Tagged Questions

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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Tricky DNA and RNA question [on hold]

Information storage and transfer are the critical functions of nucleic acids. Which of the following is/are important characteristics of the sugar phosphodiester ester linkages in the backbone of ...
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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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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 ...
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183 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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343 views

What's the longest transcript known?

What's the longest functional transcript known? I'm wondering about RNA length post splicing, so not including introns.
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34 views

How many water molecules will be generated when single nucleotides are used to make this RNA: 5’-UUAACCGUCAG-3’?

Based on what we learned on condensation reactions, how many water molecules will be generated when single nucleotides are used to make this RNA: 5’-UUAACCGUCAG-3’ I had an online biology quiz with ...
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23 views

Why can't NMR be used on large RNA molecules?

While reading my Molecular Bio textbook, I came across a sentence that stated that NMR cannot be used on large RNA molecules to determine their structure. Why is this? Is it because RNA is single ...
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47 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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63 views

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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63 views

What is the purpose of DNA? [closed]

My very basic understanding is DNA gets transcribed into RNA by effectively replacing thymine with uracil, then RNA is translated to make proteins. Looking at it from an engineering perspective, it ...
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1answer
57 views

Can we attack viruses by attaching proteins and such to their shells?

Haven't looked into this to very long, but an initial search didn't return anything. HIV uses certain co-receptors to enter our cells. Could we flood the blood stream with specially designed ...
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64 views

Remove RNAse from pipettes?

Our lab uses old Gilson Pipetman pipettes. I've been using some for making mRNA by in vitro transcription and started running into RNAse issues. I'm trying to clean everything up, including the ...
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90 views

The move from RNA to DNA and the necessity of reverse transcriptase

In this piece about giant viruses and the origin of life, in the context of the move from RNA world to DNA world, virologist Valerian Dolja states: In order to move from RNA to DNA, you need an ...
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129 views

First RNA polymerase-mRNA

We know that RNA polymerase produces mRNA by reading DNA strand. Which enzyme produces the first RNA polymerase if other RNA polymerases are synthesized in the same way like other enzymes(proteins) ?
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104 views

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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176 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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43 views

Conclusions from hybridization results

A double stranded DNA was denatured in a mixture that included mRNA from a gene in the segment. The mixture was then cooled to promote RNA and DNA hybridization. The following figure the results. ...
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36 views

Trimming of tRNA precursors

From Molecular Biology of the Cell (4th edition) by Bruce Alberts et al. (Chp 6, Pg 338) : Both bacterial and eucaryotic tRNAs are typically synthesized as larger precursor tRNAs, and these are ...
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80 views

A question related to qPCR analysis

Here is the thing. I am using a method, called TU-Tagging, to isolate cell type specific RNA. You can find more about the method here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2783170/ To explain ...
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36 views

What information do microarray image convey?

OK I have read that a cell generates 4 kinds of digital (to be precise discrete) data namely DNA, RNA, Protein (sequences that can be encoded as string sequences of nucleotides/ amino acids) and micro ...
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Do miRNA and antisense RNA do essentially the same thing?

Don't they both just disrupt RNA so it can't make a protein? If so, then what is the difference between the 2?
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128 views

Do RNA molecules bind each other?

I have a question, maybe a naive one. Let's assume that we isolated some RNA from a tissue. Do RNA molecules can bind each other if they have the complementary sequence? I know that some small RNA ...
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57 views

Which types of hydrogen bonds are known to exist in RNA secondary structures?

I'm programming an implementation of an algorithm for pattern matching in RNA structures. The algorithm assumes the following types of base pairs: Plain: No base pairs (just the primary structure of ...
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1answer
200 views

How is the transcription direction of RNA polymerase determined?

When transcription factors attach to the DNA strand - How do they know in which direction they have to initialize the transcription by rna polymerase? Is it always read in the same direction anyway? ...
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1answer
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2 types of telomerases?

As telomerase works by adding new nucleotides complementary to the RNA it contains, it cannot work for the complementary strand. Say telomerase X has RNA complementary to the 5' to 3' strand it ...
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28 views

Telomerase in tetrahymena

In this amazing video, at 26:03 we see this image We now know that the telomerase contains a sequence complementary to the telomere sequence and so is able to do what it is capable of doing in this ...
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143 views

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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69 views

Ribosomal RNA amount in a Drosophila cell

I am isolation RNA from Drosophila larvae brain with TRIzol method. What percentage of extracted RNA will be ribosomal RNA? I am only interested in mRNA, so I am trying to figure out whether I need to ...
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37 views

RNase and EtOH issue

I work with RNA and I have some RNase issues. For example I am using RNeasy mini kit and at one step I use 100% EtOH. It does not say it is RNase free or not. Does absolute EtOH inhibits or removes ...
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132 views

Why are transcripts translated from 5' to 3' direction?

