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Electrons and DNA: From Electron Attachment to DNA Strand Breaks. Michael Sevilla Chemistry Department Oakland University. What are the mechanisms of electrons reaction with DNA?. e-. e-. DNA and Electrons. - PowerPoint PPT Presentation
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Electrons and DNA: From Electron Attachment to DNA Strand Breaks
Michael SevillaChemistry DepartmentOakland University
What are the mechanisms of electrons reaction with DNA?
DNA and Electrons
• A variety of studies show that aqueous electrons add to the DNA bases and do not cause strand breaks.
• The base anion radicals undergo protonation reactions.
• Only nonsolvated electrons with kinetic energy (LEE) cause DNA strand breaks.
• At low temperatures electron in DNA are stable for long times.
-5
-3
-1
1
3
5
7
9
11
0 2 4 6 8 10 12 14
D (bp)
log 1
0(k)
(Å-1)
0.75
0.92
1.4
2.8
Vacuum
pdIdCpdIdC
DNA (salmon sperm)
pdAdTpdAdT
Electron Tunneling Decay Constant in DNA at 77 K
k = 1011exp(-D)
Z Cai and M Sevilla, in "Topics in Current Chemistry 237: Long Range Transfer in DNA II", Gary Shuster, Ed., Springer-Verlag, pages 103-128, 2004 .
DNA irradiation Studies
Irradiate hydrated DNA at 77K in frozen solutions • Direct Ionization of DNA results• Identify initial radicals by Electron Spin Resonance
Spectroscopy
Ionizing radiationDNA•+ + DNA•–DNA
Oxidative path Reductive path
"The Chemical Consequences of Radiation Damage to DNA" D. Becker and M. D. Sevilla, in Advances in Radiation Biology, Vol.17, (J. Lett, Ed.) Academic Press, 121-180 (1993).
RADICAL COMPOSITION (-irradiated DNA) ESR Spectra
• The composition of DNA radicals (77 K) is ca.:
• 25% (C-•) C(N3)H• • 25% T-•• 40% G+•• 10% Sugar•All to ±5%
C(N3)H•
Effect of scavengers on G-values
L. I. Shukla, R. Pazdro, D. Becker and M. D. Sevilla, Radiation Research: Vol. 163, 59-602 (2005).
Sug•
Oxidation pathway: formation of neutral sugar radical(s) from
sugar cation radical(s)
• Deprotonation from C1’, (C2’), C3’, C4’, C5’ may occur.
•
CH2 O BHH
HO
H
O
•CH2 O B
HH
HO
H
O
H+ + BH+
B+ 1'
2'3'
4'
5'
L. I. Shukla, R Pazdro, D Becker and M D Sevilla, RAD. RES.163, 591–602 (2005)
How do electrons damage DNA?Clues from
Ion Beam Irradiation of DNA
ca. 100 MeV/nucleon
O+8, Ar+18, Kr+36, Xe+54
D Becker, A Bryant-Friedrich, C Trzasko and M D Sevilla, Rad Res 160, 174 (2003)
PARTRAC Calculations, Hauptner et al (2006)
Cross Section of Heavy Ion Track Cross Section of Heavy Ion Track
Aloke Chatterjee and John Magee, J. Phys. Chem. Vol. 84, 3629-3536 (1980)
High Yields of Sugar radicals found in ion-beam irradiated DNA
D. Becker, A. Bryant-Friedrich, C. Trzasko, and M. D. Sevilla, Radiation Research, 160, 174-185 (2003) M. Bowman, D.Becker, M. D. Sevilla and J. Zimbrick, Radiation Research: Vol. 163, 447-454 (2005).
Excited States Important?
Yields of Sugar Radicals Increased in core of ion beam
irradiated DNA
● Sugar Radical Yield per Joule in track core
more than in the penumbra.
● New sugar phosphate species found in ion beam irradiated DNA
D. Becker, A. Bryant-Friedrich, C. Trzasko, and M. D. Sevilla, Radiation Research, 160, 174-185 (2003)
Ar ion Irradiated DNAPhosphoryl radicals - strand break radical(s)QuickTime™ and aGraphics decompressorare needed to see this picture.
