Talk:Morpholino

message: Nice editing, Daycd, the flow of the article has improved.  However, I removed your assertion that Morpholinos are in Phase III clinical trials.  While the AVI website may give that impression, there are currently no ongoing phase III trials. Jon
:Hi Jon, I'm glad you approve.  I got the phase three from the web site but obviously you should know better. David D. (Talk) 22:00, 30 August 2005 (UTC)
thread_title: 30 Aug 05

message: I removed the  tag from external links since all of the promises made in the text associated with that link are false: Morpholinos are not available from the listed suppliers, the MSDSs are not available from that page, there is no spectroscopic data available there, etc.  As Morpholinos are custom-synthesized compounds the spectroscopic data are only available from the manufacturer (Gene Tools or AVI Biopharma) and vary with the sequence of the oligo. —Preceding unsigned comment added by JonMoulton (talk • contribs)  (and added nowiki by Dirk Beetstra T C 15:56, 20 July 2006 (UTC)
replies: text: I saw the edit, I think it is right to delete the ChemicalSources template here, though now the only link there is one to a company that you are working for.  I would call that a commercial link.  Could you please think that over?  Maybe the complete external links section should go, or you should put your link into the Wikipedia:Chemical sources page (and reinstate the chemicalsources template) to avoid any commercial bias on the page.  --Dirk Beetstra T C 15:56, 20 July 2006 (UTC)
thread_title: 20 July 06

message: A lead sentance had been added saying "In biochemistry, a morpholino is a kind of molecule used for genetic engineering. "  Because Morpholinos do not modify DNA, I do not think it is appropriate to say they are used for genetic engineering, which is a field generally involving artificial genetic recombination.  Further, as Morpholinos have their direct effect at the gene expression level instead of the metabolic level, they are more closely related to molecular biology than to biochemistry.  I have changed the first sentance to:  "In molecular biology, a Morpholino is a kind of molecule used to modify gene expression. "  Overall, I think that the addition of an introductory sentance is an improvement in the article and that the general form of the sentance was very good.  These changes fine-tune the focus to the actual uses of Morpholino oligos.
JonMoulton 15:28, 19 September 2006 (UTC)
thread_title: 19 Sept 06

message: A statement that "Claim for absence of non-specific effects has been contested" has been added to the top of the Morpholino page.  As far as I can tell the page does not claim that Morpholinos have no non-specific effects.  Certainly the sequence-specificity of Morpholinos is not perfect, and targets with several mismatched bases can be knocked down.  However, the sequence specificity is better than available from other antisense types, such as phosphorothioate oligo or siRNA, due to the longer complementarity required for Morpholino activity.  I would be happy to discuss this further.  NPOV has also been challenged; I would welcome the input of experienced Morpholino users in editing this page. I have tried to maintain NPOV but I think it would be better to have strong editorial input from independent Morpholino users. JonMoulton 16:47, 19 October 2006 (UTC)
replies: text: The user who attached the NPOV tag is not registered, but I have requested clarification on the IP address' talk page. Shultzc 09:49, 26 October 2006 (UTC)
thread_title: 19 Oct 06

message: I accidentally edited the main page without signing in as JonMoulton:
00:45, 20 February 2007 65.249.23.4 (Talk) (Move Talk Board link to top level)
The last reference pointed to the siRNA vs. Morpholino discussion on the Morpholino talk board.  I did not see how this was germane to the comment on intellectual property claims, where the outside talk board was referenced within the Wikipedia article text.  I modified the link to point at the top level of the Morpholino talk board, so that a user can scan through the upper-level catagories and find a path into the discussion most useful for their needs.
JonMoulton 00:50, 20 February 2007 (UTC)
thread_title: 19 Feb 07

message: I removed this text from the section on specificity:
or the comparison with alternative antisense (for example GripNAs)
The new paper on p53 knockdowns by Steve Ekker showed that gripNA oligos caused the same "Morpholino phenotype" as the Morpholinos, and this phenotype (small head, shortened body axis, specific neurodegeneration) is caused by p53-mediated apoptosis.  Therefore it appears that the  phenotype comes not from the antisense backbone, but from the knockdown of the targeted gene, implying the apoptotic effect is independant of knockdown technology.
JonMoulton 17:00, 12 April 2007 (UTC)
thread_title: 12 April 07

message: The article was changed to claim that Morpholinos are in clinical trials as anticancer therapies:
They have been used in mammals ranging from mice[11] to humans and some are currently being tested in clinical trials as anticancer therapies.[12]
They are not; current clinical trials include West Nile virus, Hepatitis C, Duchenne's muscular dystrophy and a coronary artery bypass graft anti-stenosis trial.  Therefore I removed the claim regarding anticancer therapies.
JonMoulton 15:01, 29 May 2007 (UTC)
thread_title: 29 May 07

