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

5
votes
2answers
81 views

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?
3
votes
3answers
235 views

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 ...
5
votes
1answer
1k views

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 ...
5
votes
1answer
135 views

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
3
votes
2answers
93 views

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 ...
7
votes
2answers
153 views

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 ...
3
votes
1answer
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 ...
2
votes
0answers
119 views

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 ...
12
votes
2answers
3k views

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 ...
4
votes
1answer
106 views

Is there a DNA analogue to ribozymes? [duplicate]

If not, is it impossible for DNA to have enzymatic activity?
5
votes
1answer
146 views

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?
2
votes
1answer
127 views

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 ...
2
votes
1answer
772 views

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 ...
2
votes
4answers
5k views

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 ...
2
votes
0answers
39 views

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 ...
2
votes
1answer
622 views
+100

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 ...
2
votes
1answer
128 views

Stockholm format to dot-brackets format?

I need to convert all my sequences in a Stockholm format into this: ...
11
votes
2answers
152 views

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 ...
6
votes
1answer
338 views

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 ...
2
votes
0answers
121 views

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 ...
7
votes
1answer
226 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 ...
3
votes
1answer
141 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
211 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
1answer
82 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 ...
14
votes
4answers
13k 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 ...
8
votes
2answers
2k 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)? ...
5
votes
2answers
591 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 ...
7
votes
1answer
266 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
942 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
307 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 ...
2
votes
1answer
54 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
196 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
1answer
692 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 ...
0
votes
3answers
720 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 ...
4
votes
1answer
89 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 ...
3
votes
1answer
326 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 ...
3
votes
2answers
165 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 ...
9
votes
1answer
364 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) ?
1
vote
1answer
309 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 ...
4
votes
2answers
456 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?
1
vote
1answer
144 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
1answer
107 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
188 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
44 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
535 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
160 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 ...
2
votes
2answers
75 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 ...
2
votes
1answer
2k 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
24 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
37 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 ...