|||
-0.022
-0.017
-0.012
-0.007
-0.002
0.003
0.008
0 100 200 300 400 500 600 700 800 900 1000
ROPO2• –
8
A
B
20.0 mT
CH2
O B
HH
HO
OPH
O–
O
• •
CH2O B
HH
HO
O
P
H
O–
O
2nd Strand Break radical found in ion beam irradiated DNA
N• from DNA
Simulation using theoretical spectral
parameters
BaseO
H
HH
HH
OPO
O-
O
•
C3’dephos●
LEE Induced Strand Scission + e
–
O CH2
baseO
O
P O–
O
–O
R
2 –
O CH2
baseO
–O
O CH2
baseO
A B
•
+ +•
ROPO2–• C3'
dephos
O–
R
P O–
O
O
R
P O–
O
O
O CH2
baseO
O
R
P O–
O
O•
dry
(5%) (95%)
Path B bond scissionPath A bond scissionLEE
D. Becker, A. Bryant-Friedrich, C. Trzasko, and M. D. Sevilla, Radiation Research, 160, 174-185 (2003)
What about Excited states?• We know excitation of DNA holes forms sugar
radicals
Visible excitation converts G•+ to Sugar Radicals
A Adhikary, S Collins, D Khanduri, and M D Sevilla, JPC B 2007, 111, 7415-7421 A Adhikary, A Kumar and M D Sevilla, Rad Res 2006 165, 479–484
O
ROCH2
H
RO H
H
G
H
1'
2'3'4'
5'
•
LEE Reaction with DNA:Strand Break Formation
• LEE capture at the base or the sugar phosphate backbone?
• What energies are needed?
• Are excited states involved?
B. Boudaiffa, P. Cloutier, D. Hunting, M. A. Huels, L. Sanche,
Science 2000, 287, 1658
F. Martin, P.D. Burrow, Z. Cai, P. Cloutier, D.J. Hunting, L. Sanche, Phys. Rev. Lett. 93, 068101-1 (2004)
DNA Strand break induced by low energy electrons
DNADNA
Modeling the LEE Induced DNA Strand Break
• Li, X.; Sevilla, M. D.; Sanche, L.; J. Am. Chem. Soc., 2003, 125, 13668
Sugar-Phosphate-Sugar model
-30.0
-20.0
-10.0
0.0
10.0
20.0
30.0
40.0
50.0
60.0
1.00 1.20 1.40 1.60 1.80 2.00 2.20 2.40 2.60 2.80
C-O distance (Å)
Re
lati
ve
E (
kc
al/m
ole
)
3'C-O: neutral
5'C-O: anion
5'C-O: neutral
3'C-O: anion
The Potential Energy Surfaces
DNADNA
Basis set dependence of Spin Distribution
3-21G(d) 6-31G(d) 6-31+G(d)
Xifeng Li and Michael D. Sevilla, in Theoretical Treatment of the Interaction of Radiation with Biological Systems. J. R. Sabin and E. Brandas, Eds., Advances in Quantum Chemistry, Elsevier, Volume 52, 59-88 (2007).
New DFT Calculations on 5’-dTMPH Anion Radical
What about the vertical surface?A. Kumar; M. Sevilla, J. Phys. Chem. B 2007, 111, 5464-5474
Recent Previous Work : J. Simons, Acc. Chem. Res. 2006, 39, 772-779 Bao, X.; Wang, J.; Gu, J.; Leszczynski, J. Proc. Nat. Acad. Sci.U.S.A. 2006, 103, 5658. Gu, J.; Wang, J.; Leszczynski, J. J. Am. Chem. Soc. 2006, 128,9322.
Adiabatic Barriers of 7 kcal/mol for 3’- C-O bond and 14 kcal/mol for 5’-C-O bond
LEE Induced strand break in 5'-dTMPH as a model: Vertical or Adiabatic pathways?
vertical
adiabatic
B3LYP/6-31G* calculated adiabatic and vertical potential surfaces (PES) of C5'-O5' bond dissociation of 5'-dTMPH radical anion. The singly occupied molecular orbital (SOMO) is also shown
1.45 1.5 1.6 1.7 1.8 1.9 2.0
B3LYP/6-31G*
kcal/mol
26.0
24.0
22.0
20.0
18.0
16.0
14.0
12.0
10.0
8.0
6.0
4.0
2.0
0.0
-8.0
C5'-O5' (Å)
Vertical PES
16.5 17.6
22.5
25.5 24.4
20.7
15.5
0.7
4.8
10.8
14.81.78 Å
-7.4
TS
Adiabatic PES
B3LYP/6-31++G** calculated adiabatic and vertical potential energy surfaces (PES) of C5'-O5' bond dissociation of 5'-dTMPH radical anion.
