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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.

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Wednesday, August 2, 2017 - 08:21
Paper on Morpholino specificity and CRISPR-MO combination

Number of inadvertent RNA targets for morpholino knockdown in Danio rerio is largely underestimated: evidence from the study of Ser/Arg-rich splicing factors.

Joris M, Schloesser M, Baurain D, Hanikenne M, Muller M, Motte P.

Nucleic Acids Res. 2017;[Epub ahead of print] doi:10.1093/nar/gkx638.

https://academic.oup.com/nar/article/doi/10.1093/nar/gkx638/3984534/Numb...

Tuesday, August 1, 2017 - 14:35
Formatting sequence information for emails (splice modifying oligo designs)

To email sequence information for design of a splice-modifying Morpholino, write introns in lower case and exons in upper case and write the sense sequence 5'-3'. If you show a start codon, put parentheses around it. Here is an example:

GGTGATGTAGTACGC(ATG)GTAGACCATTTTGACAGgtgtacgttattgccgctcgcgcgcgtagcagtgacagtgacgagacgtcagGTTTTGTGCATGCGGCGTAGTAAACAAGgtgccctgcatacgcgctcgtcgaatagctctagatcccaatagcgcaagGGTGGCCCTCGAT

All I need for the design are 10 exonic and 25 intronic bases, like this:

Tuesday, July 25, 2017 - 08:02
Genetic compensation: A phenomenon in search of mechanisms

Genetic compensation: A phenomenon in search of mechanisms.

El-Brolosy MA, Stainier DYR.

PLoS Genet. 2017 Jul 13;13(7):e1006780. doi: 10.1371/journal.pgen.1006780. eCollection 2017 Jul. Review.

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

Friday, July 14, 2017 - 10:29
Book: Morpholino Oligomers

Hong and I edited a book: Morpholino Oligomers. 2017. Methods in Molecular Biology. Volume 1565. Humana Press (Springer). doi:10.1007/978-1-4939-6817-6

Links to chapters follow.

1. Summerton JE. Invention and Early History of Morpholinos: From Pipe Dream to Practical Products. Methods Mol Biol. 2017;1565:1-15. doi: 10.1007/978-1-4939-6817-6_1. Abstract: PubMed

Tuesday, April 11, 2017 - 01:57
Review of FDA-approved antisense (2017)

FDA-Approved Oligonucleotide Therapies in 2017.
Stein CA, Castanotto D.
Mol Ther. 2017 Mar 30. pii: S1525-0016(17)30122-3. doi: 10.1016/j.ymthe.2017.03.023. [Epub ahead of print] Review.
http://www.cell.com/molecular-therapy-family/molecular-therapy/fulltext/S1525-0016(17)30122-3

Thursday, April 6, 2017 - 08:40
Using Morpholinos to Control Gene Expression (in CPNAC)

Wiley has published an update to my Morpholino how-to and background review.

Moulton JD. Using Morpholinos to Control Gene Expression. Curr Protoc Nucleic Acid Chem. 2017 Mar 2;68:4.30.1-4.30.29. doi: 10.1002/cpnc.21.

http://onlinelibrary.wiley.com/doi/10.1002/cpnc.21/abstract

Saturday, March 4, 2017 - 03:26

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