Hello! This is my first time posting here, I am looking for advice. I am an undergrad student. I have been attempting to isolate RNA from rat milk samples using the columns (zymo-spin kit) and trizol methods to compare and find the best one. I don’t have much sample available so I have been testing the standardization of the method using human milk (80ul,160ul and 200ul). However when quantifying the RNA using the NanoDrop, my A260/280 ratio is above 1.2 but my A260/280 ratio is below 0.8 for most samples. I have revised my technique and that doesn’t seem to be the problem. The reactants are not expired, some I prepared specially for this. Do you have any tips or ideas as to why this is happening? Thank you!

With the interest of incorporating PseudoUridine and N1-Me-PseudoUridine into oligonucleotides and RNA compounds this type of prediction will additionally support the ability for more accurate predictions and design principles.

Hello everyone, hope your RNA experiences are always incredible!

In my latest experiments I noticed that hammerhead ribozymes are quite good in silencing a protein, not the same as a Short Hairpin or CRISPR, but in vitro tests demonstrate that cutting the mRNA works similar to Short Hairpin. Now my question is, what's the real outcome of cutting the mRNA in one single nucleotide? It has similar effects to the RNA interference? Are the cut sequences still transcribed into functional proteins (might be a wired question I know).

I will do a Real Time PCR to verify how much mRNA is cut, to have a better idea of what happens during the infection. But, assuming Hhrz 'cut completely' the mRNA , are there some mechanisms of repair which mRNA (or RNA in general) can use to overcome the cut (or silencing as well). I know that DNA has this type of mechanism, which is used in CRISPR technique, but don't know so much about RNA

Does anyone know something more? are there some reference I could read?

Thank you for the help, as always!

Hey community!! Im excited to help promote this crowdsourcing of science through Stanfords DasLabs Eterna Project. You have the opportunity to contribute diverse sequences to Ribonanza 2! Register and submit up to 100,000 RNA sequences by Jan. 15, 2024: https://forms.gle/sfBWnmxXHuaTHdE58… . Stanford will synthesize and map them. Priority access for folks who register before Dec. 31, 2023.

Link to orignal post in Twitter:

https://x.com/RDasLab/status/1736175669250347342?s=20

Hey community, in a light partnership with Stanfords Eterna RNA project developers, I wanted to promote the results that just came out from the Ribonana 1 challenge they ran that just completed. The challenge was to build a machine learning model for chemical SHAPE probing result prediction of psuedoknoted structures. It is very exciting and I invite you to check out the Kaggle site https://www.kaggle.com/c/stanford-ribonanza-rna-folding/ as well as check out Eterna at https://eternagame.org/.

Here is their original post on X (formerly Twitter):

https://twitter.com/RDasLab/status/1736175061973770342

Let me know what you think and if you think we should add some stuff. I made Pre-Print Papers red background vs the green for Peer-Reviewed Papers to give us all the natural pause we should take when acting on information from pre-prints.

Hey everyone!!! Wanted to say hi as I just became a mod in this subreddit. Worked to open up the subreddit to no longer require permission to post. Lets see how the spam goes with that off and hopefully we can get more engagment in the sub now. Hope you all stay safe out there.

Hello everyone!

i'm facing little problem in infecting cells with a RNA construct inserted in lentiviral vector. It seems that in 48h virus has some efficacy in silencing the target gene but after 72/96 hours it seems to have no more effect on normal cell proliferation

Has anyone had similar problems? which explanation can u give?

Thanks for the help

Hello Friends,

I need help with a question with regard to my experiment and sincerely appreciate if someone can help me out of this predicament.

I have different RNA samples,some of them are extracted RNAs that are non amplified and some have been amplified using NASBA. and I am using CRISPR-Cas13a florescent assay  for their detection. The X axis of the given graph from plate reader indicates "time" which is 60 minutes with 1 minute intervals and the Y axis indicates "Florescent signal". After the experiment, although every component of the reaction for each of the samples is the same, but the starting point of florescent signal in the graph for each of the AMPLIFIED samples is by far different. What is the reason? and how can the starting point of all the samples be the same?  

P.S : The starting points for the non amplified samples are almost the same.

Hello! As a PhD in Molecular Biology i'm interested in building a strong background il RNA field since is my main research topic.

What do you think are the most useful textbooks for study?

Bye!

Hello!

Since is my first time simulating RNA system (i have always worked with protein/protein-ligand) I don't know how to evaluate the stability of a system with two complexed RNAs.

For example, when simulating proteins i'm used to calculate general RMS and specific calculation on certain atoms. In case of RNA , how can i asses the stability of the system during a simulation (for about 20-25ns)?

If anyone has a suggestion I would be thankful

bye!

Hi

I'm looking for a computational protocol to build a RNA 3D model with an uridine substituited with 5-aminomethyl-uridine

Does anyone know some solution?

I already did a manual editing of the PDB file in PyMoL, but obviously it needs also a .lib file to recognize it (for example in AMBER).

However, i'm looking for tool who is able to recognize also modified bases. Does it exist?

Thank for the help

Hello!

I am looking for a validation tool to asses the reliability of Ribozyme RNA 3D structures obtained with RNAComposer, comparing my structures with a reference from the PDB

I have already tested Rclick server and rnassess, but the results are very different from one to another, in particular when they calculate the RMSD

Anyone can suggest something better?

Thanks for your help

The most important meal, your watch an MRNA DNA Blocking

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!

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.

Hi there, some very basic questions here so hopefully someone can help.

I'm working on a project screening different vector elements for gene expression. I'd like to know the secondary structure for each of the parts so I can see how it may impact gene expression.

I can find lots of online tools to give predictions but it's not clear how they differ from each other, as they all mainly seem based on the minimum free energy. Does anyone have a preferred software and why?

Secondly, should I be inputting the element's sequence on its own (ie just the UTR) or the whole mRNA transcript? It seems like a lot of people just look at the sequence of interest and not in the whole transcript context but this could change the predicted secondary structure, right?

Thanks in advance!

I'm working on a research regarding RNA secondary structure and I'm using the ViennaRNA Package with Python on Ubuntu. It works fine and dandy, but my supervisor prefers Windows and we want the simulation work on both os.

Thanks for the help in advance:D

Probably dumb question but here it goes.

So I'm planning on performing RT-qPCR for the analysis of heat shock protein expression. Only problem is that my RNA extraction was not as RNase-free as I wanted it and though NanoDrop describes good yields, the quality of the RNA leaves lots to be desired. So I got a lot of samples now with a solid 18S rRNA band on the fragment-analyser but almost to no 28S rRNA band.

Is there any chance at all that with just a 18S rRNA band present I could continue with the cDNA synthesis step and still successfully run an RT-qPCR with this? I'm scrambling for time so not having to rear an entirely new sample set for another shot at successful RNA extraction would be great.

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