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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questions with no upvoted or accepted answers
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Why can oligo-U not be used to isolate mRNAs, instead of oligo dT?
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 can we not use oligo-U instead (uracil)? I ...
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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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Travelling with tissue samples in RNAlater
I've been in Brazil collecting some samples (ants) and need to travel back to to the UK with - I've got their brains stored in RNAlater, which have been in the freezer at -4C for a bit less than a ...
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What are the reasons which make intron detection uncertain?
Intron/exon sequence detection seems to involve statistical prediction which can at best deliver a guess (until experimentally confirmed) as to where the splice site is.
What are the reasons why ...
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Is there a cellular mechanism that detects Ribosomal damage?
What kinds of options, if any, do cells (Eukary and Prokary) have for detecting, and repairing damage in Ribosomes (of all types)? I am curious as to
what happens when a cell sustains damage of some ...
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335 views
Is there a database of known riboswitches?
I'm looking for sequences and annotations of known riboswitches, but so far I haven't found a resource that actually fulfills my requirements. The best database I found so far is Rfam, which has ...
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622 views
Origin of the 260/280 ratio?
This is not a duplicate of all the other 260/280 ratio questions, I already know that DNA is supposed to be 1.8 and RNA is supposed to be 2.0. However, this might be more appropriate for chemistry, ...
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Why are riboswitches mostly present in bacteria and not in eukaryotes?
Riboswitches are a rather elegant way to regulate gene expression without any additional machinery. A small ligand binds to the mRNA and directly influences transcription or translation.
Most of the ...
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Detect differentially expressing cells
I have data (RNA expression values, obtained with in situ hybridization) collected from 1mio human cells. For each cell, I have the expression value of a negative control (non-human RNA) and single-...
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Why does M1 RNA together with C5 protein in 100mM Mg(II) fail to cleave tRNA?
Sidney Altman discovered that RNA moeity of RNAse P (M1 RNA) alone is able to perform enzymatic cleavage of ptRNA, which won him the Nobel Prize of Chemistry in 1989.
However, when I read the Nobel ...
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134 views
Sequence between PolyA signal and PolyA tail
Between the polyadenylation (PolyA) signal (AAUAAA in humans) and the start of the polyA tail, there is a short sequence of about 10~20 (G/U rich) bases, is there a special term for it?
Image credit: ...
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Smallest, specific RNA-binding protein - w/ sequence?
I'm looking to synthetically fuse an RNA-binding protein onto another protein, inside a viral vector which has a size-limit. I've considered some options, but I'm wondering what StackExchange will say....
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Can a phosphodiester bond form between RNA and DNA?
In the initiation of DNA synthesis:
the RNA segments are first synthesized by primase and then elongated
by DNA polymerase (Wikipedia).
What does 'elongated' mean in this context? Is it possible ...
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76 views
Basic molecular biology of nucleic acids book for a mathematician studying DNA and RNA formally?
I am a mathematician studying DNA and RNA language from the perspective of Formal Language Theory.
Note that I am aware of these posts:
best book for a comprehensive introduction to biology for a ...
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37 views
Validity of comparing gene expression levels between alive and <24h postmortem cohort
There is a recent paper about assessment of a suicidal risk in psychotic patients https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759104/
One of the important points is that the authors compare gene ...
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217 views
What is RNA Engineering
I've been hearing the term passed around, and my own research has led me to some very high-level papers which propose new tools for accomplishing RNA engineering.
From the abstract of one of the ...
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Link between macro lncRNA and DNA looping
I was wondering if anybody knows some publication about macro lncRNA (very long unspliced RNAs) or more generally a transcribed RNA that may lead to cis-DNA looping of genomic regions overlapped by ...
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36 views
How closely correlated is the level of an snRNA with the level of its corresponding snRNP?
Let's say I am growing cells under two conditions, and let's say I measure U1 snRNA levels in both using digital PCR. If the U1 snRNA level is reduced in one sample, how safe is it to say that U1 ...
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85 views
What is the silencing mechanism of AGO1,AGO3 and AGO4?
I read that this proteins lack of slicer activity, so what mechanism do they use to perform gene regulation?
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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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56 views
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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What prevents the translation of the negative strand of negative-sense viral genomic RNA?
Some RNA viruses contain negative-sense RNA. Then they use this negative-sense RNA to make positive-sense RNA that is then translated into protein.
My question is what prevents the translational ...
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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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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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How to map the N6-dimethyladenosine by primer extension?
I am trying to map N6-dimethyladenosine on rRNA using primer extension (low dNTPs assay) method. But i am not able to detect map my position. I went through some articles they mentioned like they ...
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Exporting RNA in extracellular vesicles (exosomes)?
I'm interested in how much is know about the process by which RNA is secreted from cells into extracellular vesicles.
Where is a good place to start reading about this?
How much is known about this ...
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UV-lamp, DNA and RNA extraction lab
I'm equipping a lab room (~3x5 meters) that's supposed to be used for DNA and RNA extractions. I know about the basic safety precautions when working with RNA and DNA extraction (fresh gloves, ...
