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Cardenas-Rodriguez M, Drummond IA. The challenge of dissecting gene function in model organisms: Tools to characterize genetic mutants and assess transcriptional adaptation in zebrafish. Methods Cell Biol. 2023;176:1-25. doi: 10.1016/bs.mcb.2022.12.019. Epub 2023 Jan 27.
A Morpholino user, accustomed to using 25-base Morpholinos in Xenopus laevis, was concerned about a design she received for a 20-base Morpholino. She wrote to ask if we had designed many short oligos and if they worked well. Here is my response.
The key factor for performance of a Morpholino is not length but Tm. Organisms grown at different temperatures will have different optimal Tm ranges. If the Tm is too low then the oligo doesn’t stick well to RNA, too high and it will stick to off-target RNAs though high-affinity subsequences.
We like to make oligos at 25 base length because this keeps the per-base affinity low. For two oligos with the same Tm, a longer oligo has a lower per-base affinity and so is less likely to have a high-affinity subsequence that could be active against an off-target RNA.
However, there are a number of good reasons to design a shorter oligo. For instance, there might be sequences present at either side of the target that put stable self-complementarities into the oligo, causing the oligo to dimerize and lose antisense activity; sometimes it is only a 20-mer that can fit between these sequences. The target region might be flanked by lots of C bases, so that a 20-mer would have good aqueous solubility but a 25-mer would have too high a G content to dissolve well. Finally, the target sequence might make high-affinity oligos, with Tm too high for the organism they are to be used in; in this case, we will shorten an oligo to bring its Tm closer to the optimal RNA affinity.
We shorten oligos to 23 bases often, especially in organisms with zebrafish temperatures (26°C) and below. We also design shorter oligos if needed, but will typically annotate our designs to mention they are short. For bacterial work, oligos conjugated with cell-penetrating peptides are often designed as short as 12 bases (to allow them to pass though the cell envelope).
For your application, you are working in an ~18°C organism so short oligos are often needed to keep the Tm low enough to favor specificity of the Morpholino for its intended RNA target.
We have been designing many short oligos for Xenopus laevis since a 2018 paper (cited below) appeared showing there was an unacceptably high level of splice-modulation in Xenopus laevis with our usual designs (at that time, almost entirely 25-mers designed as we would for a zebrafish [26°C] transcript). Since decreasing our target Tm for Xenopus laevis designs (and often shortening the oligos to produce sequences in that Tm range), we have no longer heard from the Xenopus community about dissatisfaction with the specificity of Morpholinos (though of course, off-target effects are always possible and should be controlled for).
Gentsch GE, Spruce T, Monteiro RS, Owens NDL, Martin SR, Smith JC. Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus. Dev Cell. 2018;[Epub ahead of print] doi:10.1016/j.devcel.2018.01.022.
The innate immune debate continued:
Paraiso KD, Blitz IL, Zhou JJ, Cho KWY. Morpholinos Do Not Elicit an Innate Immune Response during Early Xenopus Embryogenesis. Dev Cell. 2019;49(4):643-50. doi:10.1016/j.devcel.2019.04.019.
Gentsch GE, Spruce T, Owens NDL, Monteiro RS, Smith JC. The Innate Immune Response of Frog Embryos to Antisense Morpholino Oligomers Depends on Developmental Stage, GC Content and Dose. Dev Cell. 2019;49(4):506-7. doi:10.1016/j.devcel.2019.05.004.
Maksudov F, Kliuchnikov E, Pierson D, Ujwal ML, Marx KA, Chanda A, Barsegov V. Therapeutic Phosphorodiamidate Morpholino Oligonucleotides, an RNA mimic: Physical Properties, Solution Structures, and Folding Thermodynamics. Mol Ther Nucleic Acids. 2023;[Epub] doi:10.1016/j.omtn.2023.02.007
Sent: Wednesday, January 18, 2023 10:17 AM
To: Jon Moulton
Subject: Translation-blocking Vivo-MO reduces gene expression on the level of mRNA?
I find that the translation-blocking Vivo-MO is able to significantly reduce the copies on the level of mRNA. I use qPCR and RNAseq to confirm that the mRNA of my target gene is down-regulated by more than 4-fold at 24 hours after injection, and by more than 10-fold at 7 days after injection. Such knockdown effect is impressive, but theoretically, translation blocking MO only blocks translation, which should reduces the level of protein, rather than the level of mRNA. I am just curious about why translation-blocking MO also have effect on the mRNA level.
I also try splice-modifying Vivo-MO, which also knockdown gene expression significantly. But in my case, translation-blocking MO always induces stronger phenotype than the splice-modifying one. I hope this information will be useful to other researchers.
Have a nice day.
Binding a Morpholino to an RNA can change the stability of the RNA -- we hypothesize that this is due to change of the secondary structure making the RNA more susceptible to nucleolytic attack. However, we cannot predict what kind of change will occur: when Morpholinos bind RNA there have been reports of degradation, stabilization and lack of effect on RNA lifetime. Because of this we suggest that all translation blocking Morpholinos should be assessed at the level of protein using an immunochemical assay; this gives a more reliable signal.
Thanks for reporting your observation of a decrease in the RNA on binding a Morpholino translation-blocking oligo. May I have your permission to post these two messages on my blog? I would be happy to remove identifying information from your email if you like (let me know your preference). I think this would be useful exchange for others to read.
Lim, K.R.Q., Yokota, T. (2018). Invention and Early History of Exon Skipping and Splice Modulation. In: Yokota, T., Maruyama, R. (eds) Exon Skipping and Inclusion Therapies. Methods in Molecular Biology, vol 1828. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8651-4_1
Master’s thesis based on microarray analysis of WT, Morphant and rescue fish
Tuttle, Matthew Alan (2017)
In silico analysis of zebrafish leptin-a knockdown gene expression data reveals enrichment for metabolic and developmental pathways including morpholino artifacts
Liang H, Li Y, Li M, Zhou W, Chen J, Zhang Z, Yang Y, Ran C, Zhou Z. The effect and underlying mechanism of yeast β-glucan on antiviral resistance of zebrafish against spring viremia of carp virus infection. Front Immunol. 2022 Nov 3;13:1031962. doi: 10.3389/fimmu.2022.1031962. eCollection 2022.
"Zebrafish larvae (4dpf) were added with 25 nmol/L of CRFB1 and CRFB2 vivo MO (CRFB1 and CRFB2 vivo MO were added together during the experiment), or standard control vivo MO, and then treated with 0.05% β-glucan for 24 h. At 7 dpf, 0.1 MOI SVCV was added. At 9 dpf, zebrafish larvae were collected and SVCV replication in the larvae was measured by qPCR."