Carlos de los Santos: TODAY’S SPEAKER
Dan Bogenhagen: DNA replica6on and repair in mitochondria
Bruce Demple*: Oxida6ve DNA damage; BER; oxida6ve stress responses
Miguel Garcia‐Diaz*: DNA replica6on fidelity; protein structure; gene regula6on in mitochondria
Arthur Grollman: Mutagenesis and molecular carcinogenesis (aristolochic acid); structural biology
Francis Johnson & Charles Iden: Synthesis, purifica6on and analysis of single‐lesion DNA molecules
Orlando Schärer: Mechanisms of mammalian NER; DNA interstrand crosslinks
Kate Dickman: DNA damage and renal disease
Mark Lukin: genera6on of site‐specific DNA lesions Masaaki Moriya: translesion DNA polymerases
Mamta Naidu: Radia6on biology & BER; heavy ion studies
Thomas Rosenquist: gene6cs of aristolochic acid toxicology
*Recruited through Consor6um for InterDisciplinary Environmental Research
New insights into NER recognition: When bulky & perturbing is not enough
4/17/12
Kwong-Ngai Hung Serge Smirnov David Cullinam Zhen Lin Jenifer Bohon Raphael Hazel Omar Armstrong Tanya Zaliznyak Smita Mohanty Mahmoud El-Katheeb Kegui Tian Freda Sansaricq Dmitry Zamyatkin Kimberly Conlon Monica McTigue
Arthur Grollman Francis Johnson Charles Iden Carlos Simmerling Orlando Scharer Miguel Garcia-Diaz Masaaki Moriya Mark Lukin
NCI, NIEHS
DNA Damage Rate < Repair Rate
Healthy Genome
DNA Damage Rate > Repair Rate
Sick Cell
Cancer Ageing Repair
Diseases
Bulky Adducts Alkylating Agents
Ionizing, UV
Radiation
Chemical Degradation
Endogenous (ROS, LPO)
Exog
enou
s En
doge
nous
DSB
SSB
AP
SBD
ICl
Cl
DNA Damage and Repair
dRN
NNH
N
O
O
OH
O
dR
OOH
OH
OH
AP Sites
OH
OHOH
dA(N6) or dG(N2)
Benzo[a]Pyrene
NO2
2-Nitrofluorene
PtNH3
NH3
dG(N7)
dG(N7)
cis-platinum
N
NHNH
N
O O
OO
dR dR
Cyclobutane TT dimer 6-4 Photoproducts
NER Lesions
N
N
N
N N
O
OH
dG(N2)H
N
N N
N
NH2
O
OH
OHH
5’,8-cyclo-dA
Acrolein
NER Recognition of Bulky Adducts
Structure of a RAD4/RAD23-CPD-DNA Complex
Min, J-H & Pavletich, N.P (2007) Nature 449, 570-576
GG-NER Resistant DNA Lesions
dG-N2 Adducts (AAF, 3ABA)
dA-N6 Adducts (ALII)
NO2 2-Nitrofluorene (2-NF)
NH2 2-Aminofluorene (2-AF)
NHAc 2-Acetylaminofluorene (2-AAF)
Aminofluorene
NO2
2-NF NHAc
2-AAF
NAcOH
N-hydroxy-2-AAF
CYP1A2 CYP1A2 XO
NAcOSO3H
N-SO4-2-AAF
NHOSO3H
N-SO4-2-AF
NH2
2-AF
NHOH
N-hydroxy-2-AF
NHOAc
N-Acetoxy-2-AF
SO4 transferase SO4
transferase O-Acetylase
DNA-Adducts
N, O-Acetyl-transferase
NH N
NHN
N
O
NH2
dR
dG-C8-AF
NAc N
NHN
N
O
NH2
dR
dG-C8-AAF
NHAcN
NHN
N
O
N
dR
H
dG-N2-AAF
DNA-Adducts
dG-N2-AAF
• Is mutagenic: DNA-Pol I inserts dAMP, suggesting G → T mutations in bacteria
• It blocks mammalian Pol α activity in vitro, but TLS polymerases η and κ can bypass the lesion
• It induces G → T transversions in mammalian cells
• NER processing of dG-N2-AAF needs full study
• Is a minor guanine adduct
Mutation Research 442 1999. 9–18
• dG-N2-AAF is a persistent DNA lesion
NMR Constraints
Damaged DNA Sample
NMR Studies
Restrained MD
Structure Analysis and Validation
5’-d(C1 G2 T3 A4 C5 X6 C7 A8 T9 G10 C11)
d(G22 C21 A20 T19 G18 C17 G16 T15 A14 C13 G12)-5’
A & B, AAFH4 to G6H1’ and T19H1’ C & D, AAFH5 to G6H1’ and T19H1’
D2O NOESY
5’
3’ H1’
H1’
H6
H8
Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
5’-d(C1 G2 T3 A4 C5 X6 C7 A8 T9 G10 C11)
d(G22 C21 A20 T19 G18 C17 G16 T15 A14 C13 G12)-5’