message: This article's Good Article promotion has been put on hold. During review, some issues were discovered that can be resolved without a major re-write.  This is how the article, as of  , , compares against the  six good article criteria:
:1. Well written?: On the whole, not too bad, but my main critisism of this article would be the excessive use of jargon.  For example, the article talks about "U" this and "U" that without ever explaining what "U" is. There are many other scientific items that appear in the same way, that could be linked to help with their explaination. This really needs to be fixed before morpholino can be considered a GA.
:2. Factually accurate?: Seems pretty accurate
:3. Broad in coverage?: Could benefit from some additional sentences or sections to give the overall picture (i.e. why knockdown genes, how does it relate to the processes of translation) or to explain delivery methods and method of action a little better (a simple diagram would help here).  And the Specificity, stability and non-antisense effects section - is this the same as saying the pros and cons??
:4. Neutral point of view?: seems neutral
:5. Article stability? no edit wars are occuring
:6. Images?: as mentioned above, would benefit from a diagram to two to help visualize the activity of morpholinos. Current image meets copyright criteria
Please address these matters soon and then leave a note here showing how they have been resolved.  After 48 hours the article should be reviewed again.  If these issues are not addressed within 7 days, the article may be failed without further notice.  Thank you for your work so far
Ciar 18:22, 31 May 2007 (UTC)
thread_title: Good article nomination on hold

message: The following recent addition seems to have a few flaws:
:Knocking down gene expression is a powerful method for learning about the function of a particular protein; similarly, causing a specific exon to be spliced out of a protein can help to determine the function of the protein domain encoded by that exon. 
While it is possible that an exon MAY contain a domain this is not always the case.  I think this might be a bit misleading. David D. (Talk) 18:16, 6 June 2007 (UTC)
thread_title: Introduction

message: I am glad to say that this article which was nominated for good article status has succeeded. This is how the article, as of June 8, 2007, compares against the  six good article criteria:
:1. Well written?: The quality of writing is pretty good, and has improved a lot since initial review. This can still be made better though, so keep up the good work!
:2. Factually accurate?: To my knowledge, the information seems highly accurate.
:3. Broad in coverage?: Aspects of morpholino's are covered from structure, to function, to delivery - what else could there be?
:4. Neutral point of view?: This is a neutral article
:5. Article stability? No edit wars are occurring - it's very stable.
:6. Images?: Now several images are in place, instead of just one, that helps explain the activity of these little molecules. Much better!
If you feel that this review is in error, feel free to take it to a GA review. Thank you to all of the editors who worked hard to bring it to this status.
Ciar 05:36, 8 June 2007 (UTC)
thread_title: Successful [[Wikipedia:Good articles|good article]] nomination

message: Morpholino is used as a trade name to describe morpholino phosphorodiamidate oligomers.  Therefore it is appropriate to capitalize Morpholino, as you would capitalize Kleenex or Aspirin (http://en.wikipedia.org/wiki/Trade_name).  The word "morpholino" is also used to describe chemical structures having morpholine rings as substituants; therefore the use of the uncapitalized "morpholino" to describe the morpholino phosphorodiamidate oligomers can be confusing.  As the capitalization is appropriate for a trade name and the uncapitalized usage can be confusing, I strongly urge reversion to the capitalized usage.
JonMoulton (talk) 16:00, 23 May 2008 (UTC)
thread_title: Argument to revert to capitalized "Morpholino"

message: The word "phosphorothioate" had been make into a link, but no phosphorothioate page exists at this time.  I have removed the link.
JonMoulton (talk) 18:23, 30 November 2009 (UTC)
thread_title: removal of dead link "Phosphorothioate"

message: :This discussion is transcluded from Talk:Morpholino/GA1. The edit link for this section can be used to add comments to the reassessment.
===GA Sweeps: On hold===
As part of the WikiProject Good Articles, we're doing Sweeps to determine if the article should remain a Good article. I believe the article currently meets the majority of the criteria and should remain listed as a GA. However, in reviewing the article, I have found there are several issues that need to be addressed.
#The "Normal gene expression in eukaryotes", "Specificity, stability and non-antisense effects", and "Intellectual property" sections could use additional sourcing. 
#:"Normal gene expression in eukaryotes" looks like just a summary of the relevant details of material covered in depth with cites elsewhere. I added a  for it. Does it still need a ref here? Could copy over some of the genetics textbooks from Introduction to genetics#Further_reading, but not sure how much/what is appropriate for this type of summary-article-like section. DMacks (talk) 22:48, 14 February 2010 (UTC)
thread_title: GA Reassessment

