Interaction of 0-15 eV electrons with DNA: Resonances, diffraction and

charge transfer

The presented results represent the work of many scientists especially: Marc Michaud Sylwia Ptasinska Badia Boudaiffa Michael Huels Pierre Cloutier Darel Hunting Hassan Adoul-Carime Xiaoning Pan Luc Parenteau Andrew Bass Frederick Martin Yi Zheng Richard Wagner Xifeng Li Michael Sevilla Laurent Caron

This work was funded by:

DNA and sub-units

N N

N C6 N

NH2

Guanine

Cytosine

Thymine

Adenine

tetrahydrofuran(THF)

3-hydroxy-tetrahydrofuran

-tetrahydrofurylalcohol

+ H2O

Apparatus for productanalysis

"Electron stimulated desorption of H¯ from thin films of thymine and uracil" M.-A. Hervé du Penhoat et al., J. Chem. Phys. 114, 5755 (2001).

QuadrupoleMass

Spectrometer

Ionizer& Ion Lenses

CustomIon Lenses

Filament

Deflector

ElectronLenses

ElectronGun

Load - Lock

Chamber(Preparation)

Oven

Channeltron

Linear Transfer & Rotation

RotatableShutter

RotatableSampleHolder

MainChamber

GateValve

10 torr-10

10 torr-9

0 10 20 30 40 50 60 70 80 90 100

0.0

0.2

0.4

0.6

0.8 MDSB

(c)

0

1

2

(b)

Incident Electron Energy (eV)

DSB

0

5

10

(a)

SSB

DN

A S

tra

nd

Bre

ak

Yie

ld (

x 1

0 -

4 )

pe

r In

cid

en

t E

lect

ron

LEE Damage to Plasmid DNA M.A. Huels et al., J.A.C.S. 125, 4467 ( 2003)

LEE damage to DNA – Intro/Summary• DNA damage induced by LEE below 15 eV occurs principally

by the formation of transient anions of the subunits. The contribution from direct scattering increases with energy.

• Anion ESD yields of: H¯ arises from the bases with a small contribution from the backbone, O¯ from the phosphate group, and OH¯ from a protonated phosphate group. Other anions have been observed.

• Anion ESD yields arise from DEA below 15 eV.

• Two major pathways of LEE reactions in DNA: cleavage of the N-glycosidic bond (base release) and the phosphodiester bond (strand break).

• Phosphodiester bond breaks by C-O bond rather than P-O bond rupture.

• Between 0-5 eV, SSB are produced with a cross section of about E-14 cm2 for 3,000 bp, similar values are found at 10 and 100 eV.

Sub-excitation energy electron damage Sub-excitation energy electron damage to DNAto DNA

Barrios et al J. Phys. Chem. 106, 7991 (2002) - Electron capture by cytosine and transfer to dissociative C-O bond

Li et al JACS 125, 13668 (2003) - Scission of 5’ and 3’ C-O bond by electron attachment. Endothermic by ~0.5 eV

Dablowska et al Eur. Phys. J. D 35, 429 (2005) – Proton transfer mechanism of DNA strand breaks induced by excess electrons.

Gu et al., Nucl. Acids Res. 1-8 (2007) (in press)

[SU¯] (Eo)

[SU] [SU]*DEA+ +

e¯ (Eo) e¯ (E<<Eo)

e¯ce¯t e¯c e¯t

1

2

3SU=subunit

base

sugar

phosphate

water

+diffraction

0 1 2 3 4 50

2

4

6

8

10

12

0 1 2 3 4 50

2

4

6

8

10

12

0 1 2 3 4 50

2

4

6

8

10

12

Capture Cross Section Sum

Thymine DEA

Cro

ss S

ect

ion

Electron Energy

Cro

ss S

ect

ion

Electron Energy

Cro

ss S

ect

ion

Electron Energy

Upper curve (Martin et al, Phys. Rev. Lett. 93, 068101 (2004)):

From ETS data, sum of capture cross sections for the four bases normalized to the second peak of the DNA damage yield (full squares) and shifted by 0.4 eV.

Lower curve (Denifl et al, Chem.Phys. Lett. 377, 74 (2003)):

DEA cross section from gaseousThymine with no energy shift.

Capture cross section of the bases vs single SB

Electron transfer in DNAElectron transfer in DNA

OH

OO

O

OO

O PO

O

OO

O PO

O

OOH

O PO N

N

O

O

N N

N N

O

NH2

N

N

O

NH2

guanine

cytosine

thymine

5'

3'

1

23

45

6

X

• LEE induced cleavage reactions greatly impeded next to the abasic site below 6 eV.

• There is a shift of electron transfer to direct attachment from low to high electron energy.

• Electron transfer of LEE occurs from base moiety to the sugar-phosphate backbone in DNA.

Percentage distribution of damage by sites of cleavage, induced by 6, 10 and 15 eV electrons.

*Xp was not detected by HPLC and the yield was considered to lie below the detection limit.Total damage = SB + base release = 100

Yield functions: GCAT Yield functions: GCAT vsvs GCXT GCXT

• For strand break, a resonance shows at around 10 eV.

• Presence of an abasic site greatly decreases the yield of strand break and base release in DNA (three times less).

