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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The shape of mRNA

I was wondering about the shapes assumed by mRNA. I have read some sources quoting that it is linear (quora, so not very reliable) and also a source that says a hairpin shape is common (nature, so I ...
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Why do mutations not take place in mRNA of higher eukaryotes?

Is it because it is too short-lived to be mutated? Both DNA and RNA are nucleic acids so how is mRNA protected? RNA viruses undergo mutations to evolve so I guess it is not immune to mutations
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Where can I obtain the sequence of the E. coli ribosomal RNA precursor?

I have found separate sequences for 16S rRNA (from the small subunit) and 23S rRNA and 5S rRNA (from the large subunit). I need the full precursor rRNA sequence, which I cannot find. However the ...
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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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Non-nucleated cell-like population with RNA

We're working on invertebrate hemolymph (blood) and we have found with flow cytometry (staining with DRAQ5) a cell-like population without nucleus but it has RNA production. Does anyone any ...
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What is the difference between DNA vs RNA Editing in the context of gene therapy?

As a someone with beginner knowledge on biology, I have come across the terms "RNA editing". Take this paper for example : RNA Editing with CRISPR-Cas13 From my understanding, DNA -> RNA -> Proteins ...
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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 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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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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How do introns code for proteins? [duplicate]

The reason I am asking this is because my textbook states that: Some introns may themselves encode proteins, and some may become short non-coding lengths of RNA involved in gene regulation. Some ...
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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 does 4-thiouracil labelling to map RNA-binding proteins cause a T-C change?

I am now reading a paper about the purification and identification of mRNAs and its RNA binding proteins by using UV crosslinking and immunoprecipitation. I came upon this sentence which puzzled me ...
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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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Why does a cell need siRNA?

My question is about small non-coding RNAs. miRNA and siRNA are both known for mRNA regulation. miRNA can both transcriptionally inhibit and degrade mRNA by cutting it. For inhibition just a small ...
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2answers
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Why do we use cRNA instead of initial extracted RNA in the microarray technique?

I am recapping for the exam in transcriptomics and stumbled into a question about microarray. So, our regular workflow is to extract RNA from cells generate cDNA from the initial RNA using reverse ...
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Who created the codon wheel chart (not as a table)

I'm trying to find out who created or first used the codon wheel chart as far as we can know? (I don't mean the tabular format)
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Can I ask tip for tissue measuring(especially for RNA preparation)?

I extracted RNA at mouse liver and human blood, but degradation occurs. I think, at mouse liver, too hard to measuring 50mg liver(I am newbie for animal tissue preparation) so spend several minutes. ...
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Double stranded RNA Single stranded DNA

I have seen in textbooks referring to ds RNA and ssDNA. How a RNA can be double stranded and likewise how a DNA can single stranded and if they do exist why are there names not interchanged?
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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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Do ribosomes read mRNA?

So I understand that tRNA bonds to a codon (with an anticodon) in the translation process. I read in my biology textbook that the ribosomes "read" the mRNA strand. Why do the ribosomes need to read ...
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Name of dsRNA (or dsDNA) where all strands are identical

What is the name of dsRNA (or DNA) where all component strands are identical (i.e. where the complex consists of multiple copies of the same ssRNA)? Example: 2 identical ssRNAs forming a dsRNA ...
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What makes/breaks the hydrogen bonds between DNA and RNA during transcription?

So I know that RNA polymerase catalyzes the phosphodiester bonds that hold the sugar backbones of a growing mRNA molecule together during transcription. However, I'm less sure about the hydrogen bonds ...
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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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Why analyse transcriptome instead of proteome?

Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (...
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How does transcription end?

