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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Biopython - Big Discrepancy Calculating RNA melting Temperature over Literature

I experience big discrepancies when calculating melting temperature of RNA 7-mers with Biopython over values generated by a popular algorithm. I tried the nearest neighbour algorithm with RNA and ...
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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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Cleavage of RNA by restriction enzymes?

Six restriction enzymes discussed in Sequence-specific cleavage of RNA by Type II restriction enzymes (Murray et al.) have the ability to detect and cut RNA strands with that enzyme's recognition ...
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What physical force attracts the anti-codon on tRNA to the codon on mRNA during translation?

What physical force attracts the anti-codon on tRNA to the codon on mRNA during translation? I know that these two bond together, but what actually makes the tRNA move through the cytoplasm to the ...
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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 ...
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Why deoxyribose for DNA and ribose for RNA?

Why is DNA made out of deoxyribose and RNA made of ribose? Why can't they both use ribose or deoxyribose? I think that the deoxyribose gives an advantage in storing genes, the job of DNA and ribose is ...
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NCBI-geo differences between platforms,series and samples

This is the first time that I use NCBI-GEO and I've faced with 3 different categories inside it. They are platform, sample and ...
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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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Double stranded nucleic acids are more 'durable' than single stranded nucleic acids?

I'm struggling with a question I've been asked. "Why is double stranded genetic material more 'durable' than single stranded one?" I know that double stranded genetic material is more stable due to ...
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What is the function of the RNA primer in DNA replication?

During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?
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What is the explanation for the smaller number of tRNA than codons?

Translation, or decoding, of the four-nucleotide language of DNA and mRNA into the 20–amino acid language of proteins requires tRNAs and enzymes called aminoacyl-tRNA synthetases. To ...
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Finding Rna-Seq dataset for C. Elegans (Caenorhabditis elegans)

I want to find a RNA-Seq dataset for C. Elegans to use it in RNA-Skim software. For those who does not know RNA-Skim let me explain it a bit. It is a tool which is used to quantify RNA-Seq data using ...
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How predictably will RNA polymerase not transcribe repetitive sequences?

I am working on an (expensive) synthetic construct, which happens to have many "repetitive" sequences within it that are integral to its function. Primarily, the two sequences that are worrying me ...
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How to isolate host cell RNA (tRNA,mRNA,rRNA) from viral RNA?

A retrovirus with RNA genome infected a host cell. You would like to isolate the host cell’s RNA (rRNA, tRNA, and mRNA) from the virus RNA. What properties can you rely on to determine the three types ...
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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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Why is 5S-rRNA is different from other rRNAs in place of transcription and usage of RNA polymerase?

While transcription of rRNAs happens in nucleolus mediated by RNA Polymerase-I, we see that 5S-rRNA is transcribed elsewhere by RNA Polymerase-III. What is the cause and why?
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Time required for RNA precipitation in ethanol

I precipitated bacterial RNA during 1 hour at -80ºC after depleting rRNA with Ribo-Zero kit. Does more time lead to better results?
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Where do amino acids get attached to tRNA and where is it synthesized?

Some very basic parts of transcription/translation seem to be left out in various literature. I can't find the answer to this anywhere: How exactly is tRNA synthesized? I realize that mRNA is ...
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Naming convention of miRNAs

I'm trying to understand naming convention of miRNAs. I've found the wikipedia article about it nomenclature Based on it, I try to figure out what is hsa-let-7a. As far as I understood, hsa refers to ...
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Can bacterial RNA be degraded at -80⁰C in a SDS solution?

I would like to know if bacterial RNA in a 1.5 mL 2%SDS solution can be degraded. Comes from a pellet of pure liquid culture. Thanks
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Change solvent of bacterial solution

I have to perform an RNA extraction that should start with 900 uL of 2%SDS bacterial solution. The problem is that the sample is in 900 uL of PBS. I thought about centrifugation of the sample at ...
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Finding confidence level of miRNA disease associations

I'm an undergraduate computer engineering student, and I have a project about bioinformatics. In this manner, I need to find prediction( or association I'm not sure the correct terminology) confidence ...
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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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Is there a DNA analogue to ribozymes? [duplicate]

If not, is it impossible for DNA to have enzymatic activity?
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How does alternative splicing work?

I am trying to find out what controls what exons are spliced out, and I keep coming across the term cis regulator, but I cannot seem to find a clear explanation of what happens... Thank you in ...
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What are microRNA, siRNA and antisense RNA?