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37 views
Eukaryotic equivalent of bacterial tmRNA
According to this Wikipedia article,
tmRNA is only found in bacteria, with its purpose being to ārescue stalled ribosomesā.
This brings me to the question of is there a eukaryotic equivalent of this ...
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59 views
What is the point of storing biological samples in Trizol/TriSURE before RNA extraction?
The Wikipedia article on Trizol says that it helps break the cells and maintain RNA integrity during homogenisation of samples. Does anybody know by how much Trizol improves RNA integrity compared to ...
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58 views
Should I use glycogen in isopropanol to precipitate RNA or does glycogen have harmful consequences on downstream protocols such as RNA seq?
I have heard that one can use glycogen in isopropanol to better visualise the RNA pellet after centrifugation. What are the advantages and disadvantages of adding glycogen in isopropanol for RNA ...
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329 views
why is DNA better for storing genetic info while RNA better for transmission of it?
I do know that RNA cannot be used for transmission since it is unstable, but how does it prove to be a better transmitter of genetic information?
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How can one determine how much of a region flanking an RNA sequence of interest to include in order to look for interfering secondary structures?
I have a set of RNA sequences, and I have been analyzing slices (i.e. target frames) of these sequences in order to determine whether they conform to certain structural criteria. One of these criteria ...
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71 views
RNA isolation problem
I have isolated RNA from cell culture (T25 flask, mouse cells) with trizol. I've measured the sample on Nanodrop, and this is what I've got:
A260 (10mm): 16.408
A260/A280: 1.98
656.3 ng/ul
How is this ...
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275 views
Can a ribozyme be present on two different RNA molecules?
Suppose we have a ribozyme that consists of an 'enzyme' strand and a 'substrate' strand. (e.g. hammerhead ribozyme)
Is it possible to have the enzyme strand of the ribozyme on one RNA molecule and ...
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37 views
non-coding RNA modelling in silico
I've been trying to model a non-coding RNA molecule which binds to a RNA binding protein. I found the DNA sequence for ncRNA from NCBI. I did not find the RNA seq of the same. Hence my doubt is, ...
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Confusion about the role of capping and polyadenylation in nuclear transport
Before termination stage of transcription a GMP cap is added to the 5' end and poly-A tail to 3' end of mRNA.
The link(http://sciencing.com/role-rna-polyadenylation-5434666.html) says:
The poly(A) ...
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35 views
Modifications of free nucleotides
We know that RNA can get modified post transcriptionally (RNA modification). So when the RNA is degraded, is it possible for such modifications to still be present on the individual nucleotides -- ...
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139 views
How often does pre-mRNA processing lead to midstream off-frame errors in eukaryotic mRNAs?
As I understand it, the splicing of introns from pre-mRNAs is not incredibly precise. I've only ever seen nucleotide position ranges given in any description of the involved processes. Since there is ...
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Estimating RNA concentration from Specific Activity of Labeled RNA
The question reads, Using T7 RNA polymerase to transcribe in vitro a 100-nt RNA off a DNA template. This RNA contains 19 Adenosines. In your 100 uL transcription reaction you added 1.00 ĀµL of Ī±32Pā¢[...
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de novo gene synthesis vs cDNA library creation from plant RNA: Pros & Cons
What are the relative pros & cons of the following two approaches when one wants to insert a known, sequenced plant gene into a target host organism:
de novo gene synthesis vs
plant matter ...
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80 views
mRNA extraction from mice ears.
I am trying to extract RNA from mice ears and for some reason I don't have RNA when I perform the electrophoresis. I directly cut the ears and I put it in a tube with a bead and trizol. then I place ...
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90 views
Extraction of RNA from algae
I have used a standard protocol (I will give the bibliography below) to extract RNA from an algae (Posidonia) but I have get literally nothing, since I could not even see traces of the two rRNA. I ...
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Does the assembly of the PLC transcription complex utilize phosphorylation in binding of the GTFs?
in the recruitment of general transcription factors during transcription initiation is phosphorylation utilized?
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Since nature highly favors the pyranose forme of Ribose, what explains the fact we find it in the form of furanose in DNA and RNA?
I read in my notes that relative abundance of ribopyranose represents about 80% of all ribose in solution (including the alpha and beta anomeres).
I'm curious as to why evolution favored the use of ...
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Transcription takes place from the 5ā to the 3ā end of the m-RNA. Why?
Only one side of the DNA ladder is copied (the sense side). The sense side starts with a 3ā end. This means the corresponding mRNA will have to assemble starting from the 5ā end. This is my initial ...
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Visualizing secondary RNA structure binding to target
I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but ...
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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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34 views
How did Rna replicate according to Rna World Hypothesis?
I was studying Rna World Hypothesis in Khan Academy, and there is a line.....
The RNA world hypothesis suggests that life on Earth began with a simple RNA molecule that could copy itself without help ...
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Construct aptamer library with exact number of members
I am asked to construct an aptamer library of exactly 1024 members, each with a unique V.
I have two questions regarding this; firstly, is it wrong to construct an aptamer library using a column with ...