H2O NOESY
C1’ C1’
T A
C G C1’
C1’
Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
5’
5’
5’
5’
G6 G6
C17 C17
Refined MD Structure
Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
Space Filling Models Major Groove
5’
3’
90°
Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
Minor Groove
5’
3’
90°
Space Filling Models
Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
Minor groove width (Å) 2.0-4.7 (5.9)
Minor groove depth (Å) 5.6-7.2 (4.6)
BP propeller twist (°) 1-34 (<3.7)
Base pair buckle (°) 2-18 (0)
AAF Exposed Surface 17%
T15C5’ A8C3’
A4C5’ T19C3’
Structural Parameters
Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
Duplex Stability
45°C 15°C
20°C 50°C
25°C 60°C
14.0 13.0 12.0 11.0 10.0 PPM
30°C
14.0 13.0 12.0 11.0 10.0 PPM
65°C
10°C
T3,T9
T15
T19,G6
G2
G10,G16
G18 G6(N2H)
35°C
G6 G16
G18 G6(N2H)
Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
30 50 70
Temperature (°C)
OD
260
0
0.5
1
1.5
2
1.7
1.9
2.1
2.3
(1/T
m) x
10-
2 (1
/°K)
-14 -13.5 -13 -12.5
ln(Ct/4)
Tm (°C) ∆H0
(kCal/Mol) ∆S0
(Cal/Mol°K) ∆G0
25°C (kCal/Mol)
∆G037°C
(kCal/Mol) AAF-Duplex 60.5 -93 ± 9 -262 ± 20 -14.9 ± 0.3 -11.8 ± 0.3 Control Duplex 54.3 -98 ± 11 -285 ± 23 -13.1 ± 0.3 -9.6 ± 0.3
dG-N2-AAF Duplex Stability
Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
Adopts a regular helical structure with WC alignments
The lesion increases the duplex thermal and thermodynamics stability
The AAF moiety resides in the minor groove without protruding out of the helix boundaries
The minor groove deepens and narrows, sheltering AAF from water exposure
dG-N2-AAF Duplex
Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
1 2 3 4 5
NER Repair of dG-N2-AAF
Lane 1: Hela whole cell extracts
Lane 2: Hela whole cell extracts + plasmid DNA containing a (1,3)-N7-N7 cis-Pt adduct
Lane 3-5: Three different preparations of Hela whole cell extracts + plasmid DNA containing a dG-N2-AAF lesion
NER Recognition of Bulky Adducts
Some bulky dG-(N2) adducts of defined topology cause minimal structural perturbations and increase duplex
stability.
Thus, they evade GG-NER processing, persist in cellular DNA and are likely to
have a prevalent role in chemical mutagenesis and disease.
Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
Cosman, et al. (1992) Proc. Natl. Acad. Sci. USA 89, 1914-1918. de los Santos, et al. (1992) Biochemistry. 31, 5245-5252. Zaliznyak, et al. (2006) Chem. Res. Toxicol. 19, 745-752.
(+) and (-) trans-benzo[a]pyrene-N2-dG Lesions AAF-N2-dG Lesions
dG-N2-AAF dG-N2-3ABA
Topology of helix-stabilizing lesions
3-Nitrobenzanthrone
O
NO2
3NBA
Present in coal fly ash, diesel engine exhausts and air particulate matter
Strong mammalian mutagen
Causes DSB and induces micronuclei formation in human cells
Causes squamous cell lung tumors in rats.
Epidemiologically linked to lung cancer in humans
N
NH
N
N
O
NH
O
NH2dR
O
NO2
O
NH2
N
N
N
N
dR
NH
O
NH2
N
O
N
NH
N
N
O
dRNH2
H
O
NHOH
O
NH+
O
NHOR
NAT1NAT2
SULT1A1SULT1A2
NQO1 NQO1CYPOR CYPOR
CYP1A1CYP1A2
SOLVOLYSIS
DNA DNA
DNA
3NBA 3ABA
dG(N2)-3ABA
dG(C8)-ABA dA(N6)-3ABA1
3 4
6
7
810
N
N
N
N
O
O
OH
OHNH
O
NO2
NO2
N
N
N
N
O
O
OH
DMTONH
O
NO2
NO2
N
N
N
N
O
O
O
DMTONH
O
NO2
NO2
PO
CN
N CH3
CH3
CH3
CH3
N
N
N
N
O
O
TBDMSO
TBDMSONH
O
NO2
NO2
N
NH
N
N
O
O
OH
OHNH
O
NO2
a.
b.
c. d.
