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Autonomously replicating sequence (ARS):

Sequence  that confers the abilty on plasmids to replicate autonomously of the host chromosomes, by acting as an origin of replication (usually used to refer to sequences from yeast). Sequences from yeast chromosomes that function as ARS elements  may  also function as origins in their original chromosomal location. 

ARS consensus sequence (ACS):

Consensus sequence found in S. cerevisiae origins of DNA replication.

Checkpoint mechanism

Regulatory mechanism that arrests cell cycle when previous stages have not been completed or when a chromosome or DNA defect is present

Clamp loader

Protein such as replication factor C that can load a clamp such as PCNA onto DNA


Second stage of DNA synthesis, following initiation, where bulk DNA synthesis takes place on the leading and lagging strands

Fork regression

Occurs when a stalled replication fork reverses allowing the nascent strands to anneal.
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Fragile site

Chromosomal site in mammalian chromosomes that is prone to breakage.


First stage of DNA synthesis where the DNA double helix is unwound and an initial priming event by DNA polymerase alpha occurs on the leading strand. Priming event on lagging strand establishes a replication fork

Lagging strand

The strand which is synthesised discontinuously during elongation.

Leading strand

The strand which is synthesised continuously during elongation.


Association of Mcm2-7 proteins with DNA at ORC to form a pre-replicative complex (pre-RC) . Step requires Cdc6 and Cdt1. Synonomous with pre-RC formation

Mcm paradox

Usually refers to the high ratio of Mcm2-7 to ORC complexes (>10:1) at origins.
Has also been used to refer to the situation where MCMs do not apparently localise with replication sites.


Abbreviation for origin of DNA replication

Origin efficiency

Probability that activation of DNA replication from an origin will occur in a single S phase. Origin efficiency can be high (>80%) in S. cerevisiae, but appears to be lower in S. pombe and mammalian cells.

Origin suppression

Origin suppression refers to the inhibition of initiation at an origin by initiation at a nearby origin. Can occur passively, whereby passage of a replication fork through the unfired origin prevents initiation.

Okazaki fragment

The unit in which DNA is synthesized discontinuously on the lagging strand. Okazaki fragments are subsequently ligated together.

Polymerase switching

Process whereby DNA polymerase delta or epsilon takes over from DNA polymerase alpha. Occurs once on leading strand on initiation and is required for generation of each Okazaki fragment

Pre-initiation complex (pre-IC)

Originally used to refer to complex of Sc Cdc45 with pre-RCs before initiation. Now generally used to refer to more extensive complex of proteins at origin after pre-RC formation but before initiation of DNA synthesis.

Pre-replicative complex (pre-RC)

Originally defined as an extended in vivo footprint on S. cerevisiae origins seen in G1 phase. Now generally used to refer to origins where Mcm2-7 (together with Cdc6 and possibly Cdt1) is chromatin associated.


Synthesis of an RNA primer to allow DNA synthesis by DNA polymerase alpha. Occurs once at the origin on the leading strand and at the start of each Okazaki fragment on the lagging strand.


Ability of a DNA polymerase to synthesize consecutive nucleotides without dissociating from the template


Ability of DNA polymerases to remove incorrectly incorporated nucleotides (i.e. where the A-T, C-G base pairing rules are not observed), via transient activation of a 3’-5’ exonuclease activity

Replication focus

Cytologically defined site in nucleus where DNA synthesis is occuring

Replication fork

A site of active DNA synthesis

Replication fork barrier

Protein complex that prevents passage of replication fork in one direction

Replication origin

DNA sequence where initiation of replication occurs. In S. cerevisiae origins are sequence specific, but this appears not to be the case in most eukaryotes

Replication origin timing

Refers to the fact that replication origins can show a defined temporal pattern of activation so that individual origins can fire early or late in S phase.

Replicon hypothesis

Concept of DNA replication proposed by Brenner, Jacob and Cuzin. DNA replication was suggested to initiate at a specific origin via interaction with an origin binding protein. The unit of replication replicated from this site is the replicon.

S phase

Phase of cell cycle when DNA synthesis occurs