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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)

#61

Post by tomohelix »

eyelidlessness wrote: post #53
lsternlicht wrote: post #52

Earlier quoted context omitted.

No

Is it that simple? From a lay perspective (and granted I’m a little foggy because I actually have covid right now), I’d expect the answer is yes but with huge unintended consequences.

Ok yes, theoretically you can make something targeting the polyA tail. But everything else you body make will also get targeted because this is basically a marker of all RNA for translation.

Now making a drug that targets only viruses and not your body RNA? Possible but it is so hard not much progress has been made.

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

#62

Post by TEP_Kim_Il_Sung »

amelius wrote: post #51
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…

Can a drug target that sequence specifically?

IIRC Adenin binds to Thymin, and there are some viruses and bacteria that have alternative bases, and scientusts have discovered 82 other possible ones.

If the virus could be bound with an artificial RNA strand that had a stronger bond than natural RNA, it could be denatured, and pooped out.

https://devries.chem.ucsb.edu/research/past/base-pairing

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

#64

Post by userbinator »

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…

attachment to the ribosome during translation

There's been a lot of analogies with NOP slides in the comments here and there, but if you look at how the process of reading the genome works, this section is more like the leader/trailer on a tape:

https://en.wiktionary.org/wiki/leader#Noun "A piece of material at the beginning or end of a reel or roll to allow the material to be threaded or fed onto something, as a reel of film onto a projector or a roll of paper onto a rotary printing press."

https://en.wiktionary.org/wiki/trailer#Noun "A short blank segment of film at the end of a reel, for convenient insertion of the film in a projector."

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

#65

Post by moralestapia »

amelius wrote: post #51
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…

Can a drug target that sequence specifically?

That sequence is present everywhere in your body and living beings, so no.

https://en.wikipedia.org/wiki/Polyadenylation

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

#66

Post by worewood »

userbinator wrote: post #64
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…

attachment to the ribosome during translation There's been a lot of analogies with NOP slides in the comments here and there, but if you look at how the process of reading the genome works, this section is more like the leader/trailer on a tape: https://en.wiktionary.org/wiki/leader#Noun "A piece of material at the beginning or end of a reel or roll to allow the material to be threaded or fed onto something, as a ree…

And this fits nicely because the genome replication really looks like a roll of film being played

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

#67

Post by x-shadowban »

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…

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

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

#68

Post by koeng »

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…

ApE is one of those tools that is so old-school but just works. I used to hate using it but it's really grown on me - Snapgene is just too darn expensive and benchling isn't very power user friendly

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

#70

Post by subroutine »

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?

The number of adenine repeats that confer functional properties is quite variable but it definitely needs to be more than "just 1". I've seen anywhere from 25-250 used in designed plasmids. The exact number people use in their engineered sequence is based on a number of factors, not all of them scientific in nature (e.g. companies charge per basepair synthesize a bespoke polypeptide; e.g. you copied the sequence from a previous clone into ApE and that sequence used 30 repeats and worked fine).
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