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![Page 1: Dehydrogenation of nucleobases upon electron attachment to isolated nucleotides Steen Brøndsted Nielsen Department of Physics and Astronomy University.](https://reader036.fdocuments.us/reader036/viewer/2022062515/56649ce05503460f949aa55b/html5/thumbnails/1.jpg)
Dehydrogenation of nucleobases upon
electron attachment to isolated nucleotides
Steen Brøndsted Nielsen
Department of Physics and Astronomy
University of Aarhus
June 24-27, 2004, Lyon-France
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DNA DAMAGE
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HOW DOES UV RADIATION CAUSE GENETIC DAMAGE ?
1) Direct absorption of light by the nucleobases
followed by physical and chemical reactions
and / or
2) Ionisation of water (H2O H2O+ + e) followed
by electron attachment to nucleobases
Modification of nucleobases may lead to loss of base-pairing specificity
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Elucidate the processes at the single-molecule level.
Isolated damage to nucleotides, the basic building
blocks of DNA and RNA, upon electron attachment.
OUR APPROACH
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TOOLBOX
ELECTROSPRAY IONISATION
MASS SPECTROMETRY:
ACCELERATOR INSTRUMENT
ION STORAGE RING ELISA
LASERS
QUANTUM CHEMICAL CALCULATIONS
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BARE IONS
ELECTROSPRAY IONISATION
droplets
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ELECTROSPRAY ION SOURCE
1 mbar 10-3 mbar 10-5 mbar 10-6 mbar
Heatedcapillary
ESI needle4kV
22-pole ion trap
Tube lensSkimmer
OctapoleLenses
Acceleration tube
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GAS-PHASE EXPERIMENTS ON NUCLEOTIDE ANIONS
PROBLEM:
Attachment of an electron to a negative
ion is unlikely because of the repulsion
between the two negative charges.
SOLUTION:
High-energy collisions with sodium:
electron transfer from Na to the ion.
R 0
dianion
En
erg
y
Anion - electron distance R
dianion
Compare: the violent reaction of sodium with water !
Nielsen et al., J. Am. Chem. Soc. 125, 9592-9593 (2003).
Liu et al., Chem. Phys. Chem. 4, 1341-1344 (2003).
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ACCELERATOR INSTRUMENT
ESIsource
Magnet
Na collision cell
Electrostaticanalyser
0 V
50 kV
Channeltrondetector
+
R = 2 mB = 1.4 T
T=500 K
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COLLISION INTERACTION TIME: FEW FEMTOSECONDS
Na
-Nucleotide anion
105 m/s
1 nm
The electron transfer process is nearly vertical.
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Electron attachment to AMP anions
O
OH OH
N N
NN
NH2
CH2O
O
P
O
OH
1
2
3
4
567
8
9
1'
2'3'
4'
5'
m/q 346
Ne
Na
Liu et al., Chem. Phys. Chem. 4, 1341-1344 (2003).
80 120 160 200 240 280 320 360
dianion
[AMPAH] [AMPO]
AMP
A
H2PO
4
PO3
AMP
[AMPAH]A
H2PO
4
PO3
m/q
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164 166 168 170
High-energy collisions between dAMP anions and Na and Ne
100 150 200 250 300
m/q
dAMPdAMP2
fragment ionsm/q 330
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Spectrum obtained after collisions between AMP(H2O)13 and Na
100 200 300 400 500 600
m/q
170 190 210 230 250
AMP(H2O)13
AMP2 AMP2(H2O)9
AMP
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100 200 300 400 500 600
m/q
dG2
dT2
dC2
dA2
Electron transfer from Na to dinucleotide anions
sugar
sugar
phosphate
nucleobase
nucleobase
dianion
-
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IS THE NUCLEOTIDE DIANION INTACT ?
H loss is observed upon electron attachment to nucleobases in vacuo.
