DNA Repair Mechanisms: Mismatch, Nucleotide Excision, and Double-Strand Breaks

MutS

detects mismatches via DNA helix distortion

MutL

bridges MutS and MutH, forming a loop

MutH

binds to methylated DNA to provide strand polarity; endonuclease that nicks the unmethylated strand

MutSLH Complex

recognizes mismatch and creates a nick upstream or downstream of the lesion

DAM Methylase

methylates DNA at 3'-GATC sites, marking the parental strand

Helicase

works with exonuclease to extend the repair gap

DNA Polymerase

fills in the repaired DNA gap

Ligase

seals the final nick

Exo VII / RecJ

5'-3' exonuclease; used when the nearest methyl group is toward the 3' end

Exo VI

3'-5' exonuclease; used when the nearest methyl group is toward the 5' end

MSH2/6

eukaryotic homologue of MutS; recognizes mismatches

MLH-PMS

eukaryotic homologue of MutL; possesses nicking activity

PCNA

increases processivity of polymerase during gap filling

DNA Glycosylase

removes a damaged base, leaving an abasic site

Oxo-G DNA Glycosylase

removes oxidized guanine

Uracil DNA Glycosylase

removes uracil from DNA

Apurinic Endonuclease (APE1)

cuts 5' to the abasic site

Exonuclease

removes the abasic site

DNA Polymerase

fills in the missing nucleotide

Ligase

seals the nick in the backbone

O6-methylG Methyltransferase (MGMT)

transfers methyl group from guanine to itself; enzyme is irreversibly inactivated

DNA Photolyase

activated by visible light; cleaves thymine dimers (T-T) to repair UV damage

UvrA

scans DNA for distortions; recruits UvrB

UvrB

opens helix around lesion and recruits UvrC

UvrC

endonuclease that cleaves 8 nt upstream and 4-5 nt downstream of lesion

UvrD Helicase

removes the excised ~14 nt DNA fragment

DNA Polymerase

fills in the gap

Ligase

seals the nick

TFIIH

binds at stalled RNA polymerase site

XPD / XPB

helicases that promote NER at transcription-blocking lesions

CSA / CSB

recognize stalled RNA polymerase and mediate TCR initiation

Pol IV / Pol V

low-fidelity polymerases that bypass DNA lesions by adding bases independent of base pairing

PCNA (ubiquitinated)

triggers polymerase switching to TLS polymerases

Pol η / Pol κ

non-mutagenic TLS polymerases; Pol η correctly inserts two A's opposite T-T dimers

ATM / ATR Kinases

phosphorylate H2AX at double-strand breaks

Swr1

chromatin remodeler promoting histone ejection

Ino80

chromatin remodeler aiding histone displacement

Tip60

histone acetyltransferase; opens chromatin and activates ATM via acetylation (positive feedback loop)

Ku70/80

bind to DSB ends

DNA-PKcs

kinase that activates Artemis

Artemis

endo/exonuclease that processes DNA ends for ligation

Pol μ / Pol λ

fill in missing nucleotides

Ligase IV

seals DNA ends

MRN Complex (Mre11-Rad50-Nbs1)

performs short-range resection; ATP-bound form active

CtIP

binds MRN; initiates resection with endonuclease activity

Mre11 / Nbs1 / Rad50

components of MRN complex for sensing and resection

CtIP

initiates resection in cooperation with MRN

Blm / Wrn

helicases aiding branch migration and dissolution (Wrn stabilizes telomeres)

Dna2 / Exo1

long-range resection nucleases

RPA

binds ssDNA to prevent secondary structures

Rad51 / RecA

promote strand invasion; coat ssDNA and search for homology

Brca2

loads Rad51 onto ssDNA by replacing RPA (6 at a time)

RuvA / RuvB / RuvC

recognize and process Holliday junctions (branch migration and resolution)

Top3

relieves supercoiling during dissolution by Blm

CDK-G1 Cyclin

phosphorylates Brca2 to inhibit HR

CDK-G2/S Cyclin

phosphorylates CtIP to promote HR

Brca2

active when unphosphorylated; inactive when phosphorylated

CtIP

active when phosphorylated

Ku70/80

promote NHEJ during G1 phase

Spo11

introduces DSBs during meiosis via covalent bond with 5' phosphate

Dmc1

works with Rad51 to promote strand invasion into homologous chromosome (leading to crossover)