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Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

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Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#91

Post by userbinator »

subroutine wrote: post #24
FormerBandmate wrote: post #15

The top answer at the link explains it best: Good observation! The 3' poly(A) tail is actually a very common feature of positive-strand RNA viruses, including coronaviruses and picornaviruses. For coronaviruses in particular, we know that the poly(A) tail is required for replication, functioning in conjunction with the 3' untranslated region (UTR) as a cis-acting signal for negative strand synthesis and attachment to…

Adding a poly(A) tail when engineering rna plasmids is so common that it's part of the standard feature library of most plasmid editors. Here I have a screenshot of the ApE editor displaying one plasmid I made for a neurobio experiment involving the overexpression of two chimeric proteins (actin and profilin, respectively linked to green and red fluorophores; note the editor has autotagged the polyA tail feature): ht…

Looks almost like a hex editor.

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#92

Post by akira2501 »

uxp100 wrote: post #50
jtchang wrote: post #10

It's like a NOP slide for viruses: https://en.wikipedia.org/wiki/NOP_slide Just kidding...sort of!

User Zoe Sparks on that page covers why they don’t really feel it’s like a nop slide. I think that answer is a good supplement to the accepted one.

I think they miss the point entirely. The environment in the cell is mostly mechanical, but it's also dominated by random forces. If you are unable to guarantee where you are going to "enter the sled" or when the "tail hits the ribozyme" then the nop sled seems to be an equivalent feature.

So.. to me, it's odd they invoke "legitimate code." The comparison I'd consider would be "combative code." For example, the old game "core wars." Thinking in that mindset, I can see several uses for a "nop sled" in "legitimate code."

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#93

Post by sirsinsalot »

jkingsman wrote: post #48

If this sort of question fascinates you, you might like "Reverse Engineering the source code of the BioNTech/Pfizer SARS-CoV-2 Vaccine"[0], an article written with a tone that I've found to resonate with engineers and like-minded folk. [0] https://berthub.eu/articles/posts/reverse-engineering-source...

That was exceptionally informative and accessible. Thank you

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#94

Post by sirsinsalot »

inDigiNeous wrote: post #90

[flagged]

"Maybe" isn't a good replacement for "I don't know".

Other people do know and you can find this information out.

The body uses it in RNA for denoting the life cycle of reuse to avoid degradation.

The linked article tells you

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#96

Post by kolinko »

x-shadowban wrote: post #67
subroutine wrote: post #24

Earlier quoted context omitted.

Adding a poly(A) tail when engineering rna plasmids is so common that it's part of the standard feature library of most plasmid editors. Here I have a screenshot of the ApE editor displaying one plasmid I made for a neurobio experiment involving the overexpression of two chimeric proteins (actin and profilin, respectively linked to green and red fluorophores; note the editor has autotagged the polyA tail feature): ht…

Can you add any number of A's, or just 1, or shorten it by 1, and it still is functional?

In this case it probably works most reliably with around this number of As, and less/more would decrease reliability, butnitmwould still be functional.

Most of genetics is like that.

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#97

Post by nomercy400 »

qclibre22 wrote: post #34
ramesh31 wrote: post #28

Earlier quoted context omitted.

The biological equivalent of an endline

The stop codon is more like the '\n' or '\0' in computing. Polya tails protect against degradation and is used for nuclear export of RNA.

So it is more like a protective casing? Or like a car bumper, to protect what's inside?

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#99

Post by xg15 »

FormerBandmate wrote: post #15

The top answer at the link explains it best: Good observation! The 3' poly(A) tail is actually a very common feature of positive-strand RNA viruses, including coronaviruses and picornaviruses. For coronaviruses in particular, we know that the poly(A) tail is required for replication, functioning in conjunction with the 3' untranslated region (UTR) as a cis-acting signal for negative strand synthesis and attachment to…

As a coder, I find it a bit frustrating how often explanations in biology contain fuzzy phrases like "plays a role in" or "is required for" or "works together with" or "modulates the activity of" - without ever expected what role it plays, why it is required or how it works together.

So props to them for going a bit more into detail here - and also highlighting that the reason for the fuzzy phrases can often be that we literally don't know the details: The empirical basis may be "if this thing is removed then this other thing won't work", without us necessarily knowing why this is the case.

Re: Why does the SARS-Cov2 genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa? (2020)

#100

Post by kevviiinn »

xg15 wrote: post #99
FormerBandmate wrote: post #15

The top answer at the link explains it best: Good observation! The 3' poly(A) tail is actually a very common feature of positive-strand RNA viruses, including coronaviruses and picornaviruses. For coronaviruses in particular, we know that the poly(A) tail is required for replication, functioning in conjunction with the 3' untranslated region (UTR) as a cis-acting signal for negative strand synthesis and attachment to…

As a coder, I find it a bit frustrating how often explanations in biology contain fuzzy phrases like "plays a role in" or "is required for" or "works together with" or "modulates the activity of" - without ever expected what role it plays, why it is required or how it works together. So props to them for going a bit more into detail here - and also highlighting that the reason for the fuzzy phrases can often be that…

It isn't unknown its just complicated. There are numerous proteins involved, such as a protein that detects the poly A tail and if not present will degrade the RNA by cleavage.
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