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Answering my own question after reading the 2018 Nature review article “mRNA vaccines — a new era in vaccinology” The resources and motivation engendered by the COVID-19 pandemic are a major factor in the development of the first mRNA vaccines approved by national governments. However, before the COVID-19 pandemic, there were recent advances in mRNA vaccine ...


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Well, we can work this out empirically. We know that the average molecular mass of a base of a RNA is 339.5 g/mol. However to calculate the approximate molecular mass of a single-stranded RNA molecule, you multiply the number of bases by 320.5 and add 159 (same source). This means for a single-stranded molecule of 1000 bases, it will have a molecular mass of ...


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I would strongly recommend looking in more detail into available resources for SD and Kozak sequences, wikipedia basically answers these questions and has plenty of further reading if you desire to explore these questions. At the same time, remember that these are statistical processes involving thousands of molecules, rather than deterministic processes ...


6

I am asking this question to understand whether the cells which are used to create spike proteins are attacked by the immune system. Yes, that is the aim of RNA vaccinations! But don't worry, that's a good thing, as can be concluded from this review-paper, that emphasizes the advantage of RNA vaccinations to invoke cellular immune response: Although ...


6

The two stop codons are obviously to prevent read-through of the termination codon. Why this should be necessary is not clear to me, but the following may be relevant: The synthetic mRNA differs from the natural mRNA in a particular respect that is easier to explain with reference to the transcript map of the virus, below. The two ORFs 1a and 1b are ...


5

What you describe, creating the spike protein independently and delivering it, is exactly what is done by subunit vaccines, such as the COVID-19 vaccine developed by Novavax. As already noted in @Amanda's answer, mRNA is great at amplifying a delivery, so you need a lot less to be delivered. The manufacturing process for the vaccine itself is a lot more ...


5

The mRNA won't be entirely perfect, but the imperfections will not matter. The spike protein is big, encoded by thousands of base pairs in the virus. In the virus itself, it's not entirely homogeneous: there are always going to be small mutations that cause different variants to be produced, but nearly all of those are nearly identical. The mRNA in a vaccine ...


4

This is the temperature at which RNA is stored for long term storage without the occurance of degradation. It is also standard lab routine to store RNA at this temperature. Conviniently, this temperature can be reached by dry ice (-78°C), which makes shipping a lot easier. However, there are indications by Biontech themselves that the vaccine will be stable ...


4

What is Protein Expression Level? This was the original title of the post, which I edited myself because I regard the answer as trivial, but the question as more substantial. To deal with the trivial first: ‘Level’ is not a scientific unit, and can only be used unambiguously as a scientific term in its English sense in relation to liquids, e.g. “The level ...


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Note - This answer only covers the comparison of rA-dT (RNA:DNA) and rA-rU (RNA:RNA) duplexes, and not more exotic options involving deoxyuridine (dU) and ribothymidine (m5U). I can think of three possible reasons why oligo-dT may be preferred over oligo-rU for poly(A) hybridization and mRNA capture: The rA-dT duplex is more stable than the rA-rU duplex, ...


4

You have it wrong. Coronaviruses are part of a family of viruses that are called "enveloped viruses". These all have an "envelope" comprised of a lipid layer derived from the host cell as the virion exits. The envelope is distinct from the spike. The spike protein is produced by the virus during replication and is not found naturally in a ...


4

If I understand your question and graph correctly, your Y-axis is log(x/REF), where REF is some external standard. Your "Ref" on the x-axis you expect to be the same as REF, so that log(Ref/REF) "should be" zero, but you find it is not. However, it looks like the mean(log(Ref/REF)) is still approximately zero. This is what I would expect: ...


3

Does the mRNA of the covid19 spike protein contain any nuclear localization signals? I take it you are talking about the coronavirus SARS-CoV-2, and asking whether its RNA genome contains any nuclear localization signals that act post-translationally as signals to specifically import the spike proteins into the nucleus. I cannot find any reports where any ...


