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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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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333 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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609 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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65 views

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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48 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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24 views

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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102 views

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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70 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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36 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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199 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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35 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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84 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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34 views

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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45 views

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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49 views

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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32 views

Eukaryotic equivalent of bacterial tmRNA

According to this Wikipedia article, tmRNA is only found in bacteria, with its purpose being to “rescue stalled ribosomes”. This brings me to the question of is there a eukaryotic equivalent of this ...
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53 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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50 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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321 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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70 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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274 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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81 views

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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132 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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53 views

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 µL of α32P•[...
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75 views

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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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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Which fractions are enriched for siRNA cleavage activity by comparing electrophoresis?

Size exclusion column chromatography was used to separate the proteins in a Drosophila cell lysate to attempt to identify the protein complex responsible for processing long dsRNA into siRNAs. SDS-...
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87 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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286 views

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 5’ to the 3’ end of the m-RNA. Why?

Only one side of the DNA ladder is copied (the sense side). The sense side starts with a 3’ end. This means the corresponding mRNA will have to assemble starting from the 5’ end. This is my initial ...
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53 views

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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How to reduce the number of sequences in a Multiple Sequence Alignment?

I have a Multiple Sequence Alignment, where there are around 5000 sequences. There also exists many sequences where, there are so much of non-sequenced regions (for instance, AU----CGGGCA--NNNNNNNNNN)....
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Which database has the ready made 16S rRNA Multiple Sequence Alignment File that I can download directly from?

In my case, I need the ready made 16S rRNA Multiple Sequence Alignment File for E.coli and use it to generate the phylogenetic tree file in Newick format. I've tried using the one from utexas website, ...
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How to differentiate transportable element and non-coding RNA in genome?

I am searching for unannotated non-coding RNA in my genome at the same time i want to omit the transposable element from my genome. My sequencing libraries are paired-end and i am searching in the IGV ...
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37 views

How to detect specific mRNA dsRNA by Northern analysis?

I silenced a gene by RNAi method, for that i chose the gene and the size of the gene is 1.5kb and my insert size is 500nts. i did the transfection and i want to confirm the silencing by northern ...
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Why is snoRNA often used as a reference gene in qPCR?

I am studying non-coding RNAs and stumbled into a question about small non-coding RNAs. scaRNAs (small cajal body-specific RNAs) is a subtype of snoRNAs which are small nucleolar RNAs. It is known to ...
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396 views

Is there any evidence for the validity of RNA/DNA supplements?

Is there any evidence for the validity of RNA/DNA supplements? I've recently been seeing advertisements for RNA and DNA health supplements in the form of a pill, which claim to perform some rather ...
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1answer
69 views

What causes the complementary copy of an RNA molecule to separate?

I have recently read an article which explains that, in the RNA World hypothesis, an RNA molecule gets 'scanned' by nucleic acid, catalysed by a different specifically-folded RNA molecule, to arrange ...
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1answer
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What tools can help me determine if a plant homologous protein interacts with an ncRNA in the same way?

First post here, so bare with me if I violate any etiquette or formatting rules. Let's say I've got a protein in humans. When it interacts with an ncRNA found in humans, it does something that I'm ...
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62 views

Can an RNA anneal to its complementary (not reverse) sequence?

Say I have a target RNA strand: 5'--AAUGGCCCUUUAAA-->3' I know that this strand will readily anneal to the sequence 3'<--UUACCGGGAAAUUU--5' which is the reverse-complement. I'm wondering if ...
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79 views

Why can't nucleotides when mixed together form an RNA on their own?

Why nucleotides when mixed together in the absence of a template RNA molecule do not readily link up into a chain? We know that the bond between nucleotides side by side is stronger than the hydrogen ...
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Could DNA directly synthesize proteins without RNA?

Imagine there is no RNA. Could the DNA be modified into messenger DNA, and ribosomes made of DNA, and transfer DNAs to replace the role of RNAs to make proteins? If so, this would seem to argue that ...