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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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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Why is statistical mechanics relevant to RNA and protein folding?

This is a very naive question. As far as I understand the folding of a molecule is governed by the electromagnetic forces between its atoms and also between its atoms and the atoms in the surrounding ...
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47 views

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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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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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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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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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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197 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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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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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 ...
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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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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. ...
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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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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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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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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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Finding SNPs and Haplotypes?

I have the following alignment file. How can I identify the SNP sites and how can I find the haplotypes. I know these are related but can't seem to apply it to the below data. Any help would be ...
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What's the regulation of natural antisense transcripts?

By running an in silico approach on TF binding site prediction, I've discovered binding motif similarity on a nucleotide sequence within the EGFR-AS1. I was quite surprised, given that the ...
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Trouble identifying a gene given an Expressed sequence tag

I have an assignment where we need to answer several questions about an EST, however, I'm having trouble getting started. My sequence contained a Not I site (clipped that) and no poly A signal. We ...