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.

learn more… | top users | synonyms

1
vote
1answer
22 views

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 ...
7
votes
2answers
110 views

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 ...
3
votes
0answers
22 views

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 ...
5
votes
2answers
81 views

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 ...
51
votes
4answers
31k views

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 ...
7
votes
1answer
73 views

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 ...
1
vote
1answer
132 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 ...
2
votes
1answer
164 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: ...
2
votes
1answer
99 views

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? ...
6
votes
1answer
81 views

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 ...
5
votes
2answers
2k views

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 ...
8
votes
2answers
103 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)? ...
4
votes
1answer
36 views

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 ...
5
votes
2answers
52 views

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 ...
4
votes
1answer
185 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 ...
4
votes
2answers
352 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.
2
votes
1answer
36 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 ...
0
votes
1answer
27 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 ...
2
votes
0answers
54 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, ...
0
votes
0answers
80 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 ...
2
votes
1answer
63 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 ...
1
vote
1answer
47 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? ...
0
votes
3answers
68 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 ...
3
votes
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 ...
8
votes
1answer
137 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) ?
3
votes
2answers
91 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 ...
3
votes
1answer
72 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 ...
4
votes
2answers
186 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?
2
votes
1answer
249 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? ...
1
vote
1answer
45 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. ...
2
votes
0answers
25 views

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 ...
2
votes
1answer
39 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 ...
1
vote
1answer
90 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 ...
0
votes
1answer
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 ...
4
votes
2answers
100 views

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?
3
votes
2answers
129 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 ...
1
vote
2answers
58 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 ...
4
votes
1answer
29 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 ...
6
votes
1answer
68 views

Can two hammerhead ribozymes simultaneously cleave each other?

I am working on a project in which an XOR gate is being built by having two hammerhead ribozymes simultaneously cleave each other when both are expressed, but have these ribozymes cleave a target ...
10
votes
2answers
5k views

How do I clean phenol contaminated RNA without losing any of the sample?

I recently extracted RNA from developing plant leaves for the first time, as part of a very long and intensive experiment. The samples were extremely precious because of the amount of effort that went ...
1
vote
1answer
16 views

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 ...
4
votes
1answer
70 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 ...
0
votes
1answer
39 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 ...
0
votes
2answers
155 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 ...
2
votes
2answers
150 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? ...
2
votes
2answers
40 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 ...
2
votes
1answer
208 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 ...
1
vote
1answer
60 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, ...
1
vote
1answer
57 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 ...
3
votes
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 ...