting. When people think "aptamer," they think "a DNA or RNA ligand developed via SELEX" as the central example, and the idea of an aptamer developed via rational design, or a peptide aptamer, is a detail to treat later in the article. That's how I structured the article, with the central example up top and the details in the main body of the article. 2601:400:C100:5510:23F:84C2:22B:6429 (talk) 22:54, 5 January 2023 (UTC)

Hi @AllAmericanBreakfast: I'm afraid that approach doesn't work. You have one particular perspective, but that perspective won't be shared by others. They will vehemently disagree with "Within aptamer research, it's understood that 'aptamer' means 'nucleic acid aptamer' unless specified otherwise." Do you have a reliable source to back up your assertion?

You can't pretend for most of the article that "Aptamer = DNA/RNA Aptamer" and then suddenly introduce peptide aptamers halfway down. This is why I presented you with a choice - split the article and work up the DNA/RNA aptamer material into a GA-quality article (easy) or to integrate the peptide aptamer material fully with the rest (much more difficult). You have chosen the second option, but you are welcome to reconsider.

Best wishes Mertbiol (talk) 23:09, 5 January 2023 (UTC)

Back to the "Classification" section

Hi @AllAmericanBreakfast: I think the best thing to do now is to expand the "Classification" section. I have identified material in the "Properties" section to move up the article. The box below is an indication of how I think this section should be structured. You will obviously need to expand the text under each heading (including for the XMA aptamers, which receive very little mention in the article as it currently stands):

Nucleic acid aptamers

Most aptamers are based on a specific oligomer sequence of 20-100 bases and 3-20 kDa. Typically, DNA- and RNA-based aptamers exhibit low immunogenicity, are amplifiable via Polymerase Chain Reaction (PCR), and have complex secondary structure and tertiary structure. Chemical modifications of nucleic acid bases or backbones increase the chemical diversity of standard nucleic acid bases.

Split aptamers are composed of two or more DNA strands that are pieces of a larger parent aptamer that has been broken in two by a molecular nick. The ability of each component strand to bind targets will depend on the location of the nick, as well as the secondary structures of the daughter strands.The presence of a target molecule supports the DNA fragments joining together. This can be used as the basis for biosensors. Once assembled, the two separate DNA strands can be ligated into a single strand.

XNA aptamers

Paragraph here on XNA aptamers. XNA-based aptamers can introduce additional chemical diversity to increase binding affinity or greater durability in serum or in vivo, compared to DNA- and RNA-based aptamers.

Peptide aptamers

Peptide aptamers consist of one or more peptide loops of variable sequence displayed by a protein scaffold. The peptides that form the variable regions are synthesized as part of the same polypeptide chain as the scaffold. This structural constraint decreases the diversity of the 3D structures that the variable regions can adopt and lowers the entropic cost of molecular binding to the target.

Peptide aptamer derivatives, known as tadpoles, in which aptamer "heads" are covalently linked to unique sequence double-stranded DNA "tails", allow quantification of scarce target molecules in mixtures by PCR (using, for example, the quantitative real-time polymerase chain reaction) of their DNA tails.

Synthesis and selection

Following on from the "Classification" section, I think the next section should discuss the synthesis and selection of the different aptamer types. Again, the box below provides an indication of how I think this section should look:

Synthesis and selection

DNA, RNA and XNA aptamers

Description of SELEX and other methods go here.

Peptide aptamers

The most common peptide aptamer selection system is the yeast two-hybrid system. Peptide aptamers can also be selected from combinatorial peptide libraries constructed by phage display and other surface display technologies such as mRNA display, ribosome display, bacterial display and yeast display. These experimental procedures are also known as biopanning. All the peptides panned from combinatorial peptide libraries have been stored in the MimoDB database.

Applications

Any material remaining in the "Properties" section should then be transferred into the existing "Application" section (this includes the current "Targets" subsection).

Stopping here for now

There's a lot to do here to not only reorganise the article, but also to expand areas that are not well covered in the current text. (SELEX, for example, has a whole paragraph devoted to it in the lead section, but no mention outside the "History" section in the main part of the article.) Best wishes Mertbiol (talk) 16:25, 8 January 2023 (UTC)

@Mertbiol, it looks like the nominator is inactive and has been so for over 3 weeks now. You may need to evaluate this article based on its current state, or try to find someone else to take over the "nominator" duties of responding to comments and improving the content. ♠PMC♠ (talk) 07:08, 17 January 2023 (UTC)

@Mertbiol, you never responded to the above and the nominator is still inactive. What is your plan for this GA review? ♠PMC♠ (talk) 18:05, 3 March 2023 (UTC)

Finishing the review

Hi @AllAmericanBreakfast: There doesn't seem to have been any significant improvement in the article in the past six weeks and I am concerned that you have not engaged with this review since the start of January. The attempt to split off the material on peptide aptamers appears not to have been successful and I am also worried that there is a WP:COI with the inclusion of this website in the article.
I think it is best at this stage if I bring the review to an end. I will revert the removal of the material on peptide aptamers. I will also remove the potential WP:COI content. Best wishes Mertbiol (talk) 17:04, 6 March 2023 (UTC)

Thanks for your help in trying to make improvements - I had the impression you'd signed off from the review with your "stopping here for now" comment. If you can recover the peptide aptamer material that would be excellent, I was very frustrated with the person who decided to delete the peptide aptamer page after I had ported it over to there, and had thought it permanently lost. AllAmericanBreakfast (talk) 17:28, 6 March 2023 (UTC)

Final verdict

GA review (see here for what the criteria are, and here for what they are not)

1. It is reasonably well written.

   a (prose, spelling, and grammar): b (MoS for lead, layout, word choice, fiction, and lists):

2. It is factually accurate and verifiable.

   a (reference section): b (citations to reliable sources): c (OR): d (copyvio and plagiarism):

3. It is broad in its coverage.

   a (major aspects): b (focused):

4. It follows the neutral point of view policy.

   Fair representation without bias:

5. It is stable.

   No edit wars, etc.:

6. It is illustrated by images and other media, where possible and appropriate.

   a (images are tagged and non-free content have non-free use rationales): b (appropriate use with suitable captions):

7. Overall:

   Pass/Fail: