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Questions tagged [rna]

RNA, or ribonucleic acid, is a biological macromolecule made of nucleotides used in cells to convey genetic information to protein. RNA also plays a role in catalyzing certain biological reactions as well as carrying genetic material in some viruses.

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Relationship of disease to alternative strand - microRNA-3p or -5p

I am working in a project involving microRNAs in a cohort of patients (controls and cases of coronary artery disease). I got results from sequencing of HDL-lipoprotein involving diferentially ...
Javier Hernando's user avatar
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How do you find the template strand for a sequence where start codon is in both strands?

Maybe I'm missing something very obvious but I can't seem to understand how to find the template strand given a sequence and its complementary strand if both strands contain ATG from 5' -> 3'. ...
Naumhat's user avatar
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How to elute the protein that is bound to biotinylated RNA immobilized with streptavidin?

I would like to test the proteins that bind to biotinylated-RNA by mass spectrometry , I was using Dynabeads™ MyOne™ Streptavidin C1 (invitrogen) coupled with biotinylated-RNA,than mix these beads up ...
Fino's user avatar
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How long does therapeutic mRNA last in vivo?

How long does mRNA delivered therapeutically to cells last in the human cell once it's gotten there? I've seen sources say that endogenous mRNA lasts around 8-10 hours in humans, but wasn't sure if ...
Gumpf's user avatar
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Is there no good way to run the Vienna RNA tools on Windows?

I'm trying to get the Vienna RNA tools (particularly RNAfold) running locally (as opposed to using the web interface--because I have lots of sequences I wish to process in batch mode). On the website, ...
biohacker's user avatar
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What can be the issue during the total RNA extraction using QIAGEN kit?

I am trying to isolate total RNA using QIAGEN miRNeasy Mini Kit (50) - Cat #217004 from a 2mm biopsy. While there are only two samples (B4 and DT11) the quality of RNA is bad. The goal is to use this ...
Lara's user avatar
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Must RNA and DNA be the way it is?

We're carbon-based based life form with (mostly) iron-based oxygen transportation for apparently good reasons. Is the same true for why life on Earth developed using nucleotides, amino acids, RNA and ...
RonJohn's user avatar
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Compute a melting temperature in viennaRNA?

Posting here to get views, but may be more appropriate for bioinformatics or chemistry SE. There are a variety of utilities such as biopython or primer3 that compute melting temperatures. However, ...
Maximilian Press's user avatar
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How many cuts are done during CRISPR-Cas9 in one cell?

In a CRISPR-Cas9 experiment, the protein cuts the site matching the cRNA part of the gRNA. My question is: How many cuts are possible if multiples sites matching the cRNA are found in the cell? ...
totalMongot's user avatar
3 votes
2 answers
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Correct description of ALDH7A1 and other genes

A quote from a review paper: ALDH7A1 gene (discovered in 2006), which is located at chromosome 5q32.2, contains a transcript of 4964 base pairs and 539 amino acids divided among 18 exons [1,10,16,17]....
CopperKettle's user avatar
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What percentage of our DNA is never transcribable? What percent is never actually transcribed into RNA unless researchers force it to in a lab?

From what I gather, the vast majority (but not all) of the DNA in our genomes will transcribe and create an RNA, if only under certain conditions in a lab (forcibly unwound, among other steps). How ...
Kurt Hikes's user avatar
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Questions about ChIP-seq reads and MACS

I had a few questions raised by the below diagram in relation to how ChIP-seq reads look like (source). I would be very grateful for your insight on them! From the below diagram, it seems that, in a ...
algebroo's user avatar
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Cross correlation metric in ChIP-seq experiments

I found this explanation of cross-correlation metric in ChIP-seq. Now, the definition of Pearson's correlation coefficient between two random variables $X$ and $Y$ is $$\rho_x = \frac{Cov(X,Y)}{\...
algebroo's user avatar
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drug-dna concentration

I want to understand how you calculate the final concentration of a Drug-DNA complex. I tried to mix equal concentration and volume of drug and DNA to form a complex and tried to see the absorbance ...
dojodna's user avatar
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Genes on the reverse strand of DNA indicated by (-) in GFF

In the transcription process, RNA is produced from the template strand of DNA (that is 3'-5') so the RNA molecule produced has the direction 5'-3'. When working with genes in bioinformatics, there are ...
Homap's user avatar
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What is the relationship between stress granules and circular RNAs?

I have read that circRNAs act as sponges for miRNAs and that stress granules help reduce chronic cellular stress and they are composed of proteins and RNAs. I'm interested in the relationship between ...
Shadan Alrawi's user avatar
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Can the coding strand for an RNA act as the template for another?