What is the mechanism? In other words, how does the tRNA know whether the codon is in 5' to 3' direction? I also heard that anything that is translated from 3' to 5' direction is degraded. Is it true? ...
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146 views

How to determine the actual flux in the human metabolic model of a cell line?

The problem to be solved is to determine what the flux values are for the different reactions in the human metabolic model. As far as I understand, a good way to do that would be to use gene ...
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1answer
55 views

Does biotin affect downstream experiments, such as RT-qPCR?

I have two biotins--one of which is binding my RNA with cleavable bonds, and the other with irreversible bonds. Does biotin have an effect if it keeps its bonds with RNA? If it does, why is this the ...
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39 views

RNA secondary structure comparison

Do you know any program which can compare two and more different RNA secondary structures? I need find some (dis)similarities between lots of predicted secondary structures. And create maybe common ...
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1answer
187 views

Elution of biotinylated RNA

I am using Neutravidin Agarose beads to isolate biotinylated RNA. The thing is, in the manual it says to use 8M Guanidine-HCl, pH 1.5 for elution biotinylated molecules. As far as I know it is a very ...
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59 views

In vitro transcription, contamination problem

I am using a RNA which is in vitro transcripted before I started my project. It turned out it is not prepared properly and has DNA contamination. Instead of perform the in vitro transcription again, ...
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44 views

RNA integrity and RNA fragmentation

After RNA isolation and before following experiments, I know that RNA quality so called RNA integrity is so important. So why there is a RNA fragmentation kit? Do we need RNA intact or fragmented? ...
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55 views

Dilution question about RNA

I have a basic and probably silly question. I am isolating RNA with TRIzol. I have performed the basic steps and dissolved the pellet in 50 uL water. I ve measured the concentration and it was 3313 ...
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1answer
65 views

What's the use of RNA editing in kinetoplast?

The genes of the mitochondrion (kinetoplast) of some Kinetoplastida - e.g. Trypanosoma brucei, the parasite which causes African sleeping sickness - are "encoded" in a way that the pre mRNA requiries ...
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429 views

Gel electrophoresis after RNAse treatment

I do not understand how to solve this question. I know that RNAse will cut smaller pieces of RNA. The answer given is A
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1answer
148 views

A basic example of the interactions of 2 or more non-identical alleles leading to an advantageous outcome for an individual organism

Could someone help me out with a basic example of the interactions of 2 or more non-identical alleles leading to an advantageous outcome for an individual organism? Based on empirical research OR on a ...
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45 views

Process of Transcription

During the process of Conversion to Ribonucleoside Monophosphates the various ribonucleoside triphosphates break off their high energy bonds after linkage to the DNA.But the first ribonucleotide ...
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37 views

What is mRNA expression level?

I cannot find clear explanation of what is mRNA expression level, and how to measure it. I would appreciate if someone explained it or gave a reference. Thanks!
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53 views

How does a prophage leave the host cell's genome?

I understand that, unlike a prophage, a provirus never leaves the genome, but I don't understand how the prophage "leaves".
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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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53 views

Mutation in pre-mRNA sequence

Has there any mutations been recorded which cause harmful effects due to change in the part of pre-mRNA responsible for proper m-RNA splicing ?
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48 views

Finding RNA Loops

I was rooting through the literature, but there is too much work on the topic of detecting loops in RNA and the RNA helices that go with them. Can anyone point to a good review on this topic or even ...
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1answer
72 views

Determining sequence of oligoribonucleotide

Oligoribonucleotide X was treated with phosphatase (for removal of 3' and 5' - terminal phosphates), then with RNAase T1, which cleaves all phosphodiester bonds located in a 3' position of ...
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70 views

How predictably will RNA polymerase not translate 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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72 views

Why use DNA polymerase in making cDNA?

RT is capable of synthesizing a complementary dna strand ( as in HIV life cycle.) Then why is DNA pol used when cDNA (synthesizing the second strand of it ) has to be synthesized from mRNA ( For eg.to ...
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105 views

explanation of conjugation experiment in bacteria

In this paper (On the expression of a structural gene) I am confused about what is being plotted in Figure 6. The x-axis contains the fraction of radioactive day and y-axis contains the enzyme ...