Prokaryotic DNA Replication – Key Vocabulary

DNA Unwinding Element (DUE)

An AT-rich origin sequence that first melts, initiating strand separation during replication start-up.

DNA Assembly Regions (R1–R4 / DAR regions)

Origin boxes where host factors and DnaA bind to organize the initiation complex for replication.

DnaA

Initiator protein that binds origin boxes, oligomerizes, and introduces torsional strain to unwind DNA.

Integration Host Factor (IHF)

DNA-bending protein that binds the IHF box, increasing tension and promoting DUE melting.

DnaB helicase

Ring-shaped motor enzyme that travels 5′→3′ along DNA, unwinding the duplex ahead of the fork.

DnaC (helicase loader)

Protein that opens and loads DnaB onto single-stranded DNA at the origin.

Primase (DnaG)

Specialized RNA polymerase that synthesizes short RNA primers required for DNA polymerases.

β-clamp (sliding clamp)

Dimeric ring that encircles DNA and keeps DNA polymerase III highly processive.

Clamp loader tails (B2 loader)

Subunits that assemble the β-clamp around DNA and can tether two DNA polymerases for simultaneous leading and lagging synthesis.

Single-Stranded Binding proteins (SSB)

Tetrameric proteins that coat and stabilize exposed single-stranded DNA, preventing secondary structures.

DNA Polymerase I

Enzyme that removes RNA primers with its 5′→3′ exonuclease and fills the gaps with DNA.

Flap Endonuclease (FEN)

Nuclease that cleaves displaced RNA or DNA flaps during primer removal and processing.

DNA ligase

Enzyme that catalyzes phosphodiester bond formation, sealing nicks to join Okazaki fragments.

Tus/Ter termination system

Polar fork barrier defining a termination zone with permissive and non-permissive faces that halt replication progression.