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8

The RNA world hypothesis states that self-replicating RNA (that is, an autocatalytic RNA polymerase) was the first form or precursor of life. So, in that context, your question is basically asking how life originated. The obvious answer is that we don't know (currently anyways), but I'm going to take this opportunity to describe a few really neat experiments ...


7

The helix shape of DNA molecule is a consequence of its secondary structure. This refers to the bases contained in the molecule which pair, thus determining tertiary structure [1]. Basepairing also occurs in RNA, so it can form a double helix. In fact, RNA is composed of short helices packed together [2]. Base pairs maintain DNA's helical structure no ...


7

See this paper. They have studied RBP-protected sites in the entire human transcriptome by RNA-protein crosslinking followed by RNAse digestion and sequencing: PIPseq. Figure 1 of the paper shows distribution of protein protected sites in RNAs. They also correlate it with different regions of mRNA and its expression. They show number of protein protected ...


6

The question is a bit vague in some important parts, so I'll have to make a few assumptions about what the authors likely meant. RNAses are enzymes that degrade RNA. There are a few different ones that lead to different kinds of degradation. The type that you would use in an experiment like this is an RNAse that completely degrades RNA. The purpose of this ...


6

RNA (single or double stranded) actually can and does form a helix in the absence of certain complex 3D structures. The RNA helix is typically A-form, as opposed to B-form for typical DNA. The A-form helix is right-handed like the B-form but is more compact (2.6 Å rise versus 3.4 Å) and wider (26 Å diameter vs 20 Å). The differing helices arise from the ...


6

It's one for every phosphodiester bond formed. 11 nucleotides, but only 10 bonds needed to join them into an oligonucleotide: 1 2 3 4 5 6 7 8 9 10 11 N--N--N--N--N--N--N--N--N--N--N 1 2 3 4 5 6 7 8 9 10


6

Top 10 long processed transcripts in humans (with multiple isoforms), from gencode 19 annotations: Transcript Length(bases) ------------------------ TTN-018 108861 <-- Titin TTN-019 103988 TTN-002 101206 KCNQ1OT1-001 91666 TTN-201 82413 TTN-202 82212 TTN-003 81838 MUC16-001 43732 ...


6

You have two possibilities: When you only need a quick check if your RNA is ok and you indeed only get one band, you can try a "quick and dirty" method. Heat the sample for 5 minutes at 65°C and then immediately cool it down in an icebath and keep it there until loading. By doing so, you melt up the secondary structure of the RNA and keep it in this state. ...


5

Yes, you can find mutations in the genomic DNA which affect splice acceptor sites. Wikipedia lists the following outcome: Mutation of a splice site resulting in loss of function of that site. Results in exposure of a premature stop codon, loss of an exon, or inclusion of an intron. Mutation of a splice site reducing specificity. May result in variation in ...


5

I think a good candidate is the human titin gene. The gene itself has 363 exons, depending on the isoform it has between 27.000 and 34.000 residues. This makes up a processed mRNA length of up to 100kb for the full length isoform. See either the Wikipedia article or the one linked below for more details: The complete gene sequence of titin, expression of ...


4

The biotin-streptavidin interaction is extremely strong, one of the strongest (if not the strongest) non-covalent interaction between biomolecules. So you'll need pretty harsh conditions in any case. Extreme pH values are generally a very bad idea for RNA. I'm pretty sure that the conditions you mentioned are not meant for elution of nucleic acids. Such low ...


4

The tRNA is not acting alone, it has the help of the Ribosome. The Ribosome assembles at the beginning of the transcript and starts the translation at the first AUG codon. It then binds the first tRNA which fits to the mRNA. The tRNA is then moved from the A-position to the P-position and the next tRNA is binding (the move around and bind by chance. A ...


4

The difference between RNA and DNA is rather small, and both can form a double-helix structure. So if you had two sequences of RNA complementary to each other they would basepair and form a helix. There were also some ideas to use this for therapeutic purposes, antisense RNA, an RNA oligo complementary to a messenger RNA, can theoretically be used to ...


4

Antisense simply means that a sequence is the complement of another. miRNAs are naturally occurring antisense RNAs yes. The "difference" is that antisense RNA is often used for sequences developed in the lab and used for processes such as RNAi. miRNAs, on the other hand, are encoded by the genome and are used by the cell for regulating gene expression. They ...


