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29 Cards in this Set

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Mismatch Repair

Endonuclease

(nickase) cleaves DNA bonds within DNA molecules

(nickase) cleaves DNA bonds within DNA molecules

Exonuclease

cleaves thenucleotides at the end of aDNA molecule, requires free3’ or 5’ –OH, works with ahelicase

cleaves thenucleotides at the end of aDNA molecule, requires free3’ or 5’ –OH, works with ahelicase

Mut H

- endonuclease that creates a nick on the new strand of DNA in MR


- binds the nearest GATCmethylated sites andcuts only non-methylated DNA



Intercalating agents



	
		
		Cause the addition of base pairs by
slipping between the bases in the template strand

Cause the addition of base pairs byslipping between the bases in the template strand

Uvr

genes for nucleotide excisionrepair - loss leads to UV sensitivity

Rad

genes for double-strand breakrepair - loss leads to radiationsensitivity

Mut

genes for mismatch repair -loss results in high mutation rate

OxoG

can be mispaired to A

O6-methyl G

can be mispaired to T


(BER)

Base-Excision Repair

one of two types of excision: acts on a single damaged nucleotide
(BER and DR)
1. DNA glycolysase recognizes and removes damaged base. 2 AP endonuclease recogs abasic site. 3. replacement via polymerase and ligase

one of two types of excision: acts on a single damaged nucleotide


(BER and DR)


1. DNA glycolysase recognizes and removes damaged base. 2 AP endonuclease recogs abasic site. 3. replacement via polymerase and ligase

Hydrolytic Reactions

-deamination of cytosine to uracil


-depurination leaves an abasic site



DNA Glycolisase

flips the damaged base to expose the damaged site that will be cleaved and removes it

flips the damaged base to expose the damaged site that will be cleaved and removes it

Damage Reversal (DR)

-mostly in bacteria only


-degrades protein after process (enzyme is methylated and site is demethylated)


-uses methyltransferase to transfer methyl group from one substrate.


-focus on O6-methylG transferase


-very efficient yet consuming because methylated enzyme is degraded (sacrifice an entire protein)

Trans-letion Synthesis (TLS)

- allows damage, not repair


-flexible but causes mutation


- Uniquitination triggers the switch to a trans-lesionpolymerase in mammalian cells


- In E. Coli, Pol IV and V come in a and replace the stalled polymerase at the fork and incorporate random bases.

RPA

(Replication protein A)


damage sensor: single stranded binding protein that binds DNA ahead of the polymerase at the rep fork--->>> recruits ATR which phosphorylates H2AX




keeps the DNA unwound for repair/replication

MRN

damage sensor: recognizes DNA double strand breaks--->>> Recruits ATM which phosphorylates H2AX

Swr1 and Ino80

-chromatin remodelers


-promote strand invasion byproviding access to the donor sequence

NHEJ

-error prone, fast, G1


-doesnt require homology


-rejoines 2 ends



Single Strand Annealing (SSA)

Alt-EJ

MRN-Ctip

endonuclease that initiates resection in HR


works with wrn helicase

Endonucleases that extends resection

Dna2 (endonuclease)


blm (3'-5' helicase)


exo1 (exonuclease)

Werner syndrome

Cancer predisposition- Telomeric instability- Premature aging




due to Wrn mutation

RecA/Rad51

binds to ssDNA, replaces RPA, forms a filament around ssDNA and probes for homology (needs more than 15bp), and drives strand invasion

Brca2

-subs RPA with rad51


-mutation responsible for breast cancer



RuvAB

promotes Holliday Junction migration in bacteria only




RUV A recognizes holliday junctions


Ruv B helicase promotes movement


Ruv C resolves Holliday Junctions by cleaving acrossthe Junction



Blm helicase & top3 isomerase

requires for HJ dissolution


helicase can revert recombination intermediates by displacing rad51




topoisomerase activity counteracts positivesupercoiling during dissolution by creating breaks in the DNA to resolve topological issues





CRISPR/Cas9

-used as a research tool


-Cas9 can be directed to ANY target sequence toinduce DSBs and improve gene targeting