Complexmixture ofproducts
c.
1 2
3 4 5
Scheme 1. Synthesis of protected dG(N2)-3ABA phosphoramidite
a. 1M tetrabutylammonium fluoride, THF; b. Triethylamine trihydrofluoride:triethylamine:DMF (4:3:6);c. Dimethoxytrityl chloride, pyridine; d. Cyanoethoxy diisopropylamino chlorophosphine.
Lukin, et al. (2011) J. Nucleic Acids Epub 2011 Nov 17.
N
NH
N
N
O
O
O
ONH
O
NH2
PO
O
P
OH
OO
OH
7
DNA
DNA
N
N
N
N
O
O
O
ONH
O
NO2
NO2
PO
O
P
OH
OO
OH
6
DNA
DNA
a. , b.
Scheme 2. Deprotection and nitro reduction of dG(N2)-NBA in oligonucleotides
a.1M tetrabutylammonium fluoride, THF; b. 1M Na2S.
G1 T2 A3 T4 X5 C6 C7 G8 G9 C10 A11 T12 A13 C14
Lukin, et al. (2011) J. Nucleic Acids Epub 2011 Nov 17.
dG-(N2)-3ABA Duplex
2.88
2.90
2.92
2.94
2.96
2.98
3.00
3.02
-13.5 -13.0 -12.5 -12.0 -11.5 -11.0
ln (C)
1000
/Tm
(°C
-1)
2.88
2.90
2.92
2.94
2.96
2.98
3.00
3.02
-13.5 -13.0 -12.5 -12.0 -11.5 -11.0
ln (C)
1000
/Tm
(°C
-1)
2.88
2.90
2.92
2.94
2.96
2.98
3.00
3.02
-13.5 -13.0 -12.5 -12.0 -11.5 -11.0
2.88
2.90
2.92
2.94
2.96
2.98
3.00
3.02
-13.5 -13.0 -12.5 -12.0 -11.5 -11.0
ln (C)
1000
/Tm
(°C
-1)
0.8
1.0
1.2
1.4
1.6
1.8
35 45 55 65 75 85
Temp (°C)AU
260
0.8
1.0
1.2
1.4
1.6
1.8
35 45 55 65 75 85
Temp (°C)AU
260
0.8
1.0
1.2
1.4
1.6
1.8
35 45 55 65 75 85
0.8
1.0
1.2
1.4
1.6
1.8
35 45 55 65 75 85
Temp (°C)AU
260
dG-(N2)-3ABA Duplex
Control Duplex
Control duplex
dG(2N)-ABA duplex -1.5
ΔΔG˚37/lesion, kcal/mol
-14.9 ± 0.3
-17.9 ± 0.8
ΔG˚37, kcal/mol
-18.2 ± 0.5
-21 ± 1.1
ΔG˚25, kcal/mol
-267 ± 11
-252 ± 24
ΔS˚25, cal/mol·K
-98 ± 4
-95 ± 8
ΔH˚25, kcal/mol
dG-(N2)-3ABA Duplex
dG-N2-AAF dG-N2-3ABA
NER Recognition of Bulky Adducts
Aristolochic Acids
Aristolochia elegans
O
O
O
OH
NO2
X
AAII : X = HAAI : X = OMeAAI : X = OMe
AAII : X = H
Aristolochia clematitis
AA-I is nephrotoxic: causes interstitial fibrosis with progression to end-stage renal disease
Many patients develop urothelial cancer
Both AA-I & AA-II are genotoxic, mostly leading to AT → TA transversions
The National Toxicology Program listed the AAs as established human carcinogens
AA-dA adducts persist in chromosomal DNA for several years
Aristolochic Acids
NH
N N
N
dRib
O
NH
O
O
O
NH
X
NHN
N
N
dRib
O
O
O
NH
X
N
O
O
O
OH
NO2
X
O
O
O
NHOH
X
XO, NQO1, CYP1A2, CYP1A1,
O-acetylation SO4
transferase
O
O
O
N
X
+
AL-dG
AL-dA
dA-(N6)-ALII Duplex
C1 G2 T3 A4 C5 X6 C7 A8 T9 G10 C11 G22 C21 A20 T19 G18 T17 G16 T15 A14 C13 G12
O
N
N N
N
N H
O
O
O
N H
T B S O
T B S O
O
O
O
N H
Br
BH O
N
N N
N
N H
O
O
O
N H
D M T O
O P
O C E
N
Attaluri et al. (2010) Nucleic Acids Res., 38, 339-352.