From what I understand, microRNA binds to proteins which can cut certain mRNA strands do that this protein is not synthesised. This seems like gene silencing to me, however I have also come across the ...
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Can human mRNA be translated in vitro by prokaryotes?

As the genetic code is universal, can mRNA from a human cell be correctly translated by a prokaryote in a in vitro translation system?
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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)? ...
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Can DNA & RNA be considered as nature's programming language?

The final frontier of Biological Sciences could be considered understanding the effects of variation in the DNA (and RNA). If after fertilization the DNA of the zygote could be genetically ...
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Why do eukaryotic organisms have introns in their DNA?

We touched on introns and exons in my bio class, but unfortunately we didn't really talk about why Eukaryotes have introns. It would seem they would have to have some purpose since prokaryotes do not ...
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Why are there both stop and start codons?

Based on my understanding from wikipedia, there is the (RNA) start codon AUG and the stop codons UAA, UGA, UAG. AUG can also encode Methionine, I'm assuming if it appears in the middle of a mRNA ...
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Are codons that map to the same amino acids interchangeable?

(disclaimer - I'm just getting interested in genetics so sorry if this is an obvious/silly question.) From wikipedia, in the section on the RNA codon table, I see a mapping between codons and amino ...
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Alternative protocol for evaluating RNA integrity, using a bleach gel

I hate having to run MOPS PFA agarose gels with DEPC and everything just to verify my RNA integrity. I came across an alternative protocol that uses ordinary household bleach in the gel to inhibit ...
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How much total RNA can be extracted from Drosophila brain

I am wondering how much total RNA could be extracted from a single D. melanogaster brain. I could not find this information from the literature. The closest hit was this paper, that claims that ...
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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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Stockholm format to dot-brackets format?

I need to convert all my sequences in a Stockholm format into this: ...
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RNA isolation from Drosophila head

I need to isolate RNA from Drosophila head. I basically chop the head off and first homogenize it with a homogenizer (similar to this: ...
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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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Well to well variation in thermal cycler fluorescence?

We have an old BioRad ICycler Thermal Cycler with MyIQ single color fluorescent detector. While it's meant for RT-PCR, we've been using it for melt curves and binding assays for different types of RNA ...
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How can I purify RNA after gel electrophoresis to remove residual acrylamide?

I sometimes use denaturing gel electrophoresis on a preparative scale to purify RNA produced by in vitro transcription. The major issue with this is that the sample after extraction from the gel still ...
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Use cases of RNA secondary structure prediction

I'm an undergraduate currently writing a thesis on RNA secondary structure prediction, specifically building upon analysis done by the RNAStructure and Unafold software packages by modifying certain ...
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Why is uracil used in RNA rather than thymine?

What is the advantage gained by the substitution of thymine with uracil? I have read previously that it is due to thymine being "better protected" and therefore more suited to the storage role of ...
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How significant is RNA degradation with removal of cap/polyA's in eukaryotes, or UTR's in prokaryotes?

Question is rather self-explanatory, but segmented into two parts. I'm attempting to make use of a repression system that employs cleaving RNA at specific areas with ribozymes with the intent of ...
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Ribosomal Turing Machines, DNA/RNA computation

I'm a computer science guy, recently crossing over to do some research in computational biology on RNA secondary structure prediction. While looking through the materials I got a crazy idea, what if ...
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Mouse meta-globin mRNA problem

This is an mRNA strand of mouse meta-globin: 5'-ccccagauacggaauucgaau-3' A) Which small RNA (below) is most likely to regulate expression of meta-globin? ...
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Will eukaryotic RNA fold in the same way in prokaryotes?

As far as I know, there are no specific eukaryotic or prokaryotic factors that aid in RNA folding other than cellular environment (salt and ion concentrations, dissolved molecules, etc). Are there any ...
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Is wiping with RNAse Zap enough to destroy RNAse activity?

From the RNAseZap MSDS, it is an SDS at some unknown concentration, maybe with some NaOH? Some other links suggest there is some NaOH as well. The Ambion site states that RNAseZap destroys RNAse ...
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Are there any strictly chloroplast/mitochondrion-residing ribozymes?

A simple question that had occurred to me. Considering the small doubt of transcribed genes in both organelles, I would doubt it, but are there any known ribozymes strictly found in either ...
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How do you visualize RNA on a gel?

I have run an in vitro transcription reaction and produced some RNA of a single species and definite size. I would like to visualize it to check if the reaction worked. Can I do this on an agarose ...