Explainer: How CRISPR works | Science News for Students

Explainer: How CRISPR works

This technique lets scientists edit DNA in plants and animals
Jul 31, 2017 — 6:50 am EST

Scientists are using a tool called CRISPR/Cas9 to edit DNA.


Scientists usually shy away from using the word miracle. Unless they’re talking about the gene-editing tool called CRISPR, that is. “You can do anything with CRISPR,” some say. Others just call it amazing.

CRISPR stands for “clustered regularly interspaced short palindromic repeats.” Those repeats are elements of the genetic code in DNA. Cas9 is an enzyme that can cut apart DNA. Bacteria fight off viruses by wielding the Cas9 enzyme to reorder those repeated genetic segments. Scientists recently figured out how bacteria do this. Now, in the lab, they use a similar approach to turn the microbe’s virus-fighting system into the hottest new lab tool.

This CRISPR/Cas9 tool was first described in 2012 and 2013. Science labs around the world soon started using it to alter an organism’s genome — the entire set of its genes.

This tool can quickly and efficiently tweak almost any gene in any plant or animal. Researchers already have used it to fix genetic diseases in animals, to combat viruses and to sterilize mosquitoes. They have also used it to prepare pig organs for human transplants and to beef up the muscles in beagles.

So far CRISPR’s biggest impact has been felt in basic biology labs. This low-cost gene editor is easy to use. That has made it possible for researchers to delve into the basic mysteries of life. And they can do it in ways that used to be difficult if not impossible.

Robert Reed is a developmental biologist at Cornell University in Ithaca, N.Y. He likens CRISPR to a computer mouse. “You can just point it at a place in the genome and you can do anything you want at that spot.”

Anything, that is, as long as it involves cutting DNA. CRISPR/Cas9 in its original form is a homing device (the CRISPR part) that guides molecular scissors (the Cas9 enzyme) to a target section of DNA. Together, they work as a genetic-engineering cruise missile that disables or repairs a gene, or inserts something new where the Cas9 scissors has made some cuts.

Here’s how it works

Scientists start with RNA. That’s a molecule that can read the genetic information in DNA. The RNA finds the spot in the nucleus of a cell where some cut-and/or-paste activity should take place. (The nucleus is a compartment in a cell where most of the genetic material is stored.) This guide RNA shepherds Cas9 to the precise spot on DNA where a cut is called for. Cas9 then locks onto the double-stranded DNA and unzips it.

This allows the guide RNA to pair up with some region of the DNA it has targeted. Cas9 snips the DNA at this spot. This creates a break in both strands of the DNA molecule. The cell, sensing a problem, repairs the break.

Fixing the break might disable a gene (the easiest thing to do). Alternatively, this repair might fix a mistake or even insert a new gene (a much more difficult process).  

Cells usually repair a break in their DNA by gluing the loose ends back together. That’s a sloppy process. It often results in a mistake that disables some gene. That may not sound useful — but sometimes it is.

Scientists cut DNA with CRISPR/Cas9 to make gene changes, or mutations. By comparing cells with and without the mutation, scientists can sometimes figure out what a protein’s normal role is. Or a new mutation may help them understand genetic diseases. CRISPR/Cas9 also can be useful in human cells by disabling certain genes — ones, for instance, that play a role in inherited diseases.

“The original Cas9 is like a Swiss army knife with only one application: It’s a knife,” says Gene Yeo. He is an RNA biologist at the University of California, San Diego. But Yeo and others have bolted other proteins and chemicals to the dulled blades. That has transformed that knife into a multifunctional tool.

CRISPR/Cas9 can now be used in new ways, such as changing a single nucleotide base — a single letter in the genetic code — or adding a fluorescent protein to tag a spot in the DNA that scientists want to track. Scientists also can use this genetic cut-and-paste technology to turn genes on or off.

This explosion of new ways to use CRISPR hasn’t ended. Feng Zhang is a molecular biologist at the Massachusetts Institute of Technology in Cambridge. He was one of the first scientists to wield the Cas9 scissors. “The field is advancing so rapidly,” he says. “Just looking at how far we have come…I think what we’ll see coming in the next few years will just be amazing.”

Power Words

(for more about Power Words, click here)

application     A particular use or function of something.

base      (in genetics) A shortened version of the term nucleobase. These bases are building blocks of DNA and RNA molecules.

biology     The study of living things. The scientists who study them are known as biologists.