Can the same strand of DNA act as a sense strand and an antisense strand at two different occasions of transcription and result in two different proteins?
Khadeeja Rincy's user avatar
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Is Zayed et al.’s revision of Orthornavirae robust?

Zayed et al. (April 7, 2022) in Science “Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome” report several major hitherto-unknown Ribovirial phyla: The two most ...
alexchandel's user avatar
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Confusion regarding the meaning of the coding strand of DNA [duplicate]

I am having problems getting the ‘correct’ answer for the above question. I am assuming that mRNA uses the template strand (not the coding strand) for protein synthesis. So: ...
Chad's user avatar
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2 votes
1 answer
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Zayed et al. (2022) "Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome"; expressed sequences or transcribed?

Phys.org's Ocean water samples yield treasure trove of RNA virus data summarizes Zayed et al. (April 7, 2022) in Science Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA ...
uhoh's user avatar
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3 votes
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Difference between LIGR-seq and PARIS methods

I would like to reuse a dataset produced by LIGR-seq for ncRNA secondary structure prediction in the style of PARIS method. At ...
Marek Schwarz's user avatar
22 votes
2 answers
4k views

Is it possible to make a vaccine against cancer?

If we can make RNA vaccines against COVID-19 and we know which errors in our DNA leads to different kinds of cancer, can we make a vaccine that will teach our immune system to detect and destroy ...
Robotex's user avatar
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In what sense is PCR a "nuclear-derived" technique? [closed]

The International Atomic Energy Agency (IAEA) has launched an initiative, ZODIAC, to combat pandemics that originate in animals. In part, this involves the deployment of kits utilising real-time ...
user924308's user avatar
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How do mRNA vaccines work with respect to presentation of the antigen?

As I understand it, mRNA vaccines operate by taking a gene for some distinctive feature of the target virus and arranging for the cells of the vaccine recipient to manufacture the proteins that make ...
Imprisoned Rhesus's user avatar
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1 answer
148 views

How is RNA content distributed in daughter cells during cell division?

During cell division, DNA becomes equally distributed between the daughter cells. But how is RNA content distributed in the daughter cells?
Meera Dorle's user avatar
3 votes
1 answer
145 views

Does ribonuclease processing of pre-crRNAs happen co-transcriptionally?

I understand CRISPR-mediated bacterial immunity to occur in the following simplified steps: A CRISPR array is transcribed from promoters in the leader sequence to yield a precursor CRISPR RNA (pre-...
acvill's user avatar
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1 vote
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Where in the cell does this enhancer RNA knockdown take place?

In Pnueli et al., 2015, they knock down an enhancer RNA using RNAi, testing whether it is a mere byproduct or whether it has a key role in the enhancer's function. They find their system works: the ...
eric_kernfeld's user avatar
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1 answer
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Can Covid's RNA be nullified by an opposite RNA strand?

Firstly, I have scant knowledge of biology, epidemiology, virology, and related fields. If my question seems nonsensical or bewildering, I beg your pardon. I'm not sure how to phrase this, but I'll ...
adibak's user avatar
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1 answer
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What determines the nucleotides incorporated into RNA by polynucleotide phosphorylase?

Polynucleotide phosphorylase, in addition to its role as an exonuclease, is also involved in the post-transcriptional addition of nucleotides to RNA in a template-independent manner: “Polynucleotide ...
Samardeep singh's user avatar
2 votes
1 answer
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Does Remdesivir cause bone marrow suppression?

According to Wikipedia, Remdesivir is a prodrug of GS-441524 which is a nucleoside analog. I know that nucleotides are the building blocks of both DNA and RNA, meaning nucleotide analogues that ...
ATheCoder's user avatar
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What is the purpose of an siRNA screen in drug discovery?

In the paper "A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle" by Martin et al. the authors try to disrupt the Ebola life-cycle by ...
Seanny123's user avatar
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5 votes
1 answer
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Were nicotinic acid/amide or flavin nucleotides ever part of primary RNA sequence?

NADH and FADH2 redox reactions are built deep into our biochemistry. For example, pyridine nucleotides are involved in >500 enzymatic reactions. When we look at the structure of deamido-NAD+, it ...
Mike Serfas's user avatar
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4 votes
1 answer
132 views

Introns and miRNA

From this paper, it is stated that some introns may contain genes coding for miRNA, miRNA is essential in regulating gene expression by pairing with RNA, hence disrupting regular translation. From ...
Questions's user avatar
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7 votes
1 answer
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Why can't certain nucleoside analogs be used to label bacterial RNA?