N
N N
N
N H
N H
O
O
O 2
4
8
9 10
11
dR
dA-(N6)-ALII Duplex
A) AAH11-AAH10 B) AAH10-AAH9 C) AAH8-AAH9
Lukin et al (2012) Nucleic Acids Res. 2012 40, 2759-2770.
D2O NOESY
dA-(N6)-ALII Duplex
6.5
6.0
5.5
ppm
C1
G2
T3
A4
C5
A6
C7
A8
T9
G10C11
C7*
C1*
C11*
8.5 8.0 7.5 7.0 ppm
6.5
6.0
5.5
ppm
G12
C13
A14
T15
G16
T17
G18
T19
A20
G22
C13* C21
C21*
5’
3’ H1’
H1’
H6
H8
Lukin et al (2012) Nucleic Acids Res. 2012 40, 2759-2770.
C1 G2 T3 A4 C5 X6 C7 A8 T9 G10 C11
G22 C21 A20 T19 G18 T17 G16 T15 A14 C13 G12
H2O NOESY
G2 A20 A4 G18 G16 A8 A14
G10
Ter
dA-(N6)-ALII Duplex
C1’ C1’
T A
C G C1’
C1’
Lukin et al (2012) Nucleic Acids Res. 2012 40, 2759-2770.
N
N
O
O
H
CH3 X6•T17
N
N
O
O dRib
CH3
N
NN
N
N
dRib
NO
OO
H
H H
N
N
O
O dRib
CH3
N
NN
N
N
dRib
NO
OO
H
H
H
C1 G2 T3 A4 C5 X6 C7 A8 T9 G10 C11
G22 C21 A20 T19 G18 T17 G16 T15 A14 C13 G12
dA-(N6)-ALII Duplex
Lukin et al (2012) Nucleic Acids Res. 2012 40, 2759-2770.
H5’ H5’’
Selective H5” thymine deuteration
dA-(N6)-ALII Duplex
Lukin & de los Santos (2010) Nucleos. Nucleot. Nucleic Acids., 29, 562-573.
dA-(N6)-ALII Duplex
Lukin et al (2012) Nucleic Acids Res. 2012 40, 2759-2770.
-9.5 -11.9 -203 C - A - G 0.8
-8.7 -11.0 -190 C - X - G
-10.5 -13.1 -219 T - A - G 1.2
-9.3 -11.2 -157 T - X - G
-12.7 -15.9 -273 C - A - C 2.5
-10.2 -12.7 -211 C - X - C
42.9
39.9
46.7
43.1
51.6
45.2
Tm (°C) Duplex Sequence
-72
-68
-78
-58
-98
-76
ΔH0
(Kcal/mol) ΔS0
(cal/mol °K) ΔG0
25°C (Kcal/mol)
ΔG037°C
(Kcal/mol) ΔΔG0
37°C (Kcal/mol)
dA-(N6)-ALII causes duplex destabilization
Lukin et al (2012) Nucleic Acids Res. 2012 40, 2759-2770.
3.11
3.13
3.15
3.17
3.19
3.21
3.23
-1 4 -13.5 -13 -1 2.5 -12 -11.53.
123.
143.
143.
163.
183.
20-14.0 -13.5 -13.0 -12.5 -12.0
ln Ct10
00/T
m (K
-1)
CXC
CXG
TXG
The AL-II-dA lesion reduces the stability of the duplex
Duplex structure is perturbed at the lesion site. The AL-II moiety intercalates in the opposing strand
displacing the partner thymine in the major groove
In spite of these changes, the duplex adopts a single conformation that is stabilized mainly by hydrophobic
interactions at lesion site
Lukin et al (2012) Nucleic Acids Res. 2012 40, 2759-2770.
NER Recognition of Bulky Adducts
dA-(N6)-AL-II adduct levels are elevated in GG-NER and transcription-coupled NER deficient cells, but
not in XPC cell lines lacking GG-NER.
In vitro, plasmids containing a single dA-(N6)-AL-II adduct are resistant to the early recognition and
incision steps of NER.
Additionally, XPC-RAD23B, the GG-NER damage sensor, failed to specifically bind to dA-(N6)-AL-II
adducts. Sidorenko et al (2012) Nucleic Acids Res. 40, 2494-2505
Recognition of bulky lesions by GG-NER seems less efficient than initially thought
Topology of duplex stabilizing lesions (AAF-N2-dG, 3ABA-N2-dG)
Stability threshold
Other factors