In rho-dependent termination in prokaryotes, how does RNA polymerase “know” that it has reached the end of a gene and that it has to stop so that the rho-factor can bind mRNA’s rut site? Is there a ...
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Order of samples for RNA extraction

I want to extract RNA from various tissue samples, liver, gut etc, in different treatment groups. Due to the large amount of samples I will extract in sets. I am wondering, in reducing the potential ...
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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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If a person is infected with an RNA virus what percentage of the RNA in the blood of the person contains RNA of the virus?

Karius uses DNA sequencing of everything that's contained in a sample to detect all bacteria and DNA-viruses in the sample. Given the way that costs of sequencing are falling this approach seems to be ...
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Secondary structure and function in mRNA and single-stranded virus RNA

Although some mRNAs and the RNA of single-stranded RNA viruses do have some secondary structure, this is much less than in rRNA, tRNA etc. Why is this so? What prevents their folding to the extent ...
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RNA polymerase and DNA helicase

Is DNA helicase or RNA polymerase responsible for breaking the hydrogen bond between the 2 strands during transcription for eukaryotic cells? My textbook (WJEC Biology for AS level) says it is DNA ...
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The role of GC content in promoting or hindering transcription

This is quite a specific question, and I'm hoping someone might be able to assist in a literature hunt I've been engaged in for ages. I study some long bacterial operons, and have noticed that the GC%...
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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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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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With respect to which METRIC is my DNA 99% similar to any other person's DNA? [duplicate]

I clarified my question, by editing the title. Using the comments and links below, I have answered it myself: The answer to my question is: The similarity is between 98.4%-99.9%, depending on which ...
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Insertion of an additional base at start codon make the protein still functional?

So the question is if: a deletion of a codon for the amino acid lysine (AAG) is more or less likely to cause nonfunctionality of the protein than: Insertion of an additional base (C) within the ...
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Correct structure of RNA [closed]

Of the 2 figures, which is the correct structure of RNA, This is the link : 1: https://i.stack.imgur.com/IYgyv.jpg Sorry, the figure is not to scale. If there's any problem with the question ...
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What is the difference between alarmones and riboswitches

An Alarmone is an intracellular signal molecule that is produced due to harsh environmental factors. They regulate the gene expression at transcription level. A riboswitch is a regulatory segment of a ...
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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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How do cells determine RNA types?

I was reading about the different types of RNA polymerases, and I am confused as to how a cell determines which type of RNA it is transcribing. According to this nature article: RNA pol I ...
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1answer
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Ribosomes producing proteins, but need proteins to be produced?

So according to my textbook: RNA is used to create ribosomal RNA (known as rRNA) which is then combined with proteins to form the ribomsomes necessary for protein synthesis. I'm a bit confused ...
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Does the complimentary base pairing of rRNA with itself play a role in its transcription?

I have read that the termination of the transcription of mRNA involves a termination sequence in the form of a stem loop. As the structure of ribosomal RNA involves extensive internal base pairing, I ...
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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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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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Questions about RNA Polymerase

I'm confused about the terminology and directions described in processing DNA to proteins in this paragraph. RNA polymerase reads a DNA template in the 3’ to 5’ direction to synthesize RNA in the ...
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Complete human rDNA sequence

I've been trying to retrieve the complete human rDNA sequence (non-spacers and spacers), which should be about 43-kb in length using Biomart, NCBI, and rnacentral, but I have only been able to find ...
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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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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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Should I use RNAseZAP on my bench and pipettes before RNA extraction?

Should I spray RNAseZAP on my bench and pipettes before working with RNA? I am regularly using RNase at my bench and would like to work with RNA as well. Could traces of RNase on my equipment degrade ...
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Where is DNA during the process of RNA extraction using Trisure?

Where is DNA during the process of RNA extraction using Trisure described here? Given that DNA is also a nucleic acid, should I expect the isolated RNA to also contain DNA? However, Bioline claims RNA ...
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Assays for detecting RNA binding with protein

In a project I'm working on, we are designing a system where specific RNAs bind to proteins - an important part of this is to test whether the RNA binds when we modify the proteins in some way. What ...