message: As part of the WikiProject Good Articles, we're doing Sweeps to determine if the article should remain a Good article. I believe the article currently meets the majority of the criteria and should remain listed as a GA. However, in reviewing the article, I have found there are several issues that need to be addressed.
#The "Normal gene expression in eukaryotes", "Specificity, stability and non-antisense effects", and "Intellectual property" sections could use additional sourcing. 
#:"Normal gene expression in eukaryotes" looks like just a summary of the relevant details of material covered in depth with cites elsewhere. I added a  for it. Does it still need a ref here? Could copy over some of the genetics textbooks from Introduction to genetics#Further_reading, but not sure how much/what is appropriate for this type of summary-article-like section. DMacks (talk) 22:48, 14 February 2010 (UTC)
thread_title: GA Sweeps: On hold

message: Good work addressing the issues. I went through and made some minor changes, please review my edits. I believe the article currently meets the criteria and should remain listed as a Good Article. Continue to improve the article making sure all new information is properly sourced and neutral. If you have any questions, let me know on my talk page and I'll get back to you as soon as I can. I have updated the article history to reflect this review. --Happy editing! Nehrams2020 (talk • contrib) 03:05, 22 February 2010 (UTC)
thread_title: GA Sweeps: Kept

message: On 21 August 2012‎, user NickCT reworded the opening paragraph.  In doing so he identified Morpholino oligos as a form of small interfering RNA (siRNA).  Morpholinos are not RNA and, unlike small interfering RNA, they do not operate within the RNA-induced silencing complex (RISC).  Because their mechanism of action, structure, and targeting procedures are all different from siRNA, I reverted the lead paragraph to its original form.  Nick, feel free to edit again to bring the tradename link forward etc.
JonMoulton (talk) 20:31, 29 August 2012 (UTC)
thread_title: Reverted revision

message: On 29 January 2014, user Inferior Olive changed the case of "Morpholino" to "morpholino" at the start of paragraph 2.  This usage is inconsistant with the rest of the article and contradicts the message of the rest of paragraph 2, so I changed the case back to its original "Morpholino".  The case was similarly changed in one instance in paragraph 1, though it was left in the upper-case form in other instances in paragraph 1; likewise, I changed that back to the original usage "Morpholino". In paragraph 1, the term "nucleic acids" was added to "antisense" to describe Morpholino oligos.  Since Morpholinos are not nucleic acids (they do not occur naturally in the nucleus and they are not acidic), I removed that term; to address Inferior Olive's concern about using "antisense" as a noun, I altered the text to "a class of antisense". In paragraph 1, the link nucleic acid was changed to nucleic acids; the Wikipedia page both links refer to is named "nucleic acid" and so I changed the link back to the direct form "nucleic acid"instead of the redirected "nucleic acids" JonMoulton (talk) 17:04, 3 February 2014 (UTC)
thread_title: Some reverted revisions

message: The first sentence of the article had been:
 	
In molecular biology, Morpholino describes a molecule ...
User jmh649 altered the lead sentence to read:
Morpholino describes a molecule ...
The clause "In molecular biology," serves a specific purpose in the lead sentence.  The word "Morpholino" is used in organic chemistry to describe a specific chemical moiety (a morpholine ring covalently attached to another structure).  The usage of "Morpholino" to describe a structural family of antisense molecules is a usage specific to biologists, especially molecular and developmental biologists.  By removing the clause "In molecular biology," the lead sentence implies that "Morpholino" refers exclusively to that class of antisense molecules, but this incorrectly excludes the widespread use of the term in organic chemistry.  To avoid that implication, I am reverting the lead sentence to its previous form which restricts this definition to the field of molecular biology. JonMoulton (talk) 16:04, 14 February 2014 (UTC)
replies: text: Sure, switched ordering though. Doc James (talk · contribs · email) (if I write on your page reply on mine) 16:06, 14 February 2014 (UTC)
thread_title: reverted revision 14 Feb 2014

message: A set of revisions by FeatherPluma on 21 Sept 2015 created the sentances:
"The molecular structure has a phosphorodiamidate molecular backbone, which blocks access of other molecules to specific sequences within antisense nucleic acid sequences. Morpholinos block small (~25 base) regions of the base-pairing surfaces of ribonucleic acid (RNA)."
The structure has a backbone comprised of both the methylenemorpholine moeity and a phosphorodiamidate linkage.  It is not the backbone which blocks access to RNA, it is the entire Morpholino with its bases; the bases are in closest contact with the pairing surface of RNA. Morpholinos generally do not block antisense nucleic acid; most commonly they target sense nucleic acid. I have modified the sentances thus:
"The molecular structure has a backbone of methylenemorpholine rings and phosphorodiamidate linkages. Morpholinos block access of other molecules to small (~25 base) specific sequences of the base-pairing surfaces of ribonucleic acid (RNA)."
In revisions by FeatherPluma on 21 Sept 2015, the sentence "Most Morpholinos are used as research tools for reverse genetics by knocking down gene function" was changed to read "PMOs are used as research tools for reverse genetics by knocking down gene function. They are being studied for application in medicine."  
Because most researchers do not use the PMO designation (primarily used by drug developers) but instead call the oligos "Morpholinos", I am altering the sentences to "Morpholinos are used as research tools for reverse genetics by knocking down gene function. They are being studied for application in medicine."
JonMoulton (talk) 20:14, 12 October 2015 (UTC)
thread_title: Revisions in lead paragraph September/October 2015

