Class Time with guest speaker Rhiju Das

I asked Rhiju if he could host a class that focuses on the Lab Process and Procedures, and he agreed to give a talk this Friday, March 21st at 6:30pm EST!

Lets all welcome Rhiju to Class Time and be sure to ask him the questions you always wanted to find out about Lab procedures.

Here is an excerpt from the email to give some background information:

Hi Rhiju,

The last Class Time session that I taught had a big interest in the lab scoring.
Many of the players were interested in the lab process and procedures.

I just wanted to ask if you would like to host a session to talk about how
labs are set up and run.

What steps are taken, who is responsible for each step, how long, etc.
Some of the difficulties / challenges that you are faced with.

I know Brourd, Nando and some others are working on a Mimic project
to help with the throughput of the switch labs.

Your comments on this and possible other projects that could help you would be great.

I think this would be a big boost to the EteRNA community to have you host a session.

I know there are many brilliant players that could be motivated to help if they have the challenges outlined for them.

Let us know if you would be able to take a class.


Hi John:

How about March 21? Friday, 3:30pm PST (6:30pm EST)?
If you’re having a class this Wednesday, perhaps you could ask for questions from players who cannot make it?

Cheers, Rhiju

What a fantastic opportunity! Thank you, John for asking and Rhiju accepting!


Awesome! Thanks John and Rhiju!

Great news - thx for the initiative! :slight_smile:

Last fall, several of us put our heads together and started a Wiki page on what we knew about the lab process. The page has kind of languished since then but still, it’s a start. It would be great if Rhiju could look at it before his talk and let us know about any mis-statements we have made. Then after his talk, we can fill in more details. Actually, I’ll try to fill in some more details tomorrow to reflect my current knowledge, with the hope of getting any misconceptions I have corrected.

The class will be at 8pm EST, (changed from 6:30)

Bummer. I’ll only be able to sit in on the first half. Oh well.

My notes about the Lab Process:

First, a target structure is chosen for players to design a solution for.
Players try to choose sequences with high stability so that a large percentage of the ensemble can maintain its target (desired) fold.
Players use the dot plot tool and past experience to choose stable sequences.
The dot plot tool shows the probability that a base will pair with any other base, and a ‘clean’ dot plot is desired for better stability.
Note that the tool and the energy model is based off the Vienna 1.8.5 software which does have some flaws,
so experience in knowing what particular sequences are stable is very helpful in the lab.

The second step in the lab process is the synthesis of the RNA molecules.
Das labs orders DNA templates of each design that was selected for synthesis.
The process of transcription using T7 polymerase is carried out to create many RNA molecules.
There is a nice animation on the Wiki page showing the transcription process.
The start of every DNA template contains a fixed sequence called the T7 promoter.
This is a marker for T7 to bind to and signal the start of transcription.

The third step is the analysis.
A chemical reagent, 1M7 is used to bind to the backbone of the RNA molecule where the bases are not paired.
The RNA is denatured allowing the reagent locations to read sequentially.
A primer extension is used to bind to the tail and the unique hairpin ‘bardcode’ identifier.
This is used to separate back out the specific designs for the ‘cloud’ labs where all designs are synthesized together.
This process is known as SHAPE, Selective Hydroxyl Acylation Analyzed by Primer Extension
Please refer to the following sites for more information:……

Using gel electrophoresis,…
the following graphs are created……

Thank you jnicol, as always very informative information for the community.

Thanks jnicol for your note about the Lab Process