You are here

Jon's Blog

Post date
Targeting internal exon caused intron inclusion: example of a less-common outcome

Here is an example where targeting an internal exon of a pre-mRNA caused inclusion of the adjacent intron, an unusual outcome.

Vierstraete J, Willaert A, Vermassen P, Coucke PJ, Vral A, Claes KBM. Accurate quantification of homologous recombination in zebrafish: brca2 deficiency as a paradigm. Sci Rep. 2017;7:16518. doi:10.1038/s41598-017-16725-3

https://www.nature.com/articles/s41598-017-16725-3

Tuesday, November 28, 2017 - 08:27
Combining Vivo-Morpholinos & Endo-Porter in a hard-to-transfect cell line

These investigators report enhanced delivery of Vivo-Morpholinos by combining them with Endo-Porter to deliver the oligos into a hard-to-transfect cell line.

Adamo P, Porazinski S, Rajatileka S, Jumbe S, Hagen R, Cheung MK, Wilson I, Ladomery MR. The oncogenic transcription factor ERG represses the transcription of the tumour suppressor gene PTEN in prostate cancer cells. Oncol Lett. 2017 Nov;14(5):5605-5610. doi: 10.3892/ol.2017.6841. Epub 2017 Aug 28.

Monday, November 27, 2017 - 11:23
On the difficulty of making a good null mutant

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.10...

Anderson JL, Mulligan TS, Shen M-C, Wang H, Scahill CM, Tan FJ, Du SJ, Busch-Nentwich EM, Farber SA. mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay. PLoS Genet. 2017;13(11):e1007105. doi:10.1371/journal.pgen.1007105

Tuesday, November 21, 2017 - 12:44
ON-based drugs approved by the FDA

Here they are so far, the approved oligonucleotide drugs. Note, however, that Morpholinos are oligos but not nucleotides; Exondys 51 (eteplirsen) is the Morpholino drug.

Table 1. ON-based drugs approved by the FDA.

Tuesday, October 24, 2017 - 11:31
Guidelines for morpholino use in zebrafish

If you work with zebrafish or Morpholinos, please read this.

Stainier DYR, Raz E, Lawson ND, Ekker SC, Burdine RD, Eisen JS, Ingham PW, Schulte-Merker S, Yelon D, Weinstein BM, Mullins MC, Wilson SW, Ramakrishnan L, Amacher SL, Neuhauss SCF, Meng A, Mochizuki N, Panula P, Moens CB. Guidelines for morpholino use in zebrafish. PLoS Genet. 2017 Oct 19;13(10):e1007000. doi: 10.1371/journal.pgen.1007000. eCollection 2017 Oct. No abstract available.

Friday, October 20, 2017 - 08:31
Mechanism of uptake of Morpholino oligos in dystrophic (DMD) muscle

This work elucidates the mechanism of uptake of Morpholino oligos in dystrophic (DMD) muscle, including roles for muscle satellite cells and macrophages.

Myoblasts and macrophages are required for therapeutic morpholino antisense oligonucleotide delivery to dystrophic muscle.

Novak JS, Hogarth MW, Boehler JF, Nearing M, Vila MC, Heredia R, Fiorillo AA, Zhang A, Hathout Y, Hoffman EP, Jaiswal JK, Nagaraju K, Cirak S, Partridge TA.

Nat Commun. 2017 Oct 16;8(1):941. doi: 10.1038/s41467-017-00924-7.

Thursday, October 19, 2017 - 10:36
Time for some music! Evo-devo

Evo-Devo
https://www.youtube.com/watch?v=ydqReeTV_vk&feature=youtu.be

Wednesday, September 27, 2017 - 11:47
Confirming Specificity

There are several commonly-used strategies for confirming specificity of a Morpholino oligo. These are the five-mispair experiment, the second non-overlapping 5'-UTR oligo experiment (and the similar two oligos against one mRNA experiments), the mRNA rescue experiment, and my current favorite, the Morpholino-in-a-null-mutant experiment.

Wednesday, September 27, 2017 - 08:46
Review of eteplirsen for DMD

Mutation-Based Therapy for Duchenne Muscular Dystrophy: Antisense Treatment Arrives in the Clinic.
Elizabeth M. McNally, Eugene J. Wyatt.
Circulation. 2017;136:979-981.
doi:CIRCULATIONAHA.117.028382

http://circ.ahajournals.org/content/136/11/979.full

Monday, September 11, 2017 - 14:04
BLAST homology and specificity controls

I have had many discussions about specificity with a Morpholino user who does very careful BLAST analysis of each oligo prior to ordering. I had previously suggested that about 14 bases of complementary (without significant flanking complementarity) is probably an acceptable level of stability for off-target interactions found by BLAST. However, in light of a new report I agreed that a 13-base complementarity at a splice junction is enough to raise concern. Here is an excerpt of my response to her.

-----------------------------------------------

Wednesday, August 2, 2017 - 08:21

Pages