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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:


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

ATTTTGACAGgtgtacgttattgccgctcgcgcgc e1i1
agcagtgacagtgacgagacgtcagGTTTTGTGCA i1e2
AGTAAACAAGgtgccctgcatacgcgctcgtcgaa e2i2
tagctctagatcccaatagcgcaagGGTGGCCCTC i2e3

These can go into a .txt or .doc file. For a pair of pesudoalleles (i.e. for Xenopus laevis oligo designs), give each example of a junction like this:

ATTTTGACAGgtgtacgttattgccgctcgcgcgc e1i1 .S
ATTTTGTCAGgtgtacgttaaagccgctcgcgcgc e1i1 .L

With the sequence information in text the design should be quick.

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

2. Moulton JD. Making a Morpholino Experiment Work: Controls, Favoring Specificity, Improving Efficacy, Storage, and Dose. Methods Mol Biol. 2017;1565:17-29. doi: 10.1007/978-1-4939-6817-6_2. Abstract: PubMed

3. Chow G, Morcos PA, Moulton HM. Aggregation and Disaggregation of Morpholino Oligomers in Solution. Methods Mol Biol. 2017;1565:31-38. doi: 10.1007/978-1-4939-6817-6_3. Abstract: PubMed

4. Li YF. End-Modifications on Morpholino Oligos. Methods Mol Biol. 2017;1565:39-50. doi: 10.1007/978-1-4939-6817-6_4. Abstract: PubMed

5. Sumanas S. Inducible Inhibition of Gene Function with Photomorpholinos. Methods Mol Biol. 2017;1565:51-57. doi: 10.1007/978-1-4939-6817-6_5. Abstract: PubMed

6. Flynt AS, Rao M, Patton JG. Blocking Zebrafish MicroRNAs with Morpholinos. Methods Mol Biol. 2017;1565:59-78. doi: 10.1007/978-1-4939-6817-6_6. Abstract: PubMed

7. Thummel R, Kathryn Iovine M. Using Morpholinos to Examine Gene Function During Fin Regeneration. Methods Mol Biol. 2017;1565:79-85. doi: 10.1007/978-1-4939-6817-6_7. Abstract: PubMed

8. Materna SC. Using Morpholinos to Probe Gene Networks in Sea Urchin. Methods Mol Biol. 2017;1565:87-104. doi: 10.1007/978-1-4939-6817-6_8. Abstract: PubMed

9. Voiculescu O, Stern CD. Manipulating Gene Expression in the Chick Embryo. Methods Mol Biol. 2017;1565:105-114. doi: 10.1007/978-1-4939-6817-6_9. Abstract: PubMed

10. Daly SM, Sturge CR, Greenberg DE. Inhibition of Bacterial Growth by Peptide-Conjugated Morpholino Oligomers. Methods Mol Biol. 2017;1565:115-122. doi: 10.1007/978-1-4939-6817-6_10. Abstract: PubMed

11. Krtková J, Paredez AR. Use of Translation Blocking Morpholinos for Gene Knockdown in Giardia lamblia. Methods Mol Biol. 2017;1565:123-140. doi: 10.1007/978-1-4939-6817-6_11. Abstract: PubMed

12. Gong Q, Zhou Z. Regulation of Isoform Expression by Blocking Polyadenylation Signal Sequences with Morpholinos. Methods Mol Biol. 2017;1565:141-150. doi: 10.1007/978-1-4939-6817-6_12. Abstract: PubMed

13. Crossley MP, Krude T. Targeting Functional Noncoding RNAs. Methods Mol Biol. 2017;1565:151-160. doi: 10.1007/978-1-4939-6817-6_13. Abstract: PubMed

14. Liu G. Use of Morpholino Oligomers for Pretargeting. Methods Mol Biol. 2017;1565:161-179. doi: 10.1007/978-1-4939-6817-6_14. Abstract: PubMed

15. Levicky R, Koniges U, Tercero N. Diagnostic Applications of Morpholinos and Label-Free Electrochemical Detection of Nucleic Acids. Methods Mol Biol. 2017;1565:181-190. doi: 10.1007/978-1-4939-6817-6_15. Abstract: PubMed

16. Rajsbaum R. Intranasal Delivery of Peptide-Morpholinos to Knockdown Influenza Host Factors in Mice. Methods Mol Biol. 2017;1565:191-199. doi: 10.1007/978-1-4939-6817-6_15. Abstract: PubMed

17. Maruyama R, Echigoya Y, Caluseriu O, Aoki Y, Takeda S, Yokota T. Systemic Delivery of Morpholinos to Skip Multiple Exons in a Dog Model of Duchenne Muscular Dystrophy. Methods Mol Biol. 2017;1565:201-213. doi: 10.1007/978-1-4939-6817-6_17. Abstract: PubMed

18. Karunakaran DK, Kanadia R. In Vivo and Explant Electroporation of Morpholinos in the Developing Mouse Retina. Methods Mol Biol. 2017;1565:215-227. doi: 10.1007/978-1-4939-6817-6_18. Abstract: PubMed

19. Nizzardo M, Rizzuti M. Intracerebroventricular Delivery in Mice for Motor Neuron Diseases. Methods Mol Biol. 2017;1565:229-239. doi: 10.1007/978-1-4939-6817-6_19. Abstract: PubMed

20. Wang X, Dunlap KA. Delivery of Morpholino Antisense Oligonucleotides to a Developing Ovine Conceptus via Luminal Injection into a Ligated Uterine Horn. Methods Mol Biol. 2017;1565:241-250. doi: 10.1007/978-1-4939-6817-6_20. Abstract: PubMed

21. Boutilier J, Moulton HM. Surface Plasmon Resonance-Based Concentration Determination Assay: Label-Free and Antibody-Free Quantification of Morpholinos. Methods Mol Biol. 2017;1565:251-263. doi: 10.1007/978-1-4939-6817-6_21. Abstract: PubMed

22. Burki U, Straub V. Ultrasensitive Hybridization-Based ELISA Method for the Determination of Phosphorodiamidate Morpholino Oligonucleotides in Biological samples. Methods Mol Biol. 2017;1565:265-277. doi: 10.1007/978-1-4939-6817-6_22. Abstract: PubMed

nasal administration of delivery-enabled Morpholino in mice

This paper is an example of nasal administration of a delivery-enabled Morpholino in mice.

Soonthornvacharin S, Rodriguez-Frandsen A, Zhou Y, Galvez F, Huffmaster NJ, Tripathi S, Balasubramaniam VRMT, Inoue A, de Castro E, Moulton H, Stein DA, Sánchez-Aparicio MT, De Jesus PD, Nguyen Q, König R, Krogan NJ, García-Sastre A, Yoh SM, Chanda SK. Systems-based analysis of RIG-I-dependent signalling identifies KHSRP as an inhibitor of RIG-I receptor activation. Nat Microbio. 2017;2:17022. doi:10.1038/nmicrobiol.2017.22\

"Mice were anaesthetized ... and inoculated via the intranasal route (i.n.) with the indicated 100 μg of PPMOs or PR8 influenza virus (500 plaque-forming units (p.f.u.)) in 40 μl PBS."

Abdominal injection of Vivo-Morpholino in fish for oocyte knockdown

Injection of Vivo-Morpholinos into the abdominal cavity of medaka was used to knock down mPRα in the oocytes.

Roy SR, Wang J, Rana MR, Nakashima M, Tokumoto T. Characterization of membrane progestin receptor α (mPRα) of the medaka and role in the induction of oocyte maturation. Biomed Res. 2017;38(1):79-87. doi: 10.2220/biomedres.38.79.


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