B3LYP/6-31++G**
kcal/mol
4.85.7
10.9
18.0
21.7
19.1
14.4
0.6
4.5
10.2
13.5
1.78 Å
0.5
-5.8
20.0
18.0
16.0
14.0
12.0
10.0
8.0
6.0
4.0
2.0
0.0
-2.0
-4.0
-6.0
8.2 kcal/mol
22.0
TS
Adiabatic PES
Vertical PES
1.45 1.5 1.6 1.7 1.8 1.9 2.0C5'-O5'(Å)
B3LYP/6-31G** optimized geometries of neutral and anionic radical of 5'-dTMP with Na+ and 11 H2O.
A. Kumar; M. Sevilla, J. Phys. Chem. B 2007, 111, 5464-5474
5'-dTMPNa + 11 H2O (Neutral) 5'-dTMPNa + 11 H2O (Anion radical)
Na+ Na+
DFT (B3LYP/6-31G**) calculated adiabatic potential energy surface (PES) of C5'-O5' bond dissociation of hydrated (11 H2O) 5'-dTMP radical anion with Na+ as a counter ion.
Na+
Na+
Na+
Na+
B3LYP/6-31G**
kcal/mol
33.0
30.0
27.0
24.0
21.0
18.0
15.0
12.0
9.0
6.0
3.0
0.0
-6.0
1.5 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.5C5'-O5' (Å)
15.4
28.9
11.0
-3.3
Na+
Proposed mechanism of single strand break (SSB) due to attachment of LEE with 5'-dTMPH molecule
Why C-O not P-O?
• Experimentally only cleavage at the C-O bond is found. Y Zheng, P Cloutier, D Hunting, J R Wagner, L Sanche, JCP, 124, 064710 (2006).
• The loss of phosphate anion is the driving force for the reaction because the phosphate radical has a such a large EA.
J. Simons, Acc. Chem. Res. 2006, 39, 772-779
Base Release in Nucleosides Induced by Low Energy Electrons
OHCH2
OOH N
NH
O
O
CH3
OHCH2
CH O
OHN NH
CH
O
O
CH3
- -+.
X. Li, L. Sanche and M. Sevilla, Radiation Research, 165, 721 (2006)
J. Gu, Y. Xie and H. F. Schaefer, III, J. Am. Chem. Soc. 127, 1053–1057 (2005).
Potential Energy Surfaces (PESs) for C-N bond dissociation in Nucleoside Anion Radicals: Calculated with DFT (b3lyp, 6-31+G(d))
0.0
5.0
10.0
15.0
20.0
25.0
1.2 1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8 3.0
C-N1 distance (Å)
Rel
ativ
e E
ner
gy
(kca
l/mo
l)dT
dC
-8.0
-4.0
0.0
4.0
8.0
12.0
16.0
20.0
24.0
1.2 1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3
C1'-N distance (Å)
Re
lative
En
erg
y (
kca
l/m
ol)
dG
dA1
dA2
dA and dG anion radicals
dT and dC Anion Radicals
X. Li, L. Sanche and M. Sevilla, Radiation Research, 165, 721 (2006)
LEE Induced Excited States
• LEE induced resonances found experimentally suggest excited state involvement.
• What are the available excited state levels?
• We performed TD-DFT calculations to aid
our understanding in 5’-dTMP-●
J. Simons, Acc. Chem. Res. 2006, 39, 772-779
J. Berdys, I. Anusiewicz, P. Skurski, J. Simons JACS (2004)
Excited States of Sugar Phosphate Portion
Molecular orbital Energies and MO plots of neutral 5'-dTMPH. B3LYP/6-31G*. Scaled values by method of Modelli and Jones JPC 2006. *Experimental VOEs of thymine (Aflatooni et al. J. Phys. Chem. A (1998) 102, 6205 )
MOs Orbital Energy (eV) Scaled VOE (eV)
LUMO + 4 (σ3*)
LUMO + 3 (σ2*)
LUMO + 2 (σ1*)
LUMO + 1 (π2*)
LUMO (π1*)
HOMO (π)
1.78 2.64
1.27 2.23
0.73 1.80
0.43 1.56 (1.71)*
-0.84 0.53 (0.29)*
-6.24 ca. - 5 eV
Summary
• Strand break formation by LEE induced C-O bond scission is the lowest energy pathway in comparison to C-N, N-H or C-H bond scissions.
• LEE induced anion excited states likely provide a facile route to strand breaks.
Ph.D. Students. Amitava Adhikary Deepti Khanduri
Anil Kumar Sean Collins David Becker Alyson EngleLata Shukla Tom Casey Collaborators Leon Sanche Xifeng Li
AcknowledgmentsThis research is supported by NIH NCI RO1CA045424
DNA Radiation Chemistry Group at Oakland University
OU ESR GROUP
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