DNA REPAIR

DNA repair
DNA repair is a cellular mechanism to
correct damage to DNA before it
becomes fixed as a mutation or
chromosomal aberration, which may
lead to deleterious results such as cell
death or tumorigenesis. Mechanism of
DNA repair is important for reducing
the risk of cancer as well as
developing more effective cancer
therapies.

DNA REPAIR
perbaikan DNA adalah mekanisme seluler
untuk memperbaiki kerusakan pada DNA
sebelum menjadi tetap sebagai mutasi atau
kelainan kromosom, yang dapat
mengakibatkan hasil yang berbahaya seperti
kematian sel atau tumorigenesis.Mekanisme
perbaikan DNA sangat penting untuk
mengurangi risiko kanker serta
mengembangkan terapi kanker yang lebih
efektif.

MUTASI
Mutasi terbagi atas:
Mutasi spontan
Mutasi induksi

Types of Damage Repair

Photolyase
De-alkylation proteins (not catalytic)

Base Excision Repair

Nucleotide Excision Repair (GG and TC)
Mismatch Repair

Error-prone Repair or SOS

Double Strand Break Repair

Types of Damage Repair

Photolyase
De-alkilasi protein (tidak katalitik)
Base eksisi Perbaikan
Nukleotida eksisi Perbaikan (GG dan TC)
Ketidaksesuaian Perbaikan
Rawan kesalahan Perbaikan atau SOS
Double Strand Break Perbaikan

Repairing Damaged
Bases

Damaged bases can be repaired by

several mechanisms:
Direct chemical reversal
Excision Repair. There are three modes
of excision repair, each of which employs
specialized sets of enzymes.
Base Excision Repair (BER)
Nucleotide Excision Repair (NER)
Mismatch Repair (MMR)

Repairing Damge Bases

Basis Rusak dapat diperbaiki melalui
beberapa mekanisme:
Langsung kimia pembalikan
Perbaikan eksisi. Ada tiga mode perbaikan
eksisi, masing-masing yang mempekerjakan
set khusus enzim.
Base eksisi Perbaikan (BER)
Nukleotida eksisi Perbaikan (APM)
Perbaikan ketidaksesuaian (MMR)

Direct repair
Observation:
UVPhotoreactivation

Requires(membutuhkan) DNA photolyases

requires visible light (memerlukan cahaya) at 300
500 nm
light repair
Contrast: dark repair (BER, NER, mismatch repair)
=Kontras: perbaikan gelap (BER, APM, perbaikan
mismatch)

DNA photolyases
Structure
Generally contain 2 chromophores
Chromophore No. 1: always FADH Chromophore No. 2: folate (in E. coli and yeast)
N5,N10-methenyltetrahydrofolylpolyglutamate

Function
bind to pyrimidine dimers
resolve pyrimidine dimers into original bases

DNA PHOTOLYASES
Struktur
- Umumnya mengandung 2 chromophores
- Kromofor No 1: selalu FADH
- Kromofor No 2:folat(dalam E. coli dan ragi)
N5,N10-methenyltetrahydrofolylpolyglutamate
Fungsi
- mengikat untuk pirimidin dimer
- menyelesaikan dimer pirimidin ke basis asli

UV-responsive photolyases

Direct reversal (de-alkylating

proteins)

Base Excision Repair

not restricted to a short time post replication
similar in most organisms (bacteria
mammals)
recognizes abnormal bases in the DNA
requires four enzymes
1.DNA glycosylases
2.AP-endonucleases
3.DNA polymerase I
4.DNA ligase

Base Excision(memotong)
Repair
tidak terbatas pada replikasi posting waktu
singkat
serupa di sebagian besar
organisme (bakteri - mamalia)
mengakui basis abnormal dalam DNA
memerlukan empat enzim
- DNA glycosylases
- AP-endonuklease
- DNA polimerase I
- DNA ligase

DNA glycosylases
Relatively small
P
enzymes (20 30 KDa)
Recognize abnormal bases
deaminated bases
alkylated bases

Remove base via cleavage

at the glycosidic bond
between the deoxyribose
and the base
Cleavage creates apurinic
and apyrimidinic (AP sites)

G P
O

Before

After

DNA glycosylases
Relatif kecil
P
enzim (20 - 30 KDa)
Kenali abnormal basis
P
- deaminated basis
- dialkilasi basis
Hapus dasar melalui pemb
elahan di ikatan glikosidik a
ntara deoksiribosa&basa
Pembelahan menciptakan
apurinic dan apyrimidinic (
AP situs)

G P
O

Before

After

AP-endonucleases
5 P P P P P P P
recognize AP-sites
A G G C A G C
cleave phosphodiester
bonds near the AP site
T C C
T C G
and generate a 5
3 P P P P P P P
phosphate and 3AP endonuclease
hydroxyl
In E. coli this enzyme
also has 3-5
P P P P P P P
exonuclease activity
A G G C A G C
The 3-OH functions as
C
T
C G
a primer
5
P

