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10

I think given that you're just getting started with genetics, you can say that the codons are interchangeable. This is generally true, though not technically correct. Here are a few reasons for why this is the case, though there's probably more: Specific organisms use specific codons with different frequencies. This is usually related to the tRNA abundance ...


9

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 ...


8

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

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. ...


6

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 ...


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 ...


5

Short answer I can think of at least a dozen applications for which it would be useful to know the secondary structure of a given sequence of RNA off of the top of my head. In no particular order: Simulation/visualization of RNA Riboswitches MicroRNA RNA interference (RNAi) RNA-RNA interactions RNA-DNA interactions RNA-protein interactions Ribosomal ...


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

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


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

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

Start and stop codons are instructions for the ribosome to start and stop protein synthesis, respectively. The region between the start and stop codon (inclusive of them) is called ORF (open reading frame) or sometimes CDS (Coding sequence). Why does ribosome need explicit instructions for start and stop? Ribosome recognizes an RNA as a mRNA if it has ...


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

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 ...


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

@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

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

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

Nice question which leads to the fundamentals of DNA and RNA. DNA (Deoxyribonucleic acid) is the core of life in Earth, every known living organism is using DNA as their genetic backbone. DNA is so precious and vital to eukaryotes that its kept packaged in cell nucleus, its being copied but never removed because it never leaves the safety of nucleus. DNA ...


3

A good answer is already provided by @canadianer, but as with many things in biology it is important to keep in mind what organism and/or cell type we are talking about. Because the nuances of the answer to a question about a seemingly universal process sometimes actually depend on whether we want to know about bacteria, or fungi, or mammalian stem cells, ...


2

You've already mentioned rRNA. An interesting review (Tanner, 2006), outlines some more: Group I Introns - self-splicing; "They are abundant in fungal and plant mitochondria..." Group II Introns - some have been shown to self-splice; "...they are found in fungal and plant mitochondria, in chloroplasts of plants ... and especially in the chloroplasts of the ...


2

Removal of 5' cap is essential for degradation by 5'→3' exonucleases such as Xrn1/2. Xrn1/2 is constitutive and degradation of uncapped RNAs would be quite fast (don't have a reference for the exact lifetime). Deadenylation generally precedes 3'→5' degradation by exosome but I am not sure if that is a prerequisite. However tailless mRNAs can be stabilized by ...


2

A second telomerase is not necessary, as the lagging strand is filled in by the DNA-Polymerase, see this figure:


2

It doesn't seem like a homogenization problem. Nonetheless you can try this: Suspend the heads in trizol Homogenize by passing through 30/31G needles (insulin syringe) up to 10-15 times. Heating a little might help but I think it is unnecessary for these tissues. Insulin syringe is much better than the hand held homogenizer. Freeze-thaw 1-2 times if you ...


2

According to the Gilson Pipettman User Guide you can autoclave the following parts: Tip ejector, Tip holder and the connecting nut (have a look into the PDF linked above if you are not sure about the parts). All other parts can not be autoclaved. Gilson says the following conditions can be used (page 17 in the user guide): Autoclave for 20 minutes at 121°C, ...


2

I don't know if this is helpful in the context of moving from RNA to DNA world, but I do know that certain mutations to T7 RNA polymerase will allow that enzyme to use 2' deoxy nucleotides in addition to the normal ribonucleotides. These mutations were discovered by humans engineering the enzyme, but it's feasible that some transitional enzyme could have ...



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