4

OK, let us start from the beginning. We know what makes one cell type different from another cell type is its expression - i.e. what genes are actually being transcribed into RNA. Therefore, there should be certain RNA in one cell type that should not exit in another cell type. If you isolate RNA from a certain cell type, say a neuron and you want to show ...


4

Trimming = removing RNA sequences from one end. Splicing = removing introns and joining exons back together.


4

There are some tools for predicting the binding: TargetScan (based on seed match [primary], extra pairing, sequence context 1 — nucleotide composition around the site etc [secondary]) miRanda (based on hybridization stability and seed match[primary] and sequence context [secondary]) PicTar (adds a layer of evolutionary conservation criteria) 1 Context ...


3

Transcription always proceeds in the direction 5' (5-prime) to 3' (3-prime) on the coding strand of DNA. Binding of both transcription factors and RNA polymerase to DNA depends on sequence motifs in the DNA. Transcription always happens in the same direction with respect to the chemical structure of the coding DNA strand, while the transcription direction ...


3

The protocol you are using will not only leave the sample with rRNA but also non coding RNA. Many RNA protocols will separate mRNA by affinity of a carrier to the polyA tail. This protocol references an older paper that estimates that only 5% of RNA is mRNA. I'd be surprised if this ratio changed by more than 2-3 fold in drosophila. I assume that %age ...


3

I think that there is no reason in principle why early evolution couldn't have landed on a translation mechanism going 3'>5'. There are, however, clear biochemical reasons why the transcript itself has to be made in a 5'>3' direction. So in this alternative world where the initiation signals would have been at the 3' end of the mRNA, the message would have ...


3

You can use R-coffee of the T-coffee suite of tools. In general, the *coffee tools are excellent and work very well if you can get over their author's self obsession1. R-coffee can align RNA sequences taking into account structural information: 1 The guy actually adds his name to the output of all his programs! Seriously, he does. Apart from being ...


3

If I understand correctly what you mean by "I would like to dilute my RNA to 100 ug": Your RNA preparation is at 3.3 μg μl-1. To add 100 μg to a reaction you need to add 100/3.3 = 30 μl Then make the total volume up to 1000 μl with enzyme and buffer as appropriate.


3

You could have asked a similar question about splicing. The function of RNA editing seems to be similar: it's one of the ways to trigger production of alternative transcripts and proteins given the same DNA sequence. The question is discussed, for example, in this review. The authors describe different known effects of alternative RNA editing: Amino-acid ...


3

The RNA expression level is an estimate of the amount or proportion a given gene's RNA found in a sample of cells (such as a tissue sample) or even a single cell. Expression is used because the RNA sequence is translated from DNA to RNA according to the signals within the cells. There are various means of estimating this. They often involve a sequence ...


3

By far the most common type of base pair is the Watson-Crick base pair in an RNA helix. Those are comparably easy to predict, e.g. Mfold and the Vienna RNA package can do this. Base triples, three nucleobases that form hydrogen bonds to each other are not uncommon in RNAs with a complex tertiary structure. There is even a database of RNA triples, though ...


3

@MadScientist answer is very good. I just want to add a detail that could not fit in a comment. Double stranded RNA is nothing exceptional. You can see an RNA strand that binds to its antisense in tRNA and in RNAi for example. tRNA RNAi


3

You are almost right. I modified you picture a little bit to answer it: Structure I is indeed DNA, structure II is processed RNA. This is because in I you see loop structures which have no complementary part in the RNA anymore, these are introns (structure Q and the flanking loop regions to P). P is an exon flanked by two introns. The end of the RNA is ...


3

Yes, that should be possible. And it is one of the ways antibodies work. It is already used as a treatment against rabies. There you get a dose of immunoglobulins directed against the rabies virus together with the vaccine. The immunoglobulins neutralize the virus. The same is possible when you vaccinate against the surface proteins which a virus uses to ...


3

Imagine you want to produce a widget. You have thousands of worker, but only one blueprint. Each worker needs the blueprint to build a widget (they're really forgetful and can't build from memory). So only one worker at a time can build your widgets. What you would do is to create copies of your blueprint and distribute them to your workers. That way ...


2

Gergana is right about the effects of the Guanidine isothiocyanate, but not the details there of. Guanidine isothiocyanate absorbs strongly at 260 and NOT 230 (guanidine hcl is the one that absorbs strongly at 230). As such if your RNA is highly contaminated with guanidine isothiocyanate, which is used in at least one buffer in just about every RNA prep ...



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