Cas9     An enzyme that geneticists are now using to help edit genes. It can cut through DNA, allowing it to fix broken genes, splice in new ones or disable certain genes. Cas9 is shepherded to the place it is supposed to make cuts by CRISPRs, a type of genetic guides. The Cas9 enzyme came from bacteria. When viruses invade a bacterium, this enzyme can chop up the germs DNA, making it harmless.

cell     The smallest structural and functional unit of an organism. Typically too small to see with the naked eye, it consists of watery fluid surrounded by a membrane or wall. Animals are made of anywhere from thousands to trillions of cells, depending on their size. Some organisms, such as yeasts, molds, bacteria and some algae, are composed of only one cell.

chemical     A substance formed from two or more atoms that unite (become bonded together) in a fixed proportion and structure. For example, water is a chemical made of two hydrogen atoms bonded to one oxygen atom. Its chemical symbol is H2O.

CRISPR     An abbreviation — pronounced crisper — for the term “clustered regularly interspaced short palindromic repeats.” These are pieces of RNA, an information-carrying molecule. They are copied from the genetic material of viruses that infect bacteria. When a bacterium encounters a virus that it was previously exposed to, it produces an RNA copy of the CRISPR that contains that virus’ genetic information. The RNA then guides an enzyme, called Cas9, to cut up the virus and make it harmless. Scientists are now building their own versions of CRISPR RNAs. These lab-made RNAs guide the enzyme to cut specific genes in other organisms. Scientists use them, like a genetic scissors, to edit — or alter — specific genes so that they can then study how the gene works, repair damage to broken genes, insert new genes or disable harmful ones.

developmental     (in biology) An adjective that refers to the changes an organism undergoes from conception through adulthood. Those changes often involve chemistry, size and sometimes even shape.

DNA     (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. It is built on a backbone of phosphorus, oxygen, and carbon atoms. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

engineering     The field of research that uses math and science to solve practical problems.

field     An area of study, as in: Her field of research was biology. Also a term to describe a real-world environment in which some research is conducted, such as at sea, in a forest, on a mountaintop or on a city street. It is the opposite of an artificial setting, such as a research laboratory.

fluorescent     Capable of absorbing and reemitting light. That reemitted light is known as a fluorescence.

gene     (adj. genetic) A segment of DNA that codes, or holds instructions, for producing a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.

genome     The complete set of genes or genetic material in a cell or an organism. The study of this genetic inheritance housed within cells is known as genomics.

muscle     A type of tissue used to produce movement by contracting its cells, known as muscle fibers. Muscle is rich in a protein, which is why predatory species seek prey containing lots of this tissue.

mutation     (v. mutate) Some change that occurs to a gene in an organism’s DNA. Some mutations occur naturally. Others can be triggered by outside factors, such as pollution, radiation, medicines or something in the diet. A gene with this change is referred to as a mutant.

nucleus     Plural is nuclei. (in biology) A dense structure present in many cells. Typically a single rounded structure encased within a membrane, the nucleus contains the genetic information.

organ     (in biology) Various parts of an organism that perform one or more particular functions. For instance, an ovary is an organ that makes eggs, the brain is an organ that interprets nerve signals and a plant’s roots are organs that take in nutrients and moisture.

palindrome     (adj. palindromic) A word, a name or a phrase that has the same ordering of letters when read forwards or backwards. For instance, dad and mom are both palindromes.

protein     Compound made from one or more long chains of amino acids. Proteins are an essential part of all living organisms. They form the basis of living cells, muscle and tissues; they also do the work inside of cells. The hemoglobin in blood and the antibodies that attempt to fight infections are among the better-known, stand-alone proteins. Medicines frequently work by latching onto proteins.

RNA     A molecule that helps “read” the genetic information contained in DNA. A cell’s molecular machinery reads DNA to create RNA, and then reads RNA to create proteins.

tag     (in biology) To attach some rugged band or package of instruments onto an animal. Sometimes the tag is used to give each individual a unique identification number. Once attached to the leg, ear or other part of the body of a critter, it can effectively become the animal’s “name.” In some instances, a tag can collect information from the environment around the animal as well. This helps scientists understand both the environment and the animal’s role within it.


Journal:​ S. Wang et al. An RNA-aptamer-based two-color CRISPR labeling systemScientific Reports. Vol. 6, May 27, 2016, p. 26857. doi: 10.1038/srep26857.

Journal:​ ​A. C. Komor et al. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavageNature. Vol. 533, May 19, 2016, published online April 20, 2016, p. 420. doi:10.1038/nature17946.

Journal:​ D. A. Nelles et al. Programmable RNA tracking in live cells with CRISPR/Cas9Cell. Vol. 165, April 7, 2016, p. 488. doi: 10.1016/j.cell.2016.02.054.