2020 · Chemistry

Genetic scissors: cutting DNA at one chosen address

Q: What does the guide RNA in CRISPR-Cas9 actually do?

It tells Cas9 which DNA sequence to find. The guide RNA is the address, not the scissors. Its sequence base-pairs with a matching stretch of DNA, steering Cas9 to the target. The cutting is done by Cas9's protein domains, and the repair is done by the cell.

Q: Why must Cas9 find a PAM sequence before it cuts?

The PAM is a required signal next to the target that also stops the bacterium cutting its own DNA. No PAM, no cut. Cas9 only acts next to a short PAM such as NGG. The bacterium's own CRISPR store lacks a PAM beside its stored sequences, so it is spared, and the requirement makes targeting predictable for researchers.

Q: After Cas9 makes a double-strand cut, what most directly decides whether a gene is knocked out or precisely rewritten?

Which repair pathway the cell uses. Repair decides the outcome. Non-homologous end joining often deletes or inserts a few letters and disables the gene, while homology-directed repair copies a supplied template to write a precise sequence. Cas9 just makes the break.

Awarded to Emmanuelle Charpentier and Jennifer A. Doudna “for the development of a method for genome editing”.

What was the 2020 Nobel Prize in Chemistry awarded for?

The 2020 Chemistry prize honours CRISPR-Cas9, a tool that lets researchers cut DNA at almost any chosen spot. A short guide RNA is programmed to match a target sequence, and the Cas9 protein then snips both strands there, so a gene can be switched off or rewritten.

Predict first

A bacterium needs to chop up invading virus DNA, but it must never cut its own matching CRISPR memory of that virus. How can the same protein tell friend from foe?

It checks for a short PAM signal next to the target. The virus DNA carries a PAM, a few letters such as NGG, right beside the matching sequence, so Cas9 cuts it. The bacterium's own stored copy has no PAM in that spot, so Cas9 leaves it alone. That single safety check is also what makes Cas9 predictable once researchers reprogram it.

Predict first

CRISPR-Cas9 only makes a clean cut in the DNA. It does not actually write the new genetic text. So how does an edit get made?

The cell's own repair machinery writes it. A broken chromosome is dangerous, so the cell rushes to mend the cut. Left to itself it often drops or adds a few letters and switches the gene off. If researchers also hand the cell a matching template, it can copy that in and make a precise change. Cas9 chooses the place; repair makes the edit.

Cas9 first checks for the PAM signal, then the guide RNA confirms the match, and only then are both DNA strands cut.

Imagine your DNA is a very long instruction book written in tiny letters. Sometimes a single misspelled word causes a problem, and for a long time there was no neat way to find that exact word and fix it.

CRISPR-Cas9 works like a find-and-replace tool for that book. Scientists write a short tag, called a guide, that spells out the exact line they want. The guide leads a protein called Cas9 to that line, and Cas9 acts like a tiny pair of scissors and cuts the DNA right there.

The big idea in one line

A programmable pair of scissors

Change the guide and you change where the scissors cut. The same tool can be aimed at almost any spot in the DNA of a plant, an animal, or a person, which is why it changed biology so quickly.

Once the cut is made, the cell tries to repair it. Researchers can let that repair switch a gene off, or hand the cell a new piece of text to paste in. Bacteria invented this trick to fight viruses; two scientists turned it into a tool we can program.

CRISPR-Cas9 began as a bacterial immune system. Bacteria such as Streptococcus pyogenes keep short snippets of DNA from viruses they have met before, stored in regions called CRISPR arrays. When a virus returns, the bacterium makes RNA copies of these snippets and uses them, together with a cutting protein called Cas9, to recognise and destroy the matching viral DNA.

Emmanuelle Charpentier found a missing piece of this system. In 2011 she described a small molecule called tracrRNA that is needed to prepare the snippet RNA for action. Working with Jennifer Doudna, a specialist in RNA biochemistry, she showed that two RNA pieces could be fused into a single molecule the researchers named a guide RNA.

The 2012 experiment

Aiming the scissors on purpose

Charpentier and Doudna reprogrammed the guide RNA to match a DNA sequence of their own choosing, then showed Cas9 cut the DNA at exactly that spot. By rewriting the guide, they could aim the same protein at any target. That was the step from a natural defence system to a general editing tool.

Two details make the aiming reliable. First, Cas9 only cuts next to a short signal in the DNA called the PAM, a few letters such as NGG, which stops the bacterium from cutting its own CRISPR store. Second, once a PAM is found, the guide RNA must base-pair with the neighbouring DNA. Only when both checks pass does Cas9 cut, slicing both strands at once.

The cut itself is just the start. A cell does not leave a broken chromosome alone, so it repairs the break. If it simply glues the ends back together it often loses or gains a few letters, which switches the gene off. If researchers also supply a matching template, the cell can copy it in and write a precise new sequence.

2011

Charpentier discovers tracrRNA, a small RNA the CRISPR-Cas9 system needs to mature its guides.

Spring 2011

Charpentier and Doudna meet at a conference in Puerto Rico and begin to collaborate.

2012

They fuse two RNAs into one guide RNA and show Cas9 can be programmed to cut DNA at a chosen site.

2020

The pair share the Nobel Prize in Chemistry for the genome editing method.