A 2020 publication in Nucleic Acids Research 1 includes the following passage: A variety of nucleoside analogs have been developed for metabolic RNA labeling in various eukaryotic cells (9–16). Among ...
acvill's user avatar
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-2 votes
1 answer
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Are there ribozymes that cut double strands

the header already says: Are there any ribozymes known that cut double strands? A kind of ribozyme equivalent to the Ribonuclease III. With cut, I mean that the backbone of both strands, forming the ...
newandlost's user avatar
1 vote
2 answers
170 views

Why do genes, encoding the same proteins and in the same conditions, have different expression?

Is it possible that two genes, which come from two different cell cultures and which encodes the same protein, produces different quantity of mRNA? If yes, why? My question comes from the fact that I ...
Manuela's user avatar
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3 votes
1 answer
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With an mRNA-vaccine, would it hypothetically be possible to get that sequence transcribed into their genome for people who suffer from a retrovirus?

I recently read a bit about the mRNA-vaccines for COVID-2019. I fully understand that mRNA cannot enter the genome of a healthy person as they lack the required reverse transcriptase to transcribe RNA ...
DLCom's user avatar
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5 votes
2 answers
863 views

Is viral single-stranded RNA in the absence of reverse transcriptase infectious?

In a medical microbiology textbook I'm reading (Murray et al, 1994), the authors state the following: The retrovirus genome has a 5' cap and is polyadenylated at the 3' end. Although the genome ...
Howsikan's user avatar
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4 votes
2 answers
729 views

Does N1-methyl-pseudouridine occur naturally in any RNA?

Pseudouridine occurs naturally in some RNAs. But what about the methylated variant of it, N1-methyl-pseudouridine? The latter is a key ingredient in both the Pfizer and Moderna Covid-19 vaccines, ...
against very long user names's user avatar
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0 answers
25 views

Stability of RNA including Thymine nucleobase

Does an RNA double strand containing the nucleobase T instead of U has a lower free energy? Or more precisely: There are tabulated values for the change in free energy of the canonical neighboring ...
newandlost's user avatar
1 vote
0 answers
50 views

How does RNA polymerase II CTD bind to the RNA modification proteins if the tail is flexible?

The tail of RNA polymerase II is flexible, not folded into a fixed structure , but does each repeat have more "rigid" structure (i.e. fold into a structure that has less rotation freedom ...
jw_'s user avatar
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1 vote
1 answer
134 views

Do RNA modification proteins bind to specific repeats on the RNA polymerase II CTD?

The C-terminal domain (CTD) of human RNA polymerase II has 52 repeats of a similar heptapeptide sequence. Will the RNA modification proteins only bind to some repeats at specific locations on this (e....
jw_'s user avatar
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2 answers
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Destroying RNA of viruses using Ribonuclease

I wonder if it is possible to design some Ribonuclease to destroy only specific RNAs (like those of viruses). Then, if virus tries to infect, his RNA will be cut. Or, instead of creating Ribonuclease, ...
Dzery's user avatar
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1 vote
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RNA vaccination and Autoimmune Reactions

To my knowledge we do not have any robust experience with RNA vaccination. Most likely this will change in the near future as RNA vaccines against COVID are in the pipeline. The rationale behind this ...
friedrich's user avatar
12 votes
2 answers
1k views

Does double stranded RNA (dsRNA) exist in eukaryotic cells?

I know it sounds like a stupid question. Obviously, tRNAs and rRNAs, for example, form loops and could therefore be considered as dsRNAs... but are they really considered as such? Are there examples ...
justdoit's user avatar
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0 answers
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How to construct a sgRNA library with multiple samples?

I was wondering if anyone has already experience with constructing sgRNA libraries. We are interested in doing a knock-out experiment (loss-of-function) with 5 different conditions. I have found this ...
Assa Yeroslaviz's user avatar
1 vote
0 answers
34 views

Peak-calling in CLIP: What is the effect of RNA-concentration?

I hope it's ok to repost my question from 8 months ago from StackExchange:Bioinformatics, that is still in beta. https://bioinformatics.stackexchange.com/questions/10730/peak-calling-in-clip-what-is-...
KaPy3141's user avatar
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1 vote
1 answer
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Do DNA viroids exist?

Viroids are described as short circular ssRNA with no protein coating. Are there any analogous infectious particles that contain DNA instead of RNA? If DNA viroids do not exist, is there an obvious ...
trinitrotoluene's user avatar
-1 votes
1 answer
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Why are some parts of an rRNA structure diagram not labelled?

I've been looking at this structure diagram of the 16S rRNA and have been wondering why some parts of the diagrams have labelled base pairs while other parts are just lines and dots. I'm new to this ...
Ark Lomas's user avatar
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What is the role of pyrophosphatase in RNA polymerization?

In Molecular Cell Biology (8th edition) there's a fragment in chapter 5.2 that says: The energetics of the polymerization reaction strongly favor the addition of ribonucleotides to the growing RNA ...
micoay's user avatar
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