Mechanisms for Priming DNA Synthesis

Abstract

DNA replication is a semiconservative process in which a DNA polymerase uses one DNA strand as a template for the synthesis of a second, complementary, DNA strand. However, in contrast to RNA polymerases, which can initiate RNA synthesis on a DNA template de novo, all DNA polymerases require a preexisting primer on which to initiate DNA synthesis (Kornberg and Baker 1992). One apparent exception to this rule is a mitochondria1 DNA (mtDNA)-encoded reverse transcriptase (RT) in Neurospora (Wang and Lambowitz 1993). Preexisting primers can be classified into four groups. The simplest primer consists of the 3'-hydroxyl (3'-OH) termini of DNA chains that are complementary to the DNA template and thereby form a stable duplex structure at the site where DNA synthesis begins. This primer is used for DNA repair (Friedberg and Wood, this volume), parvovirus DNA replication (Brush and Kelly; Cotmore and Tattersall; both this volume), some RTs. The second type of primer consists of a deoxyribonucleoside monophosphate that is covalently attached to a specific serine, threonine, or tyrosine residue of a protein. Examples are bacteriophage, plasmids, and animal viruses that replicate as a linear DNA genome, and animal viruses such as hepadnaviruses whose genome is partially doublestranded and partially single-stranded. The third type of primer consists of tRNA molecules that anneal to specific sequences in the RNA The fourth class of primers consists of nascent RNA chains. These comprise nascent RNA transcripts that are processed to create a primer at a specific site in the template and short nascent oligoribonucleotides (initiator RNA) that are synthesized at many sites in the template and rapidly extended into short RNA-DNA primers by DNA polymerase-a:DNA primase (pol-a:primase). Nascent RNA transcripts are used during initiation of mtDNA replication, whereas replication forks in cellular chromosomes and double-stranded DNA (dsDNA) viral genomes that replicate within the nucleus use the initiator RNA mechanism.