Chapter 20: DNA Replication, Repair, and Recombination

DNA replication follows a semiconservative model in which each daughter molecule retains one original strand and one newly synthesized strand, beginning at specific origin sites and proceeding bidirectionally until replication forks converge at termination sites. Because DNA polymerases synthesize only in the five-prime to three-prime direction and DNA strands are antiparallel, the two strands replicate through different mechanisms: the leading strand is synthesized continuously while the lagging strand is synthesized discontinuously as short Okazaki fragments. The replisome, a coordinated protein complex, orchestrates replication through the cooperative action of multiple specialized enzymes including helicase to unwind the double helix, primase to initiate synthesis with RNA primers, DNA polymerase III to catalyze elongation with proofreading capability, and DNA ligase to join fragments into continuous strands. Eukaryotic replication is more elaborate, employing multiple origins of replication and distinct polymerases adapted to their specific roles while remaining subject to strict cell cycle regulation. The chapter explores how cells defend against genetic damage through direct repair mechanisms such as photolyase activity and excision repair pathways involving glycosylases and polymerases. Homologous recombination provides an alternative repair pathway for severe lesions like double-strand breaks, operating through strand invasion and the formation of Holliday junctions that are resolved by specific nucleases. Finally, the chapter addresses how molecular understanding of replication has enabled transformative biotechnologies including polymerase chain reaction for DNA amplification, Sanger sequencing for determining nucleotide order, and modern next-generation sequencing methods that process millions of sequences in parallel.