AP-endonucleases
5 P P P P P P P
mengakui AP-situs
A G G C A G C
bersatu fosfodiester obl
igasi dekat lokasi AP d
T C C
T C G
an menghasilkan 5 '-P
3 P P P P P P P
dan 3'-hidroksil
AP endonuclease
Pada E.
coli enzim ini juga mem
iliki aktivitas exonuclea P P P P P P P
se 3'-5
A G G C A G C
The 3'C
T
C G
OH berfungsi sebagai p
5
P P
rimer
3 P P

Base Excision Repair

The steps of BER:
1. removal of the damaged base (estimated to occur some 20,000
times a day in each cell in our body!) by a DNA glycosylase. We
have at least 8 genes encoding different DNA glycosylases each
enzyme responsible for identifying and removing a specific kind
of base damage.
2. removal of its deoxyribose phosphate in the backbone,
producing a gap. We have two genes encoding enzymes with
this function.
3. replacement with the correct nucleotide. This relies on DNA
polymerase, one of at least 11 DNA polymerases encoded by
our genes.
4. ligation of the break in the strand. Two enzymes are known that
can do this; both require ATP to provide the needed energy.

BASE EXCISION REPAIR

Langkah-langkah BER:
1. Penghapusan basis rusak (diperkirakan terjadi sekitar 20.000 kali
sehari di setiap sel dalam tubuh kita!) oleh glycosylase DNA. Kami
memiliki setidaknya 8 gen pengkodeanDNA yang berbeda setiap
glycosylases enzim yang bertanggung jawab untuk mengidentifikasi
dan menghapus jenis tertentu kerusakan dasar.
2. penghapusan deoksiribosa fosfat di tulang punggung, menghasilkan
kesenjangan.Kami memiliki dua gen enzim pengkodean dengan fungsi ini.
3. penggantian dengan nukleotida yang benar. Hal ini bergantung
pada DNA polimerase,salah satu dari sedikitnya 11 polimerase
DNA dikode oleh gen kita.
4. ligasi istirahat dalam rantai tersebut. Dua enzim
yang dikenal yang dapat melakukan hal ini, keduanya membutuhkan
ATP untuk menyediakan energi yang dibutuhkan

Base Excision Repair

Nucleotide Excision Repair

Recognizes large distortions in the DNA
structure
Repairs UV-damaged DNA
Cleaves two phosphodiester
Generally generates fragments of 12 to 13
nucleotides
Requires four different enzymes

1.Exonuclease
2.DNA helicase
3.DNA polymerase
4.DNA ligase

 Mengenali besar distorsi dalam struktur

DNA
UV-perbaikan kerusakan DNA
Memotong dua fosfodiester
Umumnya menghasilkan fragmen dari 12 sampai
13 nukleotida
Memerlukan empat berbeda enzim
- Exonuclease
- DNA helikase
- DNA polimerase
- DNA ligase

Nucleotide Excision Repair

(E.coli)
Enzyme

Exinuclease

DNA helicase
DNA
polymerase
DNA ligase

Protein

Function

UvrA (MW= 104,000)

scans DNA, binds to UvrB

UvrB (MW = 78,000)

scanner; binds DNA cleaves

phosphate bond at 3' end, 5
positions downstream of lesion

UvrC (MW = 68,000)

binds UvrB & DNA cleaves

phosphate bond at 5' end, 8
positions upstream of lesion

UvrD
DNA polymerase I
(= PolA )
Lig

removes DNA fragment

fills emerging gap
seal nick

Nucleotide Excision Repair

(E.coli)

Nucleotide Excision Repair

in E. coli
Mechanism
The (UvrA)2:UvrB complex
scans DNA
UvrA dimer dissociates from
pryimidine dimer. UvrB binds
DNA and cuts at 3 end.
UvrC associates with UvrB and
cuts DNA at 5 end of the P
pyrimidine dimer
UvrD DNA helicase removes
the DNA fragment
DNA polymerase I fills the gap
DNA ligase seals the remaining
nick.

UvrA
UvrA

UvrB

exinuclease
P

ATP
P

P
OH
DNA pol. I

UvrD DNA
helicase
P

DNA ligase

Nucleotide Excision Repair

in E. coli
Mekanisme
The (UvrA) 2: kompleks UvrB
DNA scan
Dimer UvrA memisahkan dari d
imer pryimidine. UvrB mengikat
DNA dan luka di akhir 3'.
UvrC asosiasi dengan UvrB &
DNA luka di ujung 5 'dari P
dimer pirimidin
UvrD helikase DNA menghilan
gkan fragmen DNA
DNA polimerase Saya mengisi
kesenjangan
DNA ligase segel nick tersisa.

UvrA
UvrA

UvrB

exinuclease
P

ATP
P

P
OH
DNA pol. I

UvrD DNA
helicase
P

DNA ligase

Nucleotide Excision Repair

(Global Genome Repair -Humans)

Nucleotide Excision Repair

(Transcription Coupled -Humans)

Genes Encoding Enzymes of Mismatch Repair

MISMATCH

Mismatch repair

Mismatch repair in E. coli

Scenario 1
Mismatch is at the 5 end of
cleavage site
Unmethylated DNA is
unwound via DNA helicase II

The 3-5 exonuclease activity

of exonuclease I or exo X
degrades DNA through the
mismatch

5
3

ATP
ADP+Pi
5
3

DNA polymerase III

synthesizes the new DNA
strand
DNA ligase closes the
remaining nick.

