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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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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86 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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Can a dNTP be built into a RNA strand?

DNA consists of deoxyribonucleotides, RNA consists of ribonucleotides. They differ mainly (apart from the uracil / thymine difference) in the sugar part, the deoxyribose and the ribose. Those two ...
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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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52 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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254 views

Translate DNA to Protein

Assuming the sequence shown is read left to right, what is the sequence of the protein produced? sequence: 5’-ATGTACTTCCATCTGGAATAG-3’ MY ATTEMPT: I know RNA is synthesized 5 to 3. This is ...
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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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126 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

Expression of bidirectional promoters

How are bidirectional promoters expressed ? (Won't RNA Pol have to go in 3'-5' direction?) Why are they more commonly found in eukaryotes than prokaryotes?
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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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36 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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100 views

How can a continuous RNA be transcribed in the lac operon?

The lac operon has 3 genes: lacZ , lacY and lacA. I have seen that the m-RNA transcript of these genes has stop codons in between. So, how can the RNA be made continuously? Won't the RNA Pol detach if ...
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54 views

What are the distinctive structural features of single- or double-stranded xRNA, or where can I find them?

I am interested in the structural differences caused by benzopurines and benzopyrimidines at the oligonucleotide level between RNA and xRNA, both in single-stranded and double-stranded form. I am ...
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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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38 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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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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64 views

Are there known 3- or 4-nucleotide RNA linkers with no RE sites?

Question is rather self-explanatory. I'm looking for a non-cleavable RNA sequence to act as an RNA linker. I mention 3- or 4-nucleotides only, but making such a sequence with 2 nucleotides is rather ...
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104 views

How does GTP help in the step of codon recognition?

The anticodon of an incoming tRNA base pairs with the complementary mRNA codon in the A site.Hydrolysis of GTP increases the efficiency and accuracy of this step. How does GTP do so ?
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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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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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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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275 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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61 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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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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38 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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50 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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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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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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59 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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91 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 ...
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204 views

Number of introns in a genome

Humans have approximately 21000 genes but they probably make more proteins than that. This has been explained by many mechanisms like alternative RNA splicing. My question is - If what we call as ...
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35 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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165 views

How to deduce if RNA virus infection or DNA virus infection

Is there any general rule to say this must be RNA virus infection and the other one DNA virus infection? Example of a case: 5 children develop a bright red rash on the face and turns violet after a ...
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110 views

DNA Replication

I just wanted to understand the basic steps behind the replication of the lagging strand of DNA: Have helicase unwind it first DNA Primase lays down RNA primers in fragments, called Okazaki ...
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How does one quantify T7 RNA polymerase transcription efficiency?

I am looking for a method which can help me calculate how many sequences one will get after transcription of 100-mer random sequences by T7 RNAP. The sequence pool has a known complexity and will be ...
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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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594 views

Low RNA yield, low 260/230 ratio

I extracted total RNA from animal tissue using the Qiagen RNeasy kit, however my RNA yield was extremely low and the 260/230 ratio was around 0.3. This is the protocol I followed: The animal ...
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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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118 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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46 views

How do amino acids become attached to tRNA?

Is there a protein that catalyzes this or does it happen spontaneously? In which part of the cell does this happen?
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30 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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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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43 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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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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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 ...