Jon-D's blog

I like carboxyfluorescein. It is bright, it doesn’t alter how the oligo behaves, and most labs already have a fluorescein cube (filters and dichroic mirror) for their fluorescent microscopes. The down side is that fluorescein photobleaches, so you should minimize its exposure to intense light and only observe it with the microscope when you are ready to take pictures and turn off the lamp soon. Carboxyfluorescein emits green.

Gene Tools Blue is not as bright as fluorescein but it too doesn’t alter how the oligo behaves. The problem is that it is a non-standard fluorochrome and it is expensive to purchase a cube optimized for the fluor (the wavelengths for excitation and emission are here: https://www.gene-tools.com/custom_morpholinos_controls_endmodifications#3'-GeneToolsBlue). A DAPI cube will produce some fluorescent signal, but it is not very good. Gene Tools blue emits blue.

Lissamine, also called Rhodamine B, is a bright fluorochrome and it doesn’t bleach easily but it makes the oligos less water soluble, which can be a practical problem. Lissamine emits red.

https://www.gene-tools.com/custom_morpholinos_controls_endmodifications#...

Zhong G, Wang H, He W, Li Y, Mou H, Tickner ZJ, Tran MH, Ou T, Yin Y, Diao H, Farzan M. A reversible RNA on-switch that controls gene expression of AAV-delivered therapeutics in vivo. Nat Biotechnol. 2019;[Epub ahead print] doi:10.1038/s41587-019-0357-y
Vivo-Morpholino used to control activity of an engineered ribozyme

Press release:
https://www.eurekalert.org/pub_releases/2019-12/sri-nta122419.php

Giuseppe Ronzitti. Let’s switch on AAV! Sci Transl Med. 2020;12(579) doi:10.1126/scitranslmed.aba9016 (editorial)
https://stm.sciencemag.org/content/12/529/eaba9016

Sarepta Therapeutics Announces FDA Approval of VYONDYS 53™ (golodirsen) Injection for the Treatment of Duchenne Muscular Dystrophy (DMD) in Patients Amenable to Skipping Exon 53
https://investorrelations.sarepta.com/news-releases/news-release-details...
https://www.fda.gov/news-events/press-announcements/fda-grants-accelerat...

McIntosh CS, Aung-Htut MT, Fletcher S, Wilton SD. Removal of the Polyglutamine Repeat of Ataxin-3 by Redirecting pre-mRNA Processing. Int J Mol Sci. 2019;20(21):5434. doi:10.3390/ijms20215434

https://www.mdpi.com/1422-0067/20/21/5434/htm

Excerpt from abstract:
"Here, we describe improved efficiency in the removal of the toxic polyglutamine tract of ataxin-3 in vitro using phosphorodiamidate morpholino oligomers, when compared to antisense oligonucleotides composed of 2′-O-methyl modified bases on a phosphorothioate backbone. Significant downregulation of both the expanded and non-expanded protein was induced by the morpholino antisense oligomer, with a greater proportion of ataxin-3 protein missing the polyglutamine tract. With growing concerns over toxicity associated with long-term administration of phosphorothioate oligonucleotides, the use of a phosphorodiamidate morpholino oligomer may be preferable for clinical application. These results suggest that morpholino oligomers may provide greater therapeutic benefit for the treatment of spinocerebellar ataxia type 3, without toxic effects."

Excerpt from introduction:
"Here, we describe efficient removal of the CAG containing exon 10 to produce a truncated ataxin-3
protein, lacking the polyglutamine tract, an isoform reported by Toonen et al. (2017) to be functionally
active [8]. Our study shows that by using the PMO chemistry, not only is exon 10 skipping enhanced
at the RNA level, but also significant downregulation of the protein with higher number of glutamine
repeats and an increase in production of the truncated protein is observed, when compared to the use
of the 20-Me PS AO chemistry. With robust splice switching efficiency and an established long-term
safety profile, the PMO oligomers described here are presented as lead pre-clinical candidates to treat
SCA3 patients."

Oprişoreanu A-M, Smith HL, Arya S, Webster R, Zhong Z, Wehner D, Cardozo MJ, Becker T, Talbot K, Becker CG. Interaction of Axonal Chondrolectin with Collagen XIXa1 Is Necessary for Precise Neuromuscular Junction Formation. Cell Rep. 2019;29:1082-98. doi:10.1016/j.celrep.2019.09.033

https://www.cell.com/cell-reports/fulltext/S2211-1247(19)31221-5

"Using established (Hilario et al., 2010; Zhong et al., 2012) morpholinos, we found that injection of low concentrations of either morpholino alone elicited no or only weak changes of motor axon growth (Figures 6A and 6B). However, combining these morpholinos at the same concentrations led to synergistic effects on stalling of axons at the horizontal myoseptum. Of note, total morpholino load was kept at the same level for all experiments by adding non-specific control morpholino where appropriate. This indicates a genetic interaction between chodl and col19a1(Figures 6C and 6D)."

Two Quantitative Assays for the Phosphorodiamidate #Morpholino Oligomer (PMO) SRP-4045 in Mouse Plasma Using HPLC-MS/MS Coupled with Solid Phase Micro-Extraction. Poster at ASMS 2017.

https://www.covance.com/latest-thinking/explore-library/detail.html/cova...

Development and Clinical Translation of Approved Gene Therapy Products for Genetic Disorders.

Shahryari1 A, Jazi MS, Mohammadi S, Nikoo HR, Nazari Z, Hosseini ES, Burtscher I, Mowla SJ, Lickert H.

Front Genet. 25 September 2019. doi:10.3389/fgene.2019.00868

https://www.frontiersin.org/articles/10.3389/fgene.2019.00868/full

https://www.mdpi.com/1420-3049/24/18/3287

This paper describes using a microbial transglutamase to put an azide group in a peptide onto the terminal carboxylic acid of an antibody protein, then using Cu-free click chemistry to affix an antisense oligo at that site. They didn't use Morpholinos, but in principle one could.

Huggins IJ, Medina CA, Springer AD, van den Berg A, Jadhav S, Cui X, Dowdy SF. Site Selective Antibody-Oligonucleotide Conjugation via Microbial Transglutaminase. Molecules. 2019 Sep 10;24(18). pii: E3287. doi: 10.3390/molecules24183287.

Aung-Htut MT, McIntosh CS, West KA, Fletcher S, Wilton SD. In Vitro Validation of Phosphorodiamidate Morpholino Oligomers. Molecules. 2019;24(6):2922 doi:0.3390/molecules24162922

https://www.mdpi.com/1420-3049/24/16/2922

cell culture: human dermal fibroblasts, human myoblasts
electroporation (nucelofection), Lipofectin, Lipofectamine, Endo-Porter

Gene redundancy and gene compensation: An updated view.

Peng J.

J Genet Genomics. 2019 Jul 19. pii: S1673-8527(19)30115-8. doi: 10.1016/j.jgg.2019.07.001. [Epub ahead of print] Review.

https://www.sciencedirect.com/science/article/pii/S1673852719301158