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Non-specific Effects of Morpholinos

Non-specific Effects of Morpholinos - Zebrafish Forum

Non-specific Effects of Morpholinos - Zebrafish Danio Rerio Forum. Discuss zebrafish, aquarium culture and molecular biology lab specimens.

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Old 03-31-2005, 06:13 PM
Jon D. Moulton
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Default Non-specific Effects of Morpholinos


Good day, zebrafish folks;

If anyone has more information on non-specific effects of Morpholinos,
plese post your replies to the list -- those of us at Gene Tools want to
know about these as well!

One interesting report we heard is that filter sterilization of all
materials can decrease these effects, though be careful as Morpholinos
will associate with some filter materials, leading to decreased
Morpholino concentrations. We found some Pall Acrodisc filters have
little affinity for Morpholinos.

An interesting strategy to avoid toxicity of unusually toxic sequences is
to use two translation blocking Morpholinos targeting the same
transcript, for instance a 5'-UTR oligo and a start codon oligo. Since
many groups already have two such oligos for specificity confirmation, it
is a small step to inject them in combination at decreased
concentrations. Investigators have reported to us that toxic effects
have been eliminated while preserving specific knockdown by using this

An excellent investigation of a catastrophic off-target interaction
appeared in the sea urchin literature and is available online:
Coffman JA, Dickey-Sims C, Haug JS, McCarthy JJ, Robertson AJ.
Evaluation of developmental phenotypes produced by morpholino antisense
targeting of a sea urchin Runx gene. BMC Biol. 2004 May 07;2(1):6.
[Only registered users see links. ]
I expect that similar events can occur in zebrafish, though for that
organism I have not seen such detailed documentation of off-target

When Morpholinos are designed by Gene Tools, we DO NOT BLAST the
sequences to check for potential interactions with other transcripts. We
suggest that the best strategy for ordering oligos is to submit sequences
for our free design service, BLAST the complements of the oligos to check
for potential off-target interactions, and then specify the exact
antisense sequence when you order the oligos. Ordering by specifying a
GenBank number or cDNA sequence means you won't have the opportunity to
do a BLAST search.

I usually suggest that the BLAST homology should be below about 80%, but
that cutoff % is fairly arbitrary. 15 contiguous bases of homology is
the minimum inactivating length for a Morpholino (that is, less than a
15-mer oligo won't block translation), but if you flank 10 bases of
homology with a mispair at either side and then add some homologous bases
at the outside borders, you can still get a knockdown. Five mispairs
spread throughout a 25-mer almost always gives
loss-of-knockdown (so we sell five-mispair oligos as specificity
controls). If you place all five mispairs in one end of the oligo, you
still get 20 contiguous complementary bases in a 25-mer and those 20
bases would retain considerable antisense activity. My point is that
when you find a partially-homologous region, following a rule of thumb
like "less than 80% homology is OK" can lead to trouble -- you still need
to look at distribution of the mispairs.

Another problem is that BLAST searches will not tell you if you have 12
bases of homology, 1 mismatch, and 12 more bases of homology. BLAST will
simply report this as 12 bases of homology, but it is really a
single-mismatch that would very likely lead to strong knockdown by the
Morpholino. A search tool that finds these cases would be useful for
checking the likelihood of off-target interactions by Morpholinos.

Here are a few more factors to consider when comparing mismatched
sequences: losing a C-G pair impacts the oligo activity more than losing
an A-T pair (three H-bonds for G-C compared to two for A-T) and watch for
forming G-T pairs, which are non-Watson-Crick pairing but still form two
hydrogen bonds.

Thanks for sharing your experiences with off-target effects of
Morpholinos. The more everyone understands the experimental
characteristics of the oligos, the better tool they become.


- Jon

Jon D. Moulton, Ph.D.
[Only registered users see links. ]
[Only registered users see links. ]
(541) 929-7840 x1201

SKucenas wrote:
protein of interest. I've read a lot about non-specific effects of MOs
and I know what toxicity looks like with this technology. Besides the
routine neurodegeneration and slowed development, has anyone come
neural alterations that occur without any other signs of toxicity? Any
information would be greatly appreciated. Thanks!

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