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Timing of protein measurement in a translation-blocking experiment

This was written to a researcher in response to his question about timing of assays in a translation-blocking experiment.


Friday, May 20, 2016 - 12:56
Immunology citations 2014 to early 2016

I'm headed for the American Association for Immunologists conference (AAI 2016). I assembled a citation list of many of the immunology papers published over the last couple of years. Here it is.

Some Morpholino Citations for Immunology (AAI 2016)

Furukawa R, Tamaki K, Kaneko H. Two macrophage migration inhibitory factors regulate starfish larval immune cell chemotaxis. Immunol Cell Biol. 2016 Apr;94(4):315-21. doi: 10.1038/icb.2016.6. Epub 2016 Feb 2. Patiria pectinifera (sea star)

Thursday, May 12, 2016 - 15:19
Guide for Morpholino Users: Toward Therapeutics

My open-access review paper was just published:
Moulton JD. Guide for Morpholino Users: Toward Therapeutics. Austin Journal of Drug Discovery, Development and Delivery. 2016;3(2):1023.

Wednesday, May 4, 2016 - 08:55
Brief discussion of Morpholino efficacy, specificity & controls from review in J. Cardiovasc. Dev. Dis.

Advances in the Study of Heart Development and Disease Using Zebrafish

Daniel R. Brown, Leigh Ann Samsa, Li Qian, Jiandong Liu.
J. Cardiovasc. Dev. Dis. 2016, 3(2), 13; doi: 10.3390/jcdd3020013

Keyword search "Morpholino" or go to section "3.1.2. Morpholinos" for a brief discussion of Morpholino efficacy, specificity and controls.

Monday, April 11, 2016 - 11:45
GFP targeted directly with a Morpholino - example

Makino S, Mishima Y, Inoue K, Inada T. Roles of mRNA fate modulators Dhh1 and Pat1 in TNRC6-dependent gene silencing recapitulated in yeast. J Biol Chem. 2015 Mar 27;290(13):8331-47. doi: 10.1074/jbc.M114.615088. Epub 2015 Feb 5.

"To address this question, we injected GFP reporter mRNA into zebrafish embryos and then blocked its translation using a morpholino oligomer (ATG MO) that specifically masks the start codon of the GFP ORF."

Friday, April 1, 2016 - 14:11
Morpholino for antibody validation - example

Webb AB, Lengyel IM, Jörg DJ, Valentin G, Jülicher F, Morelli LG, Oates AC. Persistence, period and precision of autonomous cellular oscillators from the zebrafish segmentation clock. Elife. 2016 Feb 13;5. pii: e08438. doi: 10.7554/eLife.08438.

Friday, April 1, 2016 - 13:41
Splicing outcomes: targeting for exon skipping or intron inclusion

Someone asked me why some Morpholinos usually cause exon skips and others cause intron inclusions...

U1 and U2 (or U11 and U12) snRNPs mark the positions on pre-mRNA of the splice junctions for the spliceosome. There is a U1 snRNP that binds in the intron near the e2i2 junction and a U2 snRNP that binds on the other side of the intron at the i2e3 junction.

Figure 1
Figure showing normal RNA splicing.

Wednesday, March 23, 2016 - 15:12
RNA therapeutics: beyond RNA interference and antisense oligonucleotides

Nice review, a few years old, describing Morpholinos and other antisense as therapeutics.

RNA therapeutics: beyond RNA interference and antisense oligonucleotides.
Kole R, Krainer AR, Altman S.
Nat Rev Drug Discov. 2012 Jan 20;11(2):125-40. doi: 10.1038/nrd3625. Review.

Tuesday, February 23, 2016 - 12:14
A nucleic acid binder, poor at binding MO

Sen D, Patel G, Patel SS. Homologous DNA strand exchange activity of the human mitochondrial DNA helicase TWINKLE. Nucl Acids Res. 2016;[Epub ahead of print] doi:10.1093/nar/gkw098

DNA binds in the protein TWINKLE, but Morpholino is very poor at that binding. No surprise, it's likely due to lack of charge, but this is a nice published example of the low-binding characteristic.

Wednesday, February 17, 2016 - 09:42
Antisense oligonucleotide-directed inhibition of nonsense-mediated mRNA decay

Here's an interesting technique: inhibition of nonsense-mediated decay with oligos. I don't think the antisense oligos were Morpholinos.

Antisense oligonucleotide-directed inhibition of nonsense-mediated mRNA decay.
Nomakuchi TT, Rigo F, Aznarez I, Krainer AR.
Nat Biotechnol. 2015 Dec 14. doi: 10.1038/nbt.3427. [Epub ahead of print]

Tuesday, February 2, 2016 - 10:24