3 5 7 9 11 13 150

30

60

90

GCAT XCAT GXAT GCXT GCAX

Ion

yie

ld (

cp

s)

Electron energy (eV)

OH-

On average 25% decrease for abasic Same results for H- and O- desorption

No diffractionSince OH- and O- originate from the backbone, these anions arise from e-

transfer unless there is a change in the resonance parameters

[base¯] (Eo)

[base] [base]*DEA+ +

e¯ (Eo) e¯ (E<<Eo)

e¯ce¯t e¯c e¯t

1

2

3

+diffraction

At higher energies, there is little coherence. Thus, creation of an abasic site has little effect on the branching ratios for electron emission in the continuum or within DNA

At low energies, transfer within DNA becomes much larger, but strongly depends on diffraction and hence is considerably decreased by formation of an abasic site

Neutral particle desorption from a single DNA strand

CN (black squares)OCN and/or H2NCN (white circles)

H and H2 desorption also observed

Ratio CN/OCN is constantResonance structures superimposed in

linearly increasing background

0 5 10 15 20 25 300

5

10

15

20

dCy6BrU

3

Fra

gmen

ts D

esor

bed

per

Ele

ctro

n (x

10-3)

Incident Electron Energy (eV)

0

2

4

dCy6T

3

0 1 2 3 4 50,0

0,5

1,0

1,5

0 1 2 3 4 5

0,0

0,5

1,0

1,5

0

2

4

6

dCy9

0 1 2 3 4 5

0,0

0,5

1,0

1,5

H. Abdoul Carime et al., Surf. Sci. 451, 102 (2000).

N

NH

R

O

O

X

N

NH

R

O

O

N

NH

R

O

O

N

R

O

O

NHC

O

NHC

+ e - + X - (1)

.

.

CN + OH

OCN + H

(3)

X + e -

+(2)

.

or

Isocyanic acid

Opinion of the presenterOpinion of the presenter

Shape resonances have high cross-section and can lead to Shape resonances have high cross-section and can lead to DEA (the only bond breaking process).DEA (the only bond breaking process).

Electron transfer is high.Electron transfer is high.

Below 3-4 eVBelow 3-4 eVBelow 3-4 eVBelow 3-4 eV

Above the energy threshold for electronic Above the energy threshold for electronic excitation excitation

Core excited shape resonances have a high cross section for decay Core excited shape resonances have a high cross section for decay into their parent neutral state and direct inelastic scattering may be into their parent neutral state and direct inelastic scattering may be significant. The magnitude of the DEA is not necessarily large significant. The magnitude of the DEA is not necessarily large compared to autoionization.compared to autoionization.

There is little coherent enhancement of the electron wavefunction There is little coherent enhancement of the electron wavefunction at the primary impact energy.at the primary impact energy.

Above the energy threshold for electronic Above the energy threshold for electronic excitation excitation

Core excited shape resonances have a high cross section for decay Core excited shape resonances have a high cross section for decay into their parent neutral state and direct inelastic scattering may be into their parent neutral state and direct inelastic scattering may be significant. The magnitude of the DEA is not necessarily large significant. The magnitude of the DEA is not necessarily large compared to autoionization.compared to autoionization.

There is little coherent enhancement of the electron wavefunction There is little coherent enhancement of the electron wavefunction at the primary impact energy.at the primary impact energy.

Proton transfer has to be re-examined in the Proton transfer has to be re-examined in the context of the present data and hypothesiscontext of the present data and hypothesis

Proton transfer has to be re-examined in the Proton transfer has to be re-examined in the context of the present data and hypothesiscontext of the present data and hypothesis

• Are transient negative ions formed within the 0-15 Are transient negative ions formed within the 0-15 eV linked directly to stable anions of the bases or eV linked directly to stable anions of the bases or other SU? other SU?

• If so how?If so how?

Possible mechanismsPossible mechanisms:

1. Vibrational stabilization triggered by the change in DNA configuration by the extra charge. The extra energy (<2eV) of the electron is dispersed in vibrational excitation of DNA and then transfered to the surrounding medium. Does not work for core-excited resonances.

2. Electron-emission decay of a core-excited shape resonance followed by vibrational stabilization.

3. Proton transfer stabilization. Neutralizes the anion charge while leaving a site with a ground state electron.

4. Superinelastic vibrational or electronic electron transfer. [Lu, Bass and Sanche, Phys. Rev. Lett. 88, 17601 (2002)].

4 6 8 10 12 14 16 18 200

25

50

75

0

25

50

75

0

25

50

75

(H2O/GCAT)-(GCAT)

H2O

D- from D2O/GCAT

Electron energy (eV)

(c)

(b)

(H2O/GCAT)-(H

2O)

GCAT

H- y

ield

(kc

ps)

H2O/GCAT

GCAT H

2O

(a)

4 6 8 10 12 14 16 18 20

0

20

40

60

80

100

120

140 16O- from GCAT

16O- from D2O/GCAT

18O- from H2

18O/GCAT

Ion

yiel

d (c

ps)

Electron energy (eV)

4 6 8 10 12 14 16 18 200

20

40

60

80

100 OH- from GCAT

OD- from D2O/GCAT

OH- from H2O/GCAT

18OH- from H2

18O/GCAT

Ion

yiel

d (c

ps)

Electron energy (eV)

| O | O = P ─ O¯ H+ (O18H) | O |

Site of Site of formationformation