Confusing aptamer shapedata

I found the lab results a bit strange this time. I’m surprised that so many of the nucleotides didn’t bind up, even in the designs that scored high. The shapedata is not very pretty, especially if one look at them in the estimate mode.

None of our designs have a functioning neck. It also looks like the top and the bottom string does not bind very well in the middle. Like more GC-pairs are needed here or more repetitative pattern.

And the neck is having problems in the middle in all the designs. In one of my designs (not synthesised) I imported a working neck from Bends and ends sampler. But I’m not sure imported necks will work as previously seen, as an aptamer is different to a multiloop. At least it seems like it. I think, certain necks will work exceptional well with aptamers - we just need to find them. And those necks might not work together with a multiloop either. Though I suspect aptamers are more sensitive. Mat said that ”the FMN must be having an effect on the target shape.

It is a clear pattern through all the lab results, that the middle of the necks is not binding. Same with the middle of the top arm and bottom arm.

I have no idea what is happening.

Hi Eli,

Thank you so much for pointing out this problem.

We have just found out that there was an alignment problem in data visualization. The scores were right, but blue/yellow data were shifted by 6 bases.

The problem has been fixed for all lab results (this happened only to the latest lab result and the round 2 of the last lab that have been published this week)

We’ll also add a news item about this - let us know if you still see a problem

Hi Jee!

Big thanks for ending my confusion. :slight_smile:

I’m also very happy, because now we have working necks. :slight_smile: