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Secret Codon

Science Snack
Secret Codon
Write a message in DNA.
Secret Codon
Write a message in DNA.

DNA is referred to as the genetic code for life, because it contains information about which amino acids join together to create different proteins. You can use the one-letter abbreviations for amino acids to make a secret message that will give new meaning to the description of DNA as beads on a string.

COVID-19 Learning Note: All living things use the same genetic code, but some viruses, including coronaviruses, use RNA instead of DNA to store their code. RNA decoding works the same way as DNA decoding, with uracil (U) swapping in for thymine (T). The host cell translates the viral RNA into amino acids that make up viral proteins. Detection of this viral RNA is how doctors verify whether a patient has been infected with this specific coronavirus.

Tools and Materials
Assembly

Assign each pony bead color to one of the four DNA bases – adenine (A), thymine (T), cytosine (C), and guanine (G). The string pictured above uses this color key:

A: red
T: yellow
C: blue
G: green

To Do and Notice

Think of a word or short phrase that you want to encode into your DNA strand. Make sure it can be spelled or sounded out without using the letters B, J, O, U, X, or Z. These letters are not abbreviations for any of the amino acids. Determine what amino acids the letters in your phrase correspond to by looking up the one-letter amino acid abbreviations in the amino acid codon table. Then, use the table to write down the DNA sequence that encodes for those amino acids. All proteins start with a methionine amino acid residue that is encoded by the DNA sequence ATG. They end when the DNA encodes one of the three stop codons. Add ATG to the beginning of your sequence, and pick one of the three stop codons for the end of your sequence. Make your DNA strand by stringing the beads so that the colors match the order of the DNA sequence that you wrote down. Don’t forget to include the proper start and stop codons in your sequence. Trade strands with a friend and see if you can decode each other’s secret message!

What’s Going On?

Proteins are long chains of individual amino acid subunits. The order of the amino acids in the chain is determined by the DNA sequence of the gene that encodes for it. This is commonly referred to as the genetic code.

DNA is a chain of four different nucleotides (adenine, thymine, cytosine, and guanine), often abbreviated A, T, C, and G. These four nucleotides (sometimes referred to as bases) give the instructions for the 20 different amino acids that compose proteins. Each amino acid is encoded by a sequence of three DNA bases, called a codon. Since it takes three DNA bases to designate an amino acid, there are enough combinations of the four different bases to represent all of the amino acids, as well as three stop codons that indicate when the protein ends. Each base can be in any position, which yields 43, or 64, possible combinations, so there is some redundancy between the 20 amino acids. This just means that a given amino acid can be encoded by more than one DNA codon sequence.

For simplicity, individual amino acids are often abbreviated using one or three letter abbreviations. For example, the amino acid arginine can be abbreviated Arg or R. The single-letter amino acid abbreviations provide a fun way to write secret messages using the genetic code. Since there are only 20 different amino acids, there are 6 letters of the alphabet that don’t stand for a specific amino acid. With the 20 letters that do, however, you can use the genetic code to determine the DNA sequence that corresponds to your amino acid message.

The message can be written with four different colors that represent the four different bases that make up DNA. The chain in the picture at the top of the page has this sequence:

RYGGBBRGRRBGGBYRRBGRYYBYYGYRYYGRGRRYYGYGRGYRR

The sequence starts with RYG. Using the color key in the Assembly section, this corresponds to the bases ATG, which is the methionine start codon that begins every protein sequence. Can you decode the rest of the message?

Going Further

In 2008, researchers at the J. Craig Venter Institute announced that they had constructed the entire genome of a small bacterium from scratch, thus creating the first example of synthetic life. To distinguish the man-made genome from the natural one, the scientists inserted “watermarks” into the DNA sequence. These sequences were decoded to their one-letter amino-acid abbreviations and revealed five watermarks commemorating those who had worked on the project: VENTERINSTITVTE, CRAIGVENTER, HAMSMITH, CINDIANDCLYDE, GLASSANDCLYDE.

This Science Snack is part of a collection that highlights Asian, Pacific Islander, and Asian Pacific American artists, scientists, inventors, and thinkers whose work aids or expands our understanding of the phenomena explored in the Snack.

Dr. Margaret Liu was born in 1956 and raised in Colorado by her mother, a Chinese immigrant. She earned her MD at Harvard University and is the former president of the International Society for Vaccines. Dr. Liu studies the immune system and works to develop new technologies for creating vaccines. While many vaccines are made from weakened viruses or viral proteins, Dr. Liu showed that injected molecules of DNA containing viral genes can be translated to protein in human cells and provoke an immune response. This key insight paved the way for a new set of vaccines made of viral sequences of DNA or RNA, including vaccines under development to protect against COVID-19. With the Secret Codon Science Snack, you can play with the DNA code to understand how scientists like Dr. Liu engineer DNA to elicit immune responses to viral proteins.