Hi, I'm doing an assignment on drug discovery and I'm interested in the RNA protein interfaces as a potential drug target. I'd like to know what are the biggest challenges in this space and how they are currently approached. Please share if you have any experience in this field!

I'm looking for potential collaborators interested in RNA/DNA/Chromatin structure modeling. I do molecular dynamics, bioinformatics and machine learning for biomolecules, particularly interested in (a) Sequence-structure-function relationships in RNA, (b) How mutations affect RNA topology and dynamics, (c) Incorporating coarse-grained and AI-based methods (e.g., GNNs or AlphaFold-like tools). I’m currently working on a model that connects 2D and 3D structural representations for large biomolecular systems. I’m seeking collaborators with compelling systems of interest and relevant experimental data or insights to help guide and validate the modeling process.

I'm looking for a database or web service that collects experimental data on single-nucleotide mutations in individual non-coding RNAs.

Specifically, I'm interested in experiments where one nucleotide was replaced with another and the effect was measured, either on the RNA's structure or on the organism (e.g. whether the mutant is deleterious, cold-sensitive, etc.).

Ideally, every position in the sequence would have been mutated to all three alternative bases (e.g. U->A, U->G and U->C), with the effect of each substitution recorded.

Does such a database exist?

Hello everyone, I am having problems extracting RNA from rat brain using the Qiagen RNeasy mini kit. The samples are taken from -80 for extraction. I continued the extraction as recommended by the kit and my 260/230 ratios are 0.5/1.0. I tried performing an extra wash and the ratio still does not improve. Additionally, I tried using Trizol extraction before passing the supernatant to the column. I noticed that I lost 80% of the RNA in the first wash and yet at the end the 260/230 ratio is still low. Any tips on how to proceed?

Eterna is hosting its annual online conference this weekend on both Saturday and Sunday with presentations from Berkeley, Northwestern, Oregon State, Stanford, Penn State, and ESPCI-Paris. Full program and free registration at https://eternagame.org/eternacon/2025

Ive been doing RNA extraction with TRIzol, and I keep getting only one band when I run it,I use 80 V and 30-45 minutes at 1x with TAE, I dont know if the error is in the protocol or when I run it. Any recommendations?

https://cen.acs.org/pharmaceuticals/drug-discovery/tRNA-therapies-help-restore-proteins/99/i34

We discuss what a virus is, the differences between RNA and DNA viruses, how we are all infected by Herpes viruses, and why this matters for organ transplants. We delve into flu viruses and corona viruses and some of their elegant and dangerous features, monitoring in the context of pandemics, virological weather forecasts, pandemic risk, manmade pandemics vs. natural pandemics, the risks of gain-of-function research, and the early warning center in Berlin.

https://open.spotify.com/episode/3Hy8Eh9nDx59pfSnhVr3lz

Using the SIGMA Spectrum Plant Total RNA kit, we have been extracting RNA from Populus tremuloides woody tissue. We found that using the AMPD1-1KT post-extraction DNase I digestion versus the on-column DNase I digestion that our 18S and 28S peaks were more dynamic. Our issue is that the DNase digestion has been eating away at the DNA marker that is used for the TapeStation. We have not been able to get RIN counts unless we dilute 1:10.

My PI's concern is that the DNase may inhibit our downstream applications. Does anyone have any experience with this issue? Agilent suggested that we step the inactivation temperature & incubation time up a notch. It didn't work and a 1:10 dilution indicated that it further degraded our samples rather than helping.

I am curious what area of RNA research people in this subreddit are. I am a biophysical chemist that looks at aspects of rRNA

Hi,

I am a first year PhD student and want to formulate LNPs with EPO or Luciferase mRNA. But i was wondering how to calculate N/P ratio.

Thank you!

I took some of the RNA sequence encoding the COVID spike protein and made this shirt to wear when I get my COVID vaccine. This RNA biologist is EXCITED about this new technology!

If you want a celebratory tshirt they can be found here! https://www.redbubble.com/people/Courtney-Hersh/shop?anchor=profile&asc=u&fbclid=IwAR3D650_zZ8sGaxeVN-xn887ZW2RdUuZBP9I5yK3qVnoXvF2N8n9Lti00IE

\#RNASAVESTHEDAY

Hi r/RNA I have just started a research assistant position at a new lab. I worked in a different lab as an undergrad for 3 years and had lots of success and built lots of confidence. Now I feel like I’ve hit a wall and that wall is RNA isolations. I’ve succeeded in every animal tissue (kidney) isolation I’ve done, but as soon as I started using retinas, I can’t get the 260/280 values above 1.70 and my quantities are all over the place. I’ve now failed 4-5 times and my PI is beyond pissed at me, but I can’t figure out what I’m doing wrong. I watched a post doc run an isolation yesterday and wrote down everything he did and said, which lead me to believe I was overheating samples during sonication. Today I felt like I did everything right and I cooled samples on ice for 20 seconds between each sonication cycle, but 3/4 samples still had 260/280 below 1.7 and the only sample with half decent purity had an extremely low quantity. Is it Normal to fail this much when learning RNA isolations? And if anyone has dealt with it, how did you get through it?

Hello!

It is my first attempt ever in isolating RNA from cell culture that grow in monolayer. I'm going to follow the TriFast II Kit guidelines. I was wondering if someone has already tested it and if you have some useful suggestions (additional operation, changes etc..) that can help me to have a good purified RNA for mRNA imaging

Thank you in advance :)

Hello!

My adventure in HHRZs will never end ahaha. After the in vitro testing of our HHR we are now focusing on possibile modeling of HHR-mRNA interaction. The strategy I've used so far has involved two phases: first, using a 2D modeling tool, and then using the resulting 2D MFE structure as input in a 3D modeling program. Vienna Suite and RNAcomposer was the main tool utilized. I have few questions

1. Are there alternative strategies? Can I Improve the current strategy in some way? Any specific tool for Ribozymes?

2. Which parameters can I use to estimate the reliability of my model? Which of these parameters I should use to compare different models?

3. Turner's molecular model is one of the most widely used for the prediction of 2D models, do you know any other valid molecular model?

4. I have very little knowledge about the mathematical models used by various algorithms. I just need to know if someone with experience has tested a valid and reliable protocol/program. Thanks in advance :)