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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Short RNA oligos modeling using FARFAR2
Does anyone have experience with modeling short RNA molecules using FARFAR2 server?
Given very short strands, ~20 bases long, I'm getting binding in all bases though only half should bind
Thanks!
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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?
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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]....
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Why don't RNA and MRNA need intracellular vesicles? [duplicate]
mRNA and RNA are hydrophilic (polar) molecules and therefore soluble in water. The cell's cytoplasm is usually full of water.
How does mRNA move to a ribosome in transcription, and RNA move elsewhere ...
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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 ...
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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 ...
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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)}{\...
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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 ...
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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 ...
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Why are hydrogen bondings in DNA-RNA hybrids weaker than hydrogen bonds between two strands of DNA or two strands of RNA?
One of our professors asked this question and mentioned that "studies proved this". I can't find any answer.if someone knows a book, article,etc that can help or can explain the reason for ...
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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 ...
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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?
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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 ...
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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:
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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?
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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-...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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, ...
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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 ...
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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 ...
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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....
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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, ...
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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 ...
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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 ...
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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 ...
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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-...
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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 ...
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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 ...
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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 ...
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VPg priming of the replication of RNA viruses
I'm doing a presentation on the replication of SARS-CoV-2 for my chemistry class, and I found that to replicate its RNA, the virus uses RNA-dependent RNA polymerase, which is primed by a VPg primer. ...
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Why does the structure of RNA change? [closed]
RNA only has one strand, but like DNA, is made up of nucleotides. RNA strands are shorter than DNA strands. RNA sometimes forms a secondary double helix structure, but only intermittently. Why does ...
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Why all negative ssRNA viruses have helical capsids?
You can always say it's a coincidence, but is there particular need to have a helical capsid? Do they need their RNA to be more protected than +ssRNA? Is it better for RdRp attachment?
This paper ...
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Why is an intron (or exon) still called intron (exon) if retained in (excluded from) mRNA?
In most explanations, the sections of RNA removed during splicing are called introns, and the remaining segments that are stitched together are called exons. That is, introns and exons are defined in ...
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What are the reasons for using oligo-dT instead of oligo-U to isolate mRNAs?
dTTP oligonucleotides are used to isolate mRNAs because mRNAs (in eukaryotes) have a poly A tail which binds to the complementary oligo-dT. However, why do we not use oligo-U instead (uracil)? I would ...
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