CH3

5
3

CH3

CH3

CH3

MutS-MutL
DNA helicase II
exonuclease I
or
exonuclease X

3
5

CH3

3
5
DNA polymerase III
SSBs
CH3

3
5

Mismatch repair in E. coli

Scenario 1

Ketidaksesuaian adalah pada

ujung 5 'situs pembelahan
Unmethylated DNA dibatalkan
melalui DNA helikase II
The 3'5 'exonuclease kegiatan exon
uclease I atau exo X DNA men
urunkan melalui
ketidakcocokan
DNA polimerase III sintesis unt
ai DNA baru
DNA ligase menutup nick tersi
sa.

5
3

CH3

ATP
ADP+Pi
5
3

5
3

CH3

CH3

CH3

MutS-MutL
DNA helicase II
exonuclease I
or
exonuclease X

3
5

CH3

3
5
DNA polymerase III
SSBs
CH3

3
5

Mismatch repair in E. coli

Scenario 2
Mismatch is at the 3 end of
cleavage site
Unmethylated DNA is
unwound via DNA helicase II

The 5-3 exonuclease activity

of exonuclease VII or RecJ
nuclease degrades DNA
through the mismatch

CH3

5
3

ATP
ADP+Pi
5
3

DNA polymerase III

synthesizes the new DNA
strand.
DNA ligase closes the
remaining nick.

5
3

CH3

CH3

CH3

MutS-MutL
DNA helicase II
exonuclease VII
or
RecJ nuclease

3
5

CH3

3
5
DNA polymerase III
SSBs
CH3

3
5

Mismatch repair in E. coli

Scenario 2

Ketidaksesuaian adalah pada

ujung 3 'situs pembelahan
Unmethylated DNA dibatalkan
melalui DNA helikase II
The 5'3 'exonuclease kegiatan exon
uclease VII atau RecJ nukleas
e DNA menurunkanmelalui ket
idakcocokan
DNA polimerase III sintesis unt
ai DNA baru.
DNA ligase menutup nick tersi
sa.

CH3

5
3

ATP
ADP+Pi
5
3

5
3

CH3

CH3

CH3

MutS-MutL
DNA helicase II
exonuclease VII
or
RecJ nuclease

3
5

CH3

3
5
DNA polymerase III
SSBs
CH3

3
5

SOS Response
SOS repair occurs when cells are
overwhelmed by UV damage - this allows
the cell to survive but at the cost of
mutagenesis.
SOS response only triggered when
other repair systems are overwhelmed
by amount of damage so that unrepaired
DNA accumulates in the cell.

SOS RESPONSE
SOS perbaikan terjadi ketika selsel kewalahan oleh kerusakan UV - ini me
mungkinkansel untuk bertahan hidup tapi
pada biaya mutagenesis.
SOS respon hanya dipicu ketika sistem pe
rbaikan lainnya kewalahan
oleh jumlahkerusakan DNA diperbaiki sehi
ngga terakumulasi dalam sel.

Error-prone repair (SOS)

Activated upon:
severe DNA damage
disruption of DNA replication

SOS-response

Inaccurate repair mechanism

Requires at least 14 proteins in E. coli
Din proteins (damage induced)
Rec poteins (recombination)
Umu proteins (UV-mutagenesis)
Uvr proteins (UV-resistance)
Others: SulA, HimA, Ssb, and PolB

Error-prone repair (SOS)

Diaktifkan pada:
parah kerusakan DNA
gangguan replikasi DNA
"SOS-respon
Tidak akurat perbaikan mekanisme
Memerlukan setidaknya 14 protein dalam E. coli
Din protein (kerusakan induksi)
Rec poteins (rekombinasi)
Umu protein (UV-mutagenesis)
UVR protein (UV-hambatan)
Lainnya: Sula, Himawan, SSB, dan PolB

Error Prone Bypass (E. coli)

Double Breaks Strand

DSB Repair Double-strand breaks (DSBs)
are perhaps the most serious form of
DNA damage because they pose
problems for transcription, replication,
and chromosome segregation. Damage
of this type is caused by a variety of
sources including exogenous agents
such as ionizing radiation, genotoxic
chemicals, and mechanical stress on the
chromosomes.

Double Breaks Strand

DSB Perbaikan istirahat Double-untai
(DSBs) mungkin adalah bentuk paling
serius kerusakan DNA karena mereka
menimbulkan masalah bagi transkripsi, re
plikasi, dansegregasi kromosom. Kerusak
an jenis ini disebabkan oleh berbagai sum
ber termasukagen eksogen seperti radiasi
pengion, bahan kimia genotoksik, dan
stres mekanispada kromosom.

THANKS.