During the genetic dissection of Drosophila melanogaster fruit flies, it was shown that certain genes such as per could affect their circadian cycles. Mammals have one or more versions of these genes. These genes contribute to a molecular clock, regulating each other so that their protein products fluctuate in an approximately 24 hour cycle. The cells in the SCN create two proteins: Clock and Cycle (Drosophila)/Bmal1 (mammals). These two proteins bind to create a dimer. The dimer binds to the cell's DNA and creates two other genes: Per and Cry. These Per and Cry proteins create a dimer as well which inhibits the activity of the Clock and Cycle genes. The Per and Cry proteins break down eventually, which causes the inhibition on the Clock and Cycle genes to disappear. This cycle takes about 24 hours, which creates a molecular circadian cycle within the SCN cells. Each SCN neuron uses this method to keep time and communicate with each other through electrical synapses. The same molecular clock exists in almost every cell in the body, and they all operate as long as the SCN is functioning, which shows that the SCN is the center for molecular rhythm.

• Entrainment of molecular circadian rhythm