Hot answers tagged rna
8
You should check out Howald C, et al[1]. This is one of the many recent papers tied to the ENCODE data. They've used RT-PCR to amplify exon-exon junctions and then sequenced the results. Supplemental table 2 shows 3076 validated exon-exon junctions in putative processed transcripts which, in the main body of the paper may be sub-classified as:
...
6
DNA-RNA triplex formation is well-documented. It was originally analysed in simple model polynucleotides where the DNA has a polypurine strand and the RNA has a polypyrimidine, e.g.
rCCCCCC
dGGGGGGGGGGGGGG
dCCCCCCCCCCCCCC
rUUUUUU
dAAAAAAAAAAAAA
dTTTTTTTTTTTTT
but it is now known to occur in more complex sequences. One of the best studied examples is ...
5
This is a question of chemical nomenclature and the principle source for this is the IUPAC (IUBMB in case of biological molecules; but not in this case). You can find all hetero-ring nomenclature references on the IUPAC web site:
http://www.acdlabs.com/iupac/nomenclature/
http://www.acdlabs.com/iupac/nomenclature/79/r79_702.htm
(I'm skipping the actual ...
5
I think the protocols to clean glassware take no chances and just care about RNA degradation rather than targeting one class of enzymes.
EtOH is supposed to denature RNAse and any other proteins on the surface.
Other chemicals such as Diethylpyrocarbonate (DEPC) used to wash glassware kill all biochemical activity by reacting with nucleophilic ...
5
Evolution - Douglas J. Futuyma, Chapter 19, p. 461
Michael Lynch and John Conery (2003) have pointed out that a variety
of genomic features that appear to have little fitness advantage for
organisms-introns, transposable elements, large tracts of noncoding
DNA-may be more prevalent in species with small effective population
sizes. They have ...
5
Thymine has a greater resistance to photochemical mutation, making the genetic message more stable. This offers a rough explanation of why thymine is more protected then uracil.
However, the real question is: Why does thymine replace uracil in DNA? The important thing to notice is that while uracil exists as both uridine (U) and deoxy-uridine (dU), ...
5
DNA is more chemically stable than RNA, which makes it ideal for long-term storage. RNA viruses like HIV have a short lifespan and must replicate to survive, which is why they can get by with a less chemically stable genome.
RNA is a useful format to transcribe since it has multiple forms and functions (e.g. rRNA, mRNA, tRNA, siRNA, snRNA, miRNA, etc.). RNA ...
4
You don't want to only inhibit or temporarily denature RNAses, if you work with RNA you have to permanently inactivate the RNAses. I work with RNA, and I haven't seen anyone use ethanol to remove RNAses, I would not trust it to work reliably. RNAses are really stable enzymes, they even survive autoclaving to some part, so I would not be suprised if they can ...
4
Yes, check out HOTAIR (in human), as well as cyrano and megamind in zebrafish -- they are all spliced.
4
Since the sequence starts with an initiation codon and ends with a stop codon I think it's safe to conclude that this is the coding strand. The coding strand has the same sequence as the transcribed RNA (except T>U). This is because it is the other strand of the DNA that is the template for the synthesis of an RNA. The RNA is indeed made 5'>3', but the ...
4
As far as I can tell from the paper you linked to (Damiana et al) it is possible but inefficient:
Naturally, we tried to translate ssDNA, but as previously described
elsewhere, direct DNA translation was not really efficient in absence
of antibiotics such as neomycin [5] and [6]. It seemed that the
elongation phase was the limiting step in the ...
3
DNA polymerases need a primer oligonucleotide (RNA or DNA) - their substrates are an existing 3'-OH group and a dNTP. The primase however is a typical RNA polymerase, capable of initiating polynucleotide synthesis de novo by positioning a complementary ribonucleoside 5'-triphosphate opposite its complementary DNA base. The primase makes an RNA primer that ...
