Fire and Mellos new method of gene silencing was able to explain the anomalous results obtained from an earlier set of experiments on petunia pigmentation. In 1990, Dr. Richard Jorgensen and colleagues attempted to produce a petunia with a deeper color by inserting the gene for purple pigment into its genome under the control of a stronger promoter. Instead of turning dark purple, the new petunias were either entirely white or streaked purple and white. Jorgensen surmised that the additional copy of the gene suppressed both itself and its endogenous counterpart, an event he called co-suppression. Fire and Mellos findings several years later explained that the inserted gene produced RNA that interfered with gene expression in a similar manner to what occurred in the C. elegans study. Scientists who described gene silencing in other plants and fungi were able to show that silencing occurred after the gene had already been transcribed.

In another paper, also published in 1998, Fire determined that dsRNA targets complementary mRNA by base-pairing to it and that regulation occurs because the targeted mRNA is degraded before translation. Soon other researchers observed the same phenomenon in fruit flies, trypanosomes, plants, planaria, hydra and zebrafish, and the focus turned to identifying this process in mammalian cells. Previous attempts with long dsRNA caused nonspecific gene regulation. A significant clue to inducing specific gene regulation emerged during the characterization of the RNAi biochemical machinery in fruit flies. Scientists discovered an enzyme that cleaved dsRNA into strands 22 nucleotides (nt) long. With this new data in mind, researchers introduced smaller dsRNA into mammalian cells. This time, the smaller dsRNA molecules specifically interfered with expression of the targeted gene.

For their work in discovering RNAi and its role in gene silencing, Fire and Mello were awarded the 2006 Nobel Prize in Physiology or Medicine.