DNA synthesis across a lesion by an appropriate polymerase. It can allow replication to continue without removing the original lesion, and its accuracy is substrate dependent.

Use of an alternative template during synthesis or damage tolerance. Appropriate switching can bypass a block; inappropriate switching can alter sequence organization.

DNA whose copying has not completed at a relevant cell-cycle transition. It can contribute to abnormal mitotic structures or breakage, but requires evidence distinct from a general DNA-damage signal.

An inhibitor of replicative DNA polymerases used to impose replication stress. Increased fragility after treatment supports replication-sensitive vulnerability without identifying every molecular intermediate.

A break involving both strands of a DNA molecule. Unrepaired breaks can prevent reliable transmission; controlled breaks also initiate meiotic homologous recombination.

Repair that recognizes and corrects mismatched sequence after copying or strand exchange. It can also inhibit homologous recombination between sufficiently divergent sequences.^[ref]

A presynaptic filament in homologous recombination is the recombinase–single-stranded DNA assembly formed before productive donor pairing. Distinguish its formation from later donor capture and DNA strand exchange.

DNA strand exchange replaces a strand's original pairing partner with another complementary strand. RecA and RAD51 organize the substrates and promote local donor opening; new pairing produces heteroduplex DNA.

A D-loop is a local strand-invasion structure in which an incoming strand pairs with one strand of a duplex and displaces the other. It is a useful intermediate and assay product in homologous recombination.

A bacterial DNA-damage response regulating repair and damage-tolerance functions; its details differ among bacterial lineages.

Repair joining broken DNA ends without an extended homologous donor. End processing can create insertions or deletions; repair need not disrupt the reading frame.

Repair using a homologous sequence as a template. An experimentally supplied donor can introduce a defined sequence, although repair-pathway competition and cell state constrain efficiency.

A protein involved in DNA-damage responses and homologous-recombination-related repair. Inherited pathogenic variants can predispose to cancer.

A protein supporting homologous-recombination repair, including control of RAD51-mediated processes. Inherited pathogenic variants can predispose to cancer.

Repair of ribonucleotides embedded in DNA, including molecules with correct base pairing. RNase H2 can initiate an incision followed by replacement synthesis and ligation.^[ref]

An enzyme acting on appropriate RNA–DNA hybrid substrates. Its substrate requirements differ from removal of a single isolated ribonucleotide by RNase H2.

Removal of a damaged base followed by processing, replacement synthesis and sealing. It repairs chemical base damage rather than every replication mismatch.

Excision of an oligonucleotide around a lesion followed by replacement and sealing, important for many bulky helix-distorting lesions.

DNA repair synthesis replaces missing or damaged DNA sequence as part of DNA repair. After a damaged region is removed, a DNA polymerase can copy the intact complementary strand to fill the gap, followed by sealing of the backbone. This uses the undamaged strand as information rather than inferring the missing sequence without a template. Incorporation of labelled nucleotides therefore need not indicate whole-genome DNA replication; localized repair can also produce incorporation. ^[ref]

Bisulfite sequencing infers cytosine modification from differential chemical conversion before DNA sequencing. Under the relevant chemistry, unmodified cytosine is converted to uracil and is subsequently read as thymine, while 5-methylcytosine is retained as cytosine. Incomplete conversion, sequence coverage and strand assignment affect interpretation. Conventional bisulfite sequencing does not by itself separate 5-methylcytosine from every other conversion-resistant modification, so its signal requires a stated chemical scope. ^[ref]