3
The only paper I found that examined the question is "Structural, Dynamical, and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases". They state
The results confirm that the structural and flexibility properties of
the canonical DNA are globally little affected by the presence of
benzo-fused bases. The most ...
3
It's hard to know what RNaseZap does since the ingredients list is a trade secret. However, I expect it is a lot more than just detergent. RNaseA is extremely hard to destroy; moreover it can easily renature once the denaturant is removed. Therefore, very minute quantities are sufficient to annihilate RNA experiments. The historical method of purification ...
3
Quick answer: we don't really know.
As WYSIWYG said, splice sites do have a sequence signature. The image below (taken from [1]) shows the consensus for human acceptor and donor sites:
In the images above, the size of a nucleotide represents its frequency at that location. As you can see, there is a clear signal around the splice sites and this signal is ...
3
Basically, all 16S genes are highly conserved, i.e., they share much identical bases. This means one can bind the 16S gene piece (after DNA was cut) to a specific other piece of DNA, even if you don't know exactly the 16S gene bases. Everything else is discarded then. Now finally, using PCR the rest is amplified and sequenced. Sequencing 16S only is much ...
2
See papers by D Bianchi for reports of miR levels in blood of pregnant humans, both of maternal and fetal origin.
A review by Steer and Subramanian offers a number of examples pertaining to your question.
Lastly, Vickers, Palmisano, et al. (2011) show that some miRs are present in the HDL-cholesterol particle and that those levels differ between normal and ...
2
If you had a complex life form which used only DNA or RNA, it would have no way to tell transcribed mXNA from genomic gXNA. This would cause problems during cellar replication, as you could also replicate your mXNA along with your gXNA. It would also cause problems repairing breaks in your gXNA, as you would run the risk of including mXNA during the repair ...
2
Prokaryotes can't have introns, because they have transcription coupled to translation. They don't have time/space for that, since intron splicing will stop the coupling. Eukaryotes evolved the nucleus, where splicing can be done. The ancestor of eukaryotes that developed the nucleus could afford more variability (because of introns) than species without it, ...
2
RNAses are enzymes, and there are various ways to inactivate them. Unfortunately, RNAses are rather stable proteins and autoclaving doesn't completely kill their activity. The common methods to inactivate are unspecific methods that will destroy any enzymes, either through covalent modification or degradation.
The most common methods for RNAse inactivation ...
1
Knockdown of lncRNA in mammals is not done via RNAi. Instead, one transfers antisense DNA oligos which bind to the RNA. This triggers the action of the RNase H enzyme, which degrades RNA-DNA duplexes. It degrades the lncRNA.
UPDATE: For reference, I learned about this from a seminar, and it is not very well documented, but after some literature search I ...
1
Nuclear RNAi happens.. check these articles:
http://www.nature.com/nrg/journal/v14/n2/execsumm/nrg3355.html
http://nar.oxfordjournals.org/content/early/2011/11/07/nar.gkr891.full
Also there is some evidence that Ago2 binds to lncRNAs.
However, you can employ other techniques to knock down lncRNAs for e.g. ribozymes.
1
The Ambion's RNAseZAP is not a detergent but contains chemicals that denature RNAse, the step of rinsing with water is necessary in order to clean up the chemicals as well as the denatured proteins left.
It is highly recommended as it completely wipes out the RNAse and the experiment can be run safely. No need to risk time, money and samples.
So, to sum up, ...
1
There are some signature sequence which mark intron-exon boundaries. Usually introns start with a GU and end with an AG. But this feature per-se is not sufficient for splicing; there are other cis-elements such as exon/intron splicing enhancers/silencers [ESE/ESS; ISE/ISS]. Refer this article.
Also, there are protein regulators of splicing such as SR ...
1
The 260/230 ratio gives you idea about the contaminants in your sample. Guanidine isothiocyanate, which is usually used for RNA isolation, absorbs at 230nm, so that might be what you see. But another explanation might be that your sample is very dilute (how much RNA did you get?), so that your A260 is also very low. Then it would be difficult to accurately ...
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