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Questions tagged [mrna]

Messenger RNA is produced during transcription before it leaves the nucleus to be be translated by a ribosome. This produces a sequence of nucleic acids for which mRNA is considered the template.

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How is mRNA read by the ribosome? [closed]

I am aware that DNA is read in the 3' to 5' direction and then the resulting mRNA strand is created by the polymerase in the 5' to 3' direction. But during translation, which direction is the mRNA ...
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What is the frequency of AUG near-cognates (as start codon) in ‘Leaderless’ mRNA?

In typical bacteria that use SD-dependent translation initiation, the AUG start codon may sometimes be replaced by near-cognates (GUG, UUG, etc.). The frequency of these near-cognates is somewhat ...
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Relationship between the ambiguity (wobble) at codon position 3 in elongation and codon position 1 in initiation

In prokaryotes the usual observed start codon frequency is AUG > GUG > UUG. An explanation for this is that AUG is the most common initiator codon because it forms the most stable interaction with ...
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172 views

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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1answer
858 views

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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1answer
40 views

mRNA bonding to itself

Does a mRNA molecule bond to itself? I heard that only tRNAs have hydrogen bonds that let them have second structures, but after searching the web i found multiple answers. If yes, does anybody have a ...
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1answer
36 views

Are RNA cleavage sites always polyadenylated?

During RNA processing (including both mRNA and non-coding RNAs), is the end of 3'UTR always polyadenylated after cleavage? I could not find the answer to my question in the Wikipedia entry for ...
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1answer
20 views

mRNA Sequencing Basepair from Polyadenylation Site?

I was wondering how many basepairs are usually sequenced with mRNA/cDNA illumina methods from upstream of the polyedenlation site? Thanks.
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1answer
84 views

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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Minimum number of cycles for effective qPCR quantification?

I have been having an apparent problem with gDNA contamination in my no-reverse transcriptase (NRT) controls by the appearance of fluorescence peaks in my qPCR data. I have/am trying multiple DNase ...
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1answer
234 views

How would one go about isolating a specific mRNA out of a pool of others? [closed]

I'm writing an essay about DNA recombinant techniques where the question asks to outline all the steps to arrive at having a colony of bacteria expressing a gene of interest.The question makes you ...
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51 views

Mutations in organisms

I was researching mutations and came across an interesting question: Do mutations occur in the DNA or mRNA of an organism? Is this more opinion that science? Thanks in advance!
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1answer
142 views

How is mRNA directed out of the nucleus to its ultimate cytoplasmic location?

In the process of translation, I learnt that following formation the mRNA must exit the nucleus through a nuclear pore and attach to a ribosome. My question is how does mRNA navigate itself out of ...
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98 views

Meaning of term ‘rapidly labeled RNA’

I encountered the term, “rapidly labeled RNA”, in the article: Rapidly labeled HeLa cell nuclear RNA. I. Identification by zone sedimentation of a heterogeneous fraction separate from ribosomal ...
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2answers
155 views

mRNA synthesis for in vivo injection

I found a commercial reagent called in vivo-jetPEI® from Polyplus-Transfection that is able to delivery mRNA in vivo. I'm planning to do an experiment with it, but I'm worry about how to synthesise ...
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0answers
54 views

What is the reason for occurence of introns in eukaryotic mRNA? [duplicate]

After transcription of the Template strand of DNA, in prokaryotes, the translation process begins immediately. But in eukaryotes the mRNA transcript has both non coding (introns) as well as coding (...
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Do exon deletions in C.elegans mutants necessarily result in nonsense mediated decay of the transcript?

I am trying to write out my research proposal about a project in C.elegans. There are multiple mutants of the factor that I want to study, each with different mutations. I know that a mutation that ...
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1answer
192 views

Which mRNAs enter P-bodies?

Processing bodies (P-bodies) are distinct foci within the cytoplasm of the eukaryotic cell consisting of many enzymes involved in mRNA turnover (ref). They play a fundamental role in RNA silencing/...
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181 views

Longest transcripts without isoforms

Does anyone know what genes produce the longest mRNAs? I am planning a project on synthetic introns and want to use stuffer fragments to vary intron size. Obviously they must not contain any splicing ...
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151 views

Consensus sequence for selection of initiation codon in eukaryotes

In bacteria the AUG (or other) codon at which translation of mRNA is initiated is preceded at a precise distance by a sequence known as the Shine and Dalgarno sequence, to which the 30S subunit ...
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Are RNA transcripts always synthesised from the same DNA strand? [duplicate]

The DNA is read 3'->5' (and RNA synthesized 5'->3'). But due to the DNA strands having to be complementary, it seems to me that the origin can only appear on the correct side of the ORF on one of the ...
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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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1answer
6k views

What is the Shine–Dalgarno sequence?

I am trying to understand the Shine–Dalgarno sequence. I currently know it is related to ribosomal binding sites, it is only found in prokaryote cells and it is in front of the initial codon. Also, ...
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485 views

DNA & mRNA During Transcription

Just a simple, quick question: how are the mRNA and the template strand of the DNA structured during transcription? I've seen models and videos of them when they're both flat/straight (is that just ...
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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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2answers
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How many proteins do all human ribosomes together produce per hour? [closed]

Very roughly how many proteins (chains) are synthesized in the human body per hour under normal conditions? (And how many ribosomes does the human body have?)
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1answer
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How do messenger RNAs regulate each other's expression levels?

