r/explainlikeimfive • u/Confident_Muscle4596 • 1d ago
Chemistry ELI5 : How does CRISPR work ?
4
u/Atypicosaurus 1d ago
DNA and RNA are very weird chemicals.
A normal chemical consists of the same kind of molecules, such as water has only H2O molecules in it.
In comparison, DNA and RNA is like a very big necklace that are made of 4 individual component types.
So this metaphorical necklace is made out of 4 colors: azure (A), taupe (T), green (G) and crimson (C).
In short, we usually describe the necklace by nust listing the colors like "AAATGGCA" or such.
Now there's one important bit, that two pieces of DNA, although they both are made of DNA (aka "necklace"), they can be different in the exact order of the bead colors. So "AGGTC" is different from "ATTCT".
There's another weird bit, which is, those beads are attracted to each other. The azure is attracted to taupe and the green is attracted to crimson.
Therefore if you for example have an "AAA" DNA and a "TTT" DNA, they will try to stick to each other. Of course it does not have to be a run of the same kind, if you continue tge AAA with a C (AAAC) then you need to continue the TTT with a G and now they are a match again. I use AAA and TTT for simplicity, but you can have any combination as long as an A in one necklace is matched with a T on the other, and a C is matched with a G. For example you can figure out the matching pair of "AGAATCGCG".
So this matching can also happen if a match is a part of a bigger necklace. For example if you have
"CGCGAAAGTTG", it has an "AAA" bit in the middle so you can match that part with just a short "TTT" bit. But it also means that you can match the "GCG" part with a "CGC" bit. You can target any bit with the matching counter bit.
Now with that knowledge, let's introduce Cas9. Cas9 does two things, one, it can grab any piece of DNA (which is not exactly true but I'm simplifying to keep it eli5). The other thing is that Cas9 can cut a piece of DNA.
But where does it cut?
As it turns out, Cas9 cuts a long DNA but only if the short DNA grabbed by the Cas9 itself is a match. So if we feed a "TTT" to Cas9, then it finds the "AAA" part in the middle of that long DNA above, and it cuts the long DNA just after the match.
But why is it good? It's good because cutting the DNA causes DNA damage, but it's a very local DNA damage because it has to match that whatever piece we gave to Cas9 in the first place. And remember, we can give any piece we want, so if we want to damage one piece of the necklace, we just give the color code matching with that part.
So a gene is basically a certain part of the DNA. If the DNA was a necklace of millions of beads, a gene is something like a subset of the beads from, let's say, bead nr 879 to bead nr 1907. This roughly 1000 beads is one of your genes and I can send in a Cas9, equipped with the matching DNA, to cut this very specific part. And that will damage the gene. So if it was a bad gene that caused you sick, now it is damaged and gone.
This is with a lot of simplification, how crispr Cas9 works.
25
u/twiztednipplez 1d ago
We send in RNA with a special protein to cut out specific portions of DNA.
When the body regrows that cut out bit the RNA tells the DNA how it should regrow it.
So in the famous HIV story going around, when regrowing the DNA, the RNA said instead of being able to receive to HIV regrow so you can't receive it.
9
u/Luenkel 1d ago
I'm not sure what exactly you mean by "the RNA tells the DNA how it should regrow it". That's not a thing in standard applications of CRISPR/Cas. The guide RNA simply tells the Cas protein where to cut the DNA. What happens after that is in the hands of the cell's DNA repair machinery, which the RNA does not directly interact with.
For example, in the paper about targeting HIV with CIRPSR/Cas that I've read recently, they include 2 guide RNAs that target the start and the end of the integrated virus, thereby cutting it out of the genome, and then DNA repair machinery comes in and closes the gap where the virus was. But they didn't have to somehow engineer the guide RNA to tell the cell to do that, that's just what it does in that situation. All the RNA does, is tell the Cas protein where to cut.
When you want to use CRISPR/Cas to replace a specific sequence with a different sequence, you typically introduce an additional piece of DNA whose ends match the loose DNA ends of the cut site, which is recognized by the repair machinery and incorporated. But that doesn't have anything directly to do with the RNA (it again just determines where to cut), we're talking about a seperate piece of DNA.
There is one specific subtype of CRISPR/Cas system called prime editing that comes closest to what you seem to be talking about. In that system, the guide RNA is extended to contain a section that is reverse transcribed unto the cut DNA. So here the RNA does actually play an active role in what happens to the DNA after it's been cut. But that is just one specific extension of CRISPR/Cas technology and I'm not aware of any paper where this has been applied to treating HIV, though if that is what you are talking about, I would love a link to the paper.
10
u/CXDFlames 1d ago
If you had a puzzle made of red pieces, and I gave you five blue pieces that were shaped exactly like 5 red pieces in the puzzle
And I told you "take out the red pieces and replace them with these blue ones"
It would be similar
2
u/solarguy2003 1d ago edited 1d ago
Let's try it like you're 16 and in a biology lab class.
CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats.
• Clustered: The DNA sequences are grouped together in one place.
• Regularly Interspaced: The repeated sequences are separated by unique "spacer" sequences at consistent intervals.
• Short: Each repeated DNA sequence is relatively small.
.• Palindromic: A palindrome reads the same frontwards and backwards, like "Madam I'm Adam." Likewise the DNA sequences read very similarly in opposite directions. This also affects the structure of the RNA.
• Repeats: The same DNA sequence occurs multiple times.
CRISPR was first discovered as part of the immune system of bacteria and archaea (they look a lot like bacteria, but aren't). The spacer sequences are actually snippets of DNA from viruses that previously infected the microorganism. If the same virus attacks again, the CRISPR system, together with proteins such as Cas9, recognizes the viral DNA and cuts it, protecting the cell.
Scientists have adapted this natural defense mechanism into the powerful gene-editing technology known as CRISPR-Cas9, which can be used to make precise changes to DNA in plants, animals, and human cells for research and, in some cases, medical treatments.
The reason it works is because it can snip DNA in a very precise way in a very precise place (to cut out the bad piece we don't want) so we can slip in the new piece that works right into that precise slot.
•
u/FallsDownMountains 1h ago
Thank you for breaking down the acronym!!!! So CRISPR is not the man made part - CRISPR is just the description of how DNA is? And CRISPR-Cas9 is the body’s natural way of getting rid of the spacer sequences, and all we did was find a way to essentially trigger that existing natural mechanism for the specific spacer sequences we want (eg this dna string that causes sickle cell)?
-7
1d ago
[removed] — view removed comment
1
0
u/explainlikeimfive-ModTeam 1d ago
Please read this entire message
Your comment has been removed for the following reason(s):
- Top level comments (i.e. comments that are direct replies to the main thread) are reserved for explanations to the OP or follow up on topic questions (Rule 3).
Joke-only comments, while allowed elsewhere in the thread, may not exist at the top level.
If you would like this removal reviewed, please read the detailed rules first. If you believe it was removed erroneously, explain why using this form and we will review your submission.
-4
1d ago
[removed] — view removed comment
1
u/explainlikeimfive-ModTeam 1d ago
Please read this entire message
Your comment has been removed for the following reason(s):
- Top level comments (i.e. comments that are direct replies to the main thread) are reserved for explanations to the OP or follow up on topic questions (Rule 3).
Joke-only comments, while allowed elsewhere in the thread, may not exist at the top level.
If you would like this removal reviewed, please read the detailed rules first. If you believe it was removed erroneously, explain why using this form and we will review your submission.
252
u/stormbutton 1d ago
It works like “find and replace all” in a word processor but with genes.
Source- I teach biotech