3

Nuclear pores control what gets in and out of the nucleus. In general, mRNAs are only allowed out, they don't go back in. Reverse transcriptases, of course, will put mRNA back into DNA, but only some viruses, like HIV, have those enzymes. https://portlandpress.com/biochemj/article-abstract/477/1/23/221793/Into-the-basket-and-beyond-the-journey-of-mRNA?...


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As was observed (by others) under related q's here on material from that site, it seems Pfzier/BioNTech has done a global optimization to increase CG contents in the sequence, generally thought to be beneficial to mRNA expression (in addition to all the other things they've done, like U -> m1Ψ global substitution, specific to mRNA therapeutics). That (...


3

The mRNA vaccines encode a mutant version of the spike protein in which the structural transition needed to to fuse membranes is blocked. This was done to make the immune response focus on the pre-fusion state, which is much better for neutralizing the virus. From https://cen.acs.org/pharmaceuticals/vaccines/tiny-tweak-behind-COVID-19/98/i38: Fortuitously, ...


3

There is a question on stackexchange that is not only related Why cytotoxic T cells don't kill dendritic cells when they present antigen? Your question refers to "some cells" (explanatory text) and "transfected cells". Thus, any cell that takes up the m-RNA-vaccine is referred to. However, any answer must be based on the different ...


2

"On MHC II, do cells present only antigen they have receptors for?" Thank you for boiling your question down to its essence. The answer is no. Professional antigen-presenting cells (APCs) such as macrophages, dendritic cells, B cells, etc., which present peptides in the context of the major histocompatibility complex (MHC) Class II to CD4+ Thelper ...


2

“Is this not toxic for the body since it is killing your own cells? ” Yes, cytotoxic T cells do kill mRNA vaccine-transfected cells, but not to the extent of harming your body. This is because the mRNA vaccine cannot be not integrated into the host genome, mRNA then will be degraded after translation within hours, preventing spike proteins variants to be ...


2

It is entirely possible that different cell-lines express the same genes at drastically different levels. The proteinatlas provides data and analyses on differences between certain tissues or cell types / cell-lines. If your cells are of the same line/tissue, then they might still differ dependent on the cell-cycle, age and external factors. There are ...


2

I believe the news report you cited is not accurate in its reporting. Of course, it's not actual science, and we will wait for the release of the actual science, but here's my understanding (which may end up being wrong): if vaccinated people get infected anyway, they have as much virus in their bodies as unvaccinated people. This seems to be incorrect. ...


2

Although specific time is not yet clear, the coronavirus mRNA vaccine is expected to be degraded within hours after translation, according to Rebecca Dutch, Ph.D., a virologist at the University of Kentucky. "It’s unclear how long this degradation takes. With regular mRNA, it’s within hours. The special coating involved with mRNA coronavirus vaccines ...


2

The short answer to how vaccines are spread around the body is, quickly. What is the process in which they spread from there to the rest of the body? The reason vaccines are often delivered into muscle tissue is because muscle tissue is highly vascularized with both blood and lymphatic vessels. Immediately after a vaccine injection, the delivery vehicle (...


1

Your question is a good one, and has given rise to decades of intensive research, which continues today. The short answer is that many factors are involved, ranging from sequences within the gene up to chromatin-level changes. De Conti et al. in their review "Exon and intron definition in pre-mRNA splicing" (2012 DOI: 10.1002/wrna.1140) note: Most ...


1

I'm answering my own question for the benefit of anyone else who might be wondering about this. (Please note that I'm just a programmer, not a biologist, but thanks to David's comment, I was able to come to what I think are some correct conclusions.) A single mRNA strand can be translated more than once, even more than once at the same time. The polysome ...


1

Why is the mRNA not damaged at -70 C temperature Corona vaccine? Actually they use Sucrose as cryoprotectant. https://medicalsciences.stackexchange.com/questions/25289/why-use-sucrose-rather-than-glucose-in-an-injectable-vaccine/25290


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According to the person who made this video's response to my comment asking this question, the transfected cells are killed by cytotoxic T cells, but the amount of transfected cells dying is not enough to cause irreparable harm since the cells regenerate themselves fairly quickly through division. Plus, the acquired cell-mediated in addition to humoral ...


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