I tested different influenza strains in vitro on TLR7 reporter lines and saw differences but want to know if the differences are due to the sequence.
I was thinking something similar as with MHC epitopes but with the RNA sequences.
Dear Jose,
It is too early to link your results to RNA sequences of Influenza strains. There are several factors to note.
1. the response to your viruses might be due to different amounts of viruses in your samples (you need to check the virus titer is equal in terms of RNA copy number.
2. It also depends on infectivity or entry of the virus into endosomes of the cells. I am sure each strain is different in terms of entry into the cells.
3. The whole genomic RNA is too big to conclude on RNA specificity towards the TLR7 as it needs just small motifs to bind and so the affinity.
4. to study the interaction between TLR7/8 and the RNA, you need to use a specific sequence that is shorter enough and pure.
5. if you really want to study the affinity, you need to do a kind of biophysical studies with pure TLR7/8 and pure RNA motifs.
The following article might be interesting to you
http://www.jimmunol.org/content/180/6/3729.long
I hope this information helps. Goodluck.
Great, Thank you.
We are measuring the the viral entry and also making sure the amount of RNA is equal.
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