CRISPR-Cas9 is a class 2, type II CRISPR system, meaning a single multidomain protein, Cas9, carries out both target recognition and cleavage. In its natural form Cas9 is guided by two RNAs: a CRISPR RNA (crRNA) that carries the roughly 20-nucleotide spacer matching the target, and a trans-activating CRISPR RNA (tracrRNA) that pairs with the crRNA and scaffolds the complex. Charpentier's identification of tracrRNA supplied the missing component. Charpentier and Doudna then engineered the two into a single-guide RNA (sgRNA), collapsing the system to one protein plus one programmable RNA.

Target search

PAM first, then the seed

Cas9 does not scan by base-pairing alone. It first interrogates the DNA for a protospacer adjacent motif (PAM), the sequence 5'-NGG-3' for Streptococcus pyogenes Cas9, which sits just 3-prime of the intended target on the non-target strand. PAM recognition licenses local unwinding, and the guide then tests complementarity starting from a PAM-proximal seed region. A correct match drives formation of an R-loop, in which the guide RNA pairs with the target strand while the non-target strand is displaced.

Cleavage is carried out by two nuclease domains. The HNH domain cuts the target strand, the one paired with the guide, and the RuvC domain cuts the displaced non-target strand. Both cuts fall about three base pairs upstream of the PAM, producing a blunt double-strand break at a defined position. The same PAM requirement protects the bacterium's own CRISPR array, which lacks a PAM next to its stored spacers, so the feature that keeps Cas9 safe for its host also makes it predictable as a tool.

After the break

The edit is written by repair, not by Cas9

Cas9 only breaks the DNA; the cell's repair pathways decide the outcome. Non-homologous end joining (NHEJ) religates the ends and frequently introduces small insertions or deletions, which shift the reading frame and knock the gene out. Homology-directed repair (HDR) instead copies a supplied donor template across the break, allowing a precise sequence to be inserted or corrected, though it is largely restricted to dividing cells.

What the tool opened up

Functional genomics: programmable knockouts and genome-wide CRISPR screens that test what each gene does.
Medicine: in November 2023 the UK regulator approved Casgevy (exagamglogene autotemcel), a CRISPR-Cas9 therapy that edits a patient's own blood stem cells to treat sickle cell disease and transfusion-dependent beta thalassaemia.
Agriculture: crops edited for traits such as disease resistance, often without adding any foreign genes.
The open problems: off-target cuts, getting the machinery into the right tissue efficiently, and the ethics of editing human embryos.

Worth knowing

Bacteria had this technology long before we did

CRISPR is an ancient bacterial immune system, a genetic memory of past virus attacks. Charpentier and Doudna did not invent the cutting machine. They worked out its rules and reprogrammed it, turning a microbe's defence into a tool that can rewrite the code of almost any living thing in a matter of weeks.

Check yourself

What does the guide RNA in CRISPR-Cas9 actually do?

Why: The guide RNA is the address, not the scissors. Its sequence base-pairs with a matching stretch of DNA, steering Cas9 to the target. The cutting is done by Cas9's protein domains, and the repair is done by the cell.

Why must Cas9 find a PAM sequence before it cuts?

Why: No PAM, no cut. Cas9 only acts next to a short PAM such as NGG. The bacterium's own CRISPR store lacks a PAM beside its stored sequences, so it is spared, and the requirement makes targeting predictable for researchers.

After Cas9 makes a double-strand cut, what most directly decides whether a gene is knocked out or precisely rewritten?

Why: Repair decides the outcome. Non-homologous end joining often deletes or inserts a few letters and disables the gene, while homology-directed repair copies a supplied template to write a precise sequence. Cas9 just makes the break.

Key terms

CRISPR-Cas9: A bacterial defence system, repurposed as a tool, in which a guide RNA directs the Cas9 protein to cut DNA at a chosen sequence.
Guide RNA (sgRNA): A short RNA whose sequence is written to match a DNA target. It base-pairs with that DNA and steers Cas9 to the right spot.
tracrRNA: A small trans-activating RNA, discovered by Charpentier in 2011, that the CRISPR system needs to mature its guide and activate Cas9.
PAM: Protospacer adjacent motif, a short DNA signal such as NGG that must sit next to the target. Cas9 cuts only beside a PAM, which also spares the bacterium's own CRISPR store.
Double-strand break: A clean cut through both strands of the DNA, made by Cas9 about three base pairs from the PAM, that the cell then has to repair.
NHEJ: Non-homologous end joining, a repair route that glues the cut ends back together and often loses or adds a few letters, switching the gene off.
HDR: Homology-directed repair, a route that copies a supplied template across the break to write a precise new sequence, mostly in dividing cells.

The laureates

Emmanuelle Charpentier

Max Planck Unit for the Science of Pathogens, Berlin, Germany

Born in France in 1968, Charpentier is a microbiologist who studied how the bacterium Streptococcus pyogenes defends itself against viruses. In 2011 she discovered tracrRNA, a small RNA the CRISPR system needs, which pointed straight at the Cas9 cutting machinery and led to her collaboration with Doudna. She now directs the Max Planck Unit for the Science of Pathogens in Berlin.

Photo: Bianca Fioretti, Hallbauer & Fioretti, CC BY-SA 4.0 (via Wikimedia Commons)

Jennifer A. Doudna

University of California, Berkeley, CA, USA

Born in the United States in 1964, Doudna is a biochemist at the University of California, Berkeley, who specialises in the structure and chemistry of RNA. Working with Charpentier, she helped fuse two natural RNA pieces into a single programmable guide RNA and showed the pair could direct Cas9 to cut DNA at a location the researchers chose.

Photo: Duncan.Hull, CC BY-SA 4.0 (via Wikimedia Commons)

Sources

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