I know that researchers learn gene regulatory networks from microarray experiments that measure the mRNA expression levels. However, I do not understand how mRNAs regulate each other's levels. Do they ...
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1answer
84 views

Is the technology “identitas v1 forensics chip” related to microarray technology?

Available resource but difficult for me to make scence Relation about crime scene and identitas v1 forensics chip Is the technology "identitas v1 forensics chip" related to microarray technology? ...
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siRNA designing problem [closed]

I have a gene sequence with 15 alternative splicing forms. I want to design a siRNA for 1 isoform, I select the exon intron junction that is unique for this isoform, and I must design siRNA for this ...
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1answer
27 views

Method of figuring out how much of a certain mRNA is present in a bacterium

I am trying to develop a method for figuring out how much of a certain mRNA is present in a bacterium. This is what I have so far: Perform a mRNA extraction Using Electrophoresis, to isolate the ...
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1answer
53 views

What is the rate of mRNA decay in saccharomyces cerevisiae?

I am just looking for a number whether that is a mean or an estimate. I am having trouble finding this value on papers because the papers mention only the methods for calculating such a value. Is ...
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1answer
491 views

What is the transcriptome in layman's term?

I am new to the bioinformatics field and am trying to understand a research paper that includes some terminology without definitions. The term transcriptome in particular is banded around in the ...
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3answers
2k views

Relationship of the DNA of a eukaryotic gene to the 5'-UTR of its mRNA

In eukaryote pre-mRNA I am having a little trouble grasping exactly what the 5 prime untranslated region is defined as. It seems that it could be defined as the difference in pre-mRNA between the ...
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0answers
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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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1answer
874 views

How does the splicing enzyme recognize where to splice the introns?

When the DNA from the nucleus is transcribed to an mRNA, the mRNA is spliced by an enzyme before it goes outside through the nuclear pore. What is the name of this enzyme and how does it recognize ...
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75 views

Blood sampling at home

I want to collect small blood samples at regular intervals (e.g. every 8 hours or more often) over a longer period (weeks to months). To avoid having to go to a lab or doctor to have this done, I want ...
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3answers
129 views

miRNA targets mRNAs

If we observe that a miRNA, say hsa-mir-233, targets a mRNA, say XXX, in a given tissue in disease condition, can we say that always hsa-mir-233 targets mRNA XXX regardless of type of tissue and ...
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1answer
273 views

Why do bacteria need messenger RNA?

Why do bacteria need mRNA? Isn't the DNA free floating without nuclear membrane so why doesn't the tRNA read the code directly off of the split DNA strands? (ofcourse after helicase splits them). ...
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1answer
90 views

Difference between micro RNA and short-interfering RNA and CRISPR Cas 9 system?

I read this article https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/ and am slightly puzzled as to why the CRISPR/Cas 9 system is seen as being so revolutionary. It seems like the ...
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1answer
530 views

How can I find the mRNA sequence for a specific prokaryotic gene?

What I want to find out is the start of the transcription for a specific gene, how long the UTR is before the actual coding sequence starts. I've looked at various databases like NCBI Gene, Refseq or ...
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1answer
113 views

RNAi in nematode resistant plants

Background : Certain plants have been genetically engineered to have sense-antisense gene of a parasitic nematode. The dsRNA produced by the plant then inactivates the mRNA produced in the nematode, ...
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164 views

What is the meaning of conservation site in miRNA-mRNA pairing context?

I am not biologist and just work in Bioinformatics field. Does anyone know what is the meaning of conservation in the context of miRNAs and their pairings to mRNAs? Example: Each of these duplexes ...
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3answers
5k views

Mutation That Loses Stop Codon

Someone asked this in my class and my instructor wasn't sure in her answer, doesn't anyone know what happens in protein synthesis if a mutation causes mRNA to not possess a stop codon? Would the ...
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4answers
241 views

Are there constraints on where intron/exon boundaries occur with respect to the triplet codons of the reading frame?

I did a quick search (here and elsewhere) and couldn't find anything on this subject. If all introns in a given primary transcript were spliced out in the same way, then this wouldn't matter. But ...
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2answers
941 views

How can 3' end polyadenylation protect cellular RNA from ribonuclease degridation?

In this link, it states: It is worth noting that all intracellular RNAs are protected from RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding ...
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1answer
191 views

Are both (partial) copies of DNA transcribed in S and G2 phases of cell cycle?

For a little less than half the cell cycle, a significant number of genes are represented twice (just before dividing). Does the cell differentiate between these DNA in any way or are transcription ...
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Which data format for mRNA expression matrix is necessary to run pathway analysis with Paradigm?

I am running Paradigm on a matrix of mRNA expression. I read Vaske, Charles J., et al. "Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM."...
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0answers
32 views

Gene expression for mouse feeder cells (inactivated MEFs)

I'm looking for a paper with gene expression data for mouse feeder cells, inactivated by gamma radiation or mitomycin C. Ideally I'd like RNA-seq data but I'll use microarray data if that's all there ...
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2answers
5k views

How to find miRNA binding sites on a specific gene?

I am trying to find miRNAs that bind to the 3'UTR of a specific gene. What is the best way of doing that (that is, with a good scoring analysis that is most commonly used by researchers in this area)? ...
9
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1answer
348 views

How many RNA-binding proteins can simultaneously bind on a single mRNA?

Typically, how many RNA-binding proteins can simultaneously bind to a single mRNA? Or said differently, how many "binding sites" does an mRNA have? What order of magnitude? I am interested in RNA ...