message: One at least has reached late stage clinical trials : Eteplirsen.  (drisapersen is similiar but not a Morpholino ?) ? - Rod57 (talk) 17:03, 23 April 2016 (UTC)
thread_title:  Can we start a section listing the ones in clinical use or trials 

message: Substituted at 00:27, 30 April 2016 (UTC)
thread_title: Assessment comment

message: Another Morpholino drug has been approved by the US FDA, golodirsen.  I have declared COI and should not add the link myself.  https://investorrelations.sarepta.com/news-releases/news-release-details/sarepta-therapeutics-announces-fda-approval-vyondys-53tm  https://www.fda.gov/news-events/press-announcements/fda-grants-accelerated-approval-first-targeted-treatment-rare-duchenne-muscular-dystrophy-mutation
JonMoulton (talk) 21:04, 13 December 2019 (UTC)
replies: text: . — kashmīrī TALK 02:27, 14 December 2019 (UTC)
thread_title: Request for someone to add drug approval

message: It would be useful to add a link to the Antisense_therapy page in the first paragraph, which already contains the (unlinked) term "antisense therapies".  This would provide context, showing where Morpholinos fit into the broader field of antisense therapeutics. I have been asked not to modify this page myself due to conflict of interest. JonMoulton (talk) 15:43, 11 March 2020 (UTC)
thread_title:  Link to Antisense Therapy page would be useful. 

message: A recent change to the Morpholino page ruined the meaning of a sentence and should be changed back.  I have been asked not to make changes in the page due to a conflict of interest, so I must request that someone else helps out.
On 12 May 2020, Timegg113 modified the Morpholino page, changing a "to" to a "too" in the following sentence.
Original:
Morpholinos block access of other molecules to small (~25 base) specific sequences of the base-pairing surfaces of ribonucleic acid (RNA). (note: this is two revisions back) 
Modified:
Morpholinos block access of other molecules too small (~25 base) specific sequences of the base-pairing surfaces of ribonucleic acid (RNA). 
The Morpholinos are not, however, "too small" (overly tiny).  Instead, the Morpholino is blocking access of a molecule "to" a specific sequence.  The modification (to->too) broke the grammar of the sentence and should be changed back.
Thanks in advance,
JonMoulton (talk) 19:14, 12 May 2020 (UTC)
replies: text: This is an unambigous grammatical error. In this case, and for all minor edits, you may make your requested changes. 's talk page! 19:27, 12 May 2020 (UTC)
thread_title:  Revision was ungrammatical - please change back 

message: On the Morpholino page, in the first paragraph, the word "modify" was changed by TheBartgry on 02 Jan 2021 to "specifically suppress".  However, suppression of gene expression is only one of the applications of Morpholinos, which can be used to upregulate gene expression (e.g. by blocking a miRNA target) or to target transcripts with frameshift mutations to restore the reading frame and cause gain-of-function (the basis for the four Morpholino drugs approved by the FDA).  Therefore, the term "specifically suppress" is inappropriate to describe the range of applications of Morpholino antisense oligos.  I reverted the text.  JonMoulton (talk)  — Preceding undated comment added 16:20, 1 March 2021 (UTC)
replies: text: Thank you for correcting me. I was misinformed by one of my sources. --TheBartgry (talk) 16:32, 1 March 2021 (UTC)
thread_title: 1 Mar 2021

message: The Journal of Visualized Experiments (JoVE) has published a Science Education video for Morpholinos.  That would probably be a useful link for the Morpholino page.  As I am categorized as a conflict-of-interest person, I should not add it myself.
Gene Silencing with Morpholinos. 
JoVE, Cambridge, MA, (2022).
JoVE Science Education Database. 
https://www.jove.com/v/5326/gene-silencing-with-morpholinos
::::  — Preceding unsigned comment added by JonMoulton (talk • contribs) 19:41, 23 August 2022 (UTC)
thread_title: 23 Aug 22

message: I am no longer an employee of Gene Tools LLC, and so I no longer have a commercial conflict of interest with the topic of this page (Morpholino).
JonMoulton (talk) 20:33, 1 April 2024 (UTC)
thread_title: 01 Apr 2024