The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets

guide RNA could indeed direct the base-editing enzyme to any site in the genome that needed to be “fixed,” and the enzyme would change a single letter—for example, a C to a T—in the DNA without ever causing a double-strand break.

Once a bacterium had a snippet of a particular phage sequence stored in its CRISPR cluster, it was immune to attack by a phage of that type.

The RNAs that emerge from this dark matter are called long noncoding RNAs (lncRNAs).

The CRISPR-Cas9 bacterial defense complex (left) has a guide RNA that recognizes a target phage DNA sequence and a tracrRNA that base-pairs with the guide RNA and holds on to the Cas9 protein. Cas9 then cleaves both strands of the DNA. An engineered form of CRISPR-Cas9 used for genome editing (right) has the two natural RNAs fused to form a single-

After CRISPR-Cas9 cleaves its target DNA at a specific sequence, cellular DNA-repair machines take over and do the gene editing. Non-homologous end joining (NHEJ) is a quick-and-sloppy repair system that usually leaves a small insertion or deletion of DNA at the site of repair. Homologous recombination is accurate and requires a donor template DNA

These are not messenger RNAs, but rather noncoding RNAs—the same general category as ribosomal RNA, transfer RNA, telomerase RNA, and microRNAs. But what they’re doing is still, for the most part, a mystery.

CRISPR DNA caught their attention as something new and unusual. It contained repeated sequences that were palindromic, reading the same forward and backward,

the bacteria had the immunity embedded in their DNA so it was passed from one generation to the next.

The total number of RNAs made from DNA’s “dark matter” has been estimated to be several hundred thousand.