One way to silence a gene is to prevent it from being transcribed in the first place. To accomplish this, scientists can insert pieces of DNA that are very similar in sequence to the gene in question. Having excess quantities of DNA sequences that the organism recognizes as one of its own genes prevents transcription of the organism's actual gene. This silencing occurs because gene expression typically operates by a feedback mechanism, whereby the expression of a sufficient amount of a gene prevents further expression of that gene.
Genes can also be silenced by altering the nucleotide sequence of the genes. Each triplet of nucleotides in mRNA encodes one amino acid, the building blocks of proteins. The exceptions to this rule are that three specific triplets, called stop codons, cause translation to stop instead of attaching another amino acid to the growing protein. There are three stop codons: UAA, UAG and UGA. By using restriction enzymes to cut and paste sequences of DNA, scientists can insert a stop codon into the middle of a gene. When this gene gets translated, the stop codon causes protein synthesis to terminate early, before a functional protein is formed.
RNAi (RNA interference) is a genetic technology in which double-stranded RNA (dsRNA) is introduced into a cell. The dsRNA then gets cut into smaller fragments and associates with an RNA-destroying complex. In the process, the dsRNA separates into single-stranded RNA. The RNA complex binds to complementary mRNA in the organism's cells and destroys it.
The effects of a gene can be silenced after translation as well. Genes encode proteins, most of which are enzymes. Many enzymes have inhibitors which are molecules that will specifically bind to that enzyme and prevent it from functioning. Therefore, after a gene has been expressed into an enzyme, an inhibitor may be added to silence the effect of that enzyme as if it had not been produced in the first place.