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 meant by “Expression” of Non-Coding RNA?

I was having a look at lncRNAdb and its help says: The ENCODE project gene annotation list, GENCODE, has predicted that the human genome contains 14,470 lncRNAs whereas only a small proportion of ...
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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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Do transcripts always start and end with exons?

I realized that in all cases of "RefSeq Genes" annotations of hg19 I looked at spliced transcripts start (and end) with an exon. From the annotation there is no evidence of any sequence upstream or ...
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46 views

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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22 views

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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273 views

Why is DNA double stranded and RNA single stranded? [closed]

Why is DNA present as a double helix structure and RNA as a single helix? What causes the difference between them? Why they are not the same? what is the role of these differences?
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1answer
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Do residue sequence numbers in PDB files correspond to the positions in the backbone?

In other words if two residues have sequence numbers, say, 20 and 21 then are they next to each other in the backbone? If no (or not necessarily) then is there any way to find consecutive residues ...
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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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126 views

Is there any virus that contains both DNA and RNA in its genome?

It is known that viruses contain DNA or RNA- either one and not both. I came across a question: Which virus contains both DNA and RNA?
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1answer
25 views

What's the difference between CREs and DHSs?

I would like to know what's the difference between cis-regulating elements and DNase I–hypersensitive sites, in order to produce a meaningful segregation of non coding elements affecting gene ...
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1answer
32 views

Why do RNAi pathway proteins exist in the nematode when they can cause them harm?

When dsRNA is injected in plant, Dicer cuts it and prevents disease. Why would the plant parasite, M. incognita - a nematode, die when dsRNA was injected in it? It should have saved it. Again, to 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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1answer
50 views

Questions on adding a protein to a DNA library [closed]

Two questions regarding finding the DNA sequence of a amino acid sequence (AA): 1) If you are able to find out the mRNA sequence of an AA, then don't you automatically know the DNA sequence? 2) ...
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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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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 ...
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1answer
16 views

RNAse activity review

I was searching for any review unravelling the structure-function motifs responsible for RNAse activity. Or at least a well-composed review of RNAse superfamilies that are described nowadays (with ...
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1answer
17 views

Why are minor introns bounded by nucleotides AT-AC, where T is not normally in RNA?

Major intron boundary nucleotides are GU-AG. Minor intron boundary nucleotides are AT-AC. Why does the former use RNA Uracil and the latter use DNA thymine? Since introns are in the primary RNA ...
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1answer
42 views

Accessing Expression Levels for Genes of Interest from GEO Experiments

I have a list of 100 lncRNAs (long non-coding RNAs). For each of these RNAs, I would like to query GEO to find any experiments that used a high throughput sequencing platform and detected expression ...
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1answer
25 views

H3K36me3 role in RNA polymerase II elongation

I found a paper describing the association of RNA polymerase II with the histone methyltransferase Set2 that methylates H3K36. At the end they say: While our results strongly implicate K36 ...
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3answers
613 views

Bioinformatics tool for “pairwise alignment” of complementary sequences?

I'm currently working on some ribozyme binding, and I'm looking for a tool that will essentially analyze the regions of the degree of complementarity in two sequences in order to extrapolate ...
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1answer
46 views

Does RNA serve as the genetic material of some plants and animals along with viruses?

My teacher mentioned that some plants and animals have RNA as genetic material but did not substantiate his statement with examples. I'm wondering if it is so? I have searched the internet but have ...
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1answer
33 views

Why is mRNA used as a biomarker for cancer over tRNA or rRNA?

I cannot find a clear explanation for why mRNA is used as cancer biomarker and not tRNA or rRNA. Is there something peculiar about mRNA which cannot be fulfilled by tRNA or rRNA?
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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
53 views

Do snRNAs exit the nucleus or not?

In Molecular Biology of The Cell (Alberts, et al., 2015), it lists the various RNAs that are trafficked through the Nuclear Pore Complex (NPC) into the cytoplasm. The list includes snRNAs, but I ...
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44 views

Which secondary structures of RNA are symmetric? [closed]

I'm trying to understand what is the meaning of this statement. A088518 Symmetric secondary structures of RNA molecules with n nucleotides. 4 %I %S ...
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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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238 views

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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3answers
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Are non-coding RNAs introns?

I am slightly confused as to what part of the genome codes for non-coding RNAs. Is it the introns? This would make sense to me as to why they are not transcribed as the introns are not transcribed. Or ...
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2answers
441 views

How much ATP is consumed during protein synthesis?

I'm trying to find out how many molecules of nucleoside triphosphates (ATP, GTP, UTP and/or CTP) it takes to release enough energy to link two amino acid monomers together with a peptide bond, ...
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1answer
46 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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64 views

Are the ribosomes specific for each organism

If we removed one ribosome from human and we put it inside horse, would the ribosome perform the as it would in humans or it will not work or somewhere inbetween?
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30 views

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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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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481 views

What is the biological significance of finding palindromes in DNA sequence?

I found a function called palindromes in Matlab that finds palindromes from DNA sequence. Now what is the biological intention behind incorporating this function? What the biological significance of ...
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1answer
39 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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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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1answer
135 views

How do eukaryotes terminate transcription? (clarification on Campbell Biology)

I'm having trouble understanding how eukaryotes terminate transcription. Studying Campbell Biology (pg. 342, 10th ed.), I read: In eukaryotes, RNA polymerase II transcribes the polyadenylation ...
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255 views

How to Extract RNA and perform RT-qPCR from very few cells ( ~5,000)?

I am currently conducting an experiment which involves FACS-sorting a specific population of cells using an antibody of interest. In order to validate the type of cells I have collected using this ...
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What are some (bioinformatic) methods to characterize potentially novel gene transcripts?

I am working with a few novel transcripts of genes- before I confirm their existence experimentally, I would like to perform some bioinformatic analysis. I have already considered coding potential, ...
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441 views

What makes DNA helical?

Why isn't DNA like RNA; why isn't RNA like DNA, that is, helical? Why are RNA chains straight?
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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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2answers
215 views

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 ...
6
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1answer
264 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 ...
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1answer
44 views

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 ...
2
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2answers
122 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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218 views

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 ...