C. Desfrancois, H. Abdoul-Carime, and J. P. Schermann, J. Chem. Phys. 104, 7792 (1996).S. Gohlke, H. Abdoul-Carime, and E. Illenberger, Chem. Phys. Lett. 380, 595 (2003). G. Hanel, B. Gstir, S. Denifl, P. Scheier, M. Probst, B. Farizon, M. Farizon, E. Illenberger, and T. D. Märk, Phys. Rev. Lett. 90, 188104 (2003). H. Abdoul-Carime, S. Gohlke, and E. Illenberger, Phys. Rev. Lett. 92, 168103 (2004).
H loss is observed upon electron attachment to deoxyribose in vacuo.
S. Ptasińska, S. Denifl, P. Scheier, and T. D. Märk, J. Chem. Phys. 18, 8505 (2004).
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1.5 1 0.5 0m/q
# of D in AMP
0
1
2
3
Intact dianion H D
AMP dissolved in CD3OD:
Selection of deuterium-
labelled ions for collision
experiments
O
OH OH
N N
NN
NH2
CH2O
O
P
O
OH
1
2
3
4
567
8
9
1'2'3'
4'
5'
Exchangeable hydrogens
Liu et al., J. Chem. Phys., issued for Sept. 1 (2004).
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WHAT IS THE ORIGIN OF THE HYDROGEN ?
POH phosphoric acid group
OH sugar
NH2 nucleobase
CH sugar or nucleobase
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Electron attachment to nucleotides:
dehydrogenation at nitrogen sites
N
NH
O
OCH3
N
NH
O
O
Thymine Uracil Adenine Cytosine Guanine
N N
N N
NH2
N
N
O
NH2
N N
N NH
O
NH2
1 2 3
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0 1 2 30.0
0.1
0.2
0.3
0.4
(Å
2 )
Number of nitrogen hydrogens
RNA nucleotide DNA nucleotide
Cross section for formation of dehydrogenated dianion
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• H-loss from N
• No D-loss from C
H. Abdoul-Carime, S. Gohlke, and E. Illenberger,
Phys. Rev. Lett. 92, 168103 (2004).
Dissociative electron attachment to deuterated thymine
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THE DNA DOUBLE HELIX
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Watson-Crick base pairs Base mispairing
Biological relevance?
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WHAT IS THE LIFETIME OF THE DIANION ?
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1 m
Micro-channel platedetector
Accelerator with electrospray ion source
Magnet
Ion bunch
Injection
ELectrostatic Ion Storage Ring Aarhus (ELISA)
S.P. Møller, NIM A 394, 281 (1997).
J.U. Andersen, J.S. Forster, P. Hvelplund, T.J.D. Jørgensen, S.P Møller, S. Brøndsted Nielsen, U.V. Pedersen, S. Tomita, and H. Wahlgreen, Rev. Sci. Instrum. 73, 1284-1287 (2002).
Channeltron
Sodium
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0.0 0.5 1.0 1.5 2.0
100
101
102 298 K 203 K
Dec
ay r
ate
[a.u
.]
Time [ms]
= 0.2 ms
Electron autodetachment from the AMP dianion
Liu et al., J. Chem. Phys., issued for Sept. 1 (2004).
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1 m
Micro-channel platedetector
Accelerator with electrospray ion source
Magnet
Ion bunch
Injection
Channeltron
Long-lived component ?
Dump of a remaining beam in the micro-channel plate detector after 34 ms of storage time.
Sodium
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34.00 34.05 34.10 34.150
30
60
90
Cou
nts
Time [ms]
40 s
Dump of beam in the detector after 34 ms of storage time
AMP2
(m/q 172.5)
13C-AMP2
(m/q 173)
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CONCLUSIONS
• Electron transfer to nucleotide anions occurs in
collisions with sodium vapour.
• Electron attachment leads to dehydrogenation of
the nucleobase nitrogens.
• The dehydrogenated dianion is longlived.
Other fragmentation channels than H-loss upon electron attachment ?
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ACKNOWLEDGEMENTS
University of Aarhus:
Preben Hvelplund Jens Ulrik Andersen
Shigeo Tomita Bo Liu
Jimmy Rangama
Leopold-Franzens Universität Innsbruck:
Paul Scheier Gabriel Hasan
FUNDING
The Danish Natural Science Research Council
Aarhus Center for Atomic Physics (ACAP)