One of the two strands of the invading DNA molecule is digested by nucleases, The surviving DNA strand aligns with a complementary region of the bacterial chromosome and replaces it, producing a heteroduplex region where the two strands of DNA are not perfectly complementary.

Following DNA replication and cell division, one cell contains the original DNA sequence, while the other has been transformed to possess the foreign gene.

This process can be used to establish "linkage", since bacterial genes that are close together have a high probability of cotransformation, and relative mapping distances between linked genes can be determined.