Phage phi29 and Nf terminal protein-priming domain specifies the internal template nucleotide to initiate DNA replication.

Bacteriophages phi29 and Nf from Bacillus subtilis start replication of their linear genome at both DNA ends by a protein-primed mechanism, by which the DNA polymerase, in a template-instructed reaction, adds 5'-dAMP to a molecule of terminal protein (TP) to form the initiation product TP-dAMP. Mutational analysis of the 3 terminal thymines of the Nf DNA end indicated that initiation of Nf DNA replication is directed by the third thymine on the template, the recovery of the 2 terminal nucleotides mainly occurring by a stepwise sliding-back mechanism. By using chimerical TPs, constructed by swapping the priming domain of the related phi29 and Nf proteins, we show that this domain is the main structural determinant that dictates the internal 3' nucleotide used as template during initiation.