1. Metal ion induced pairing of cytosine bases
formation of i-motif structures identified by ion spectroscopy
Anouk Rijs
Juehan Gao, Giel Berden, Jos Oomens
FELIX Laboratory
Radboud University, Nijmegen, The Netherlands
© M. Molle

2. Cytosine: one of the four nucleobases in DNA4 5 3 6 2 1
cytosine

3. Non-Watson-Crick base pairing: mismatch pairing
i-motif
Cytosine pairing with cytosine, sharing one proton:
Hemi-protonated cytosine dimer

4. Spectroscopic evidence for the gaseous i-motif
(1-MeCy-d2)2 D+
wavenumber (cm-1)
Oomens, Moehlig, Morton, JPCL 2010, 1, 2891

5. IR ion spectroscopy – experimental

6. FELIX - Free Electron Laser
International user facility
2 calls for proposals per year
Range of ancillary equipment
Contact Britta Redlich!
undulator magnets
IR-beam
Wavelength tunable 3 – 150 mm
Pulse energy <100 mJ per 5 ms pulse
FWHM bandwidth >0.4% of l
International user facility
gun
e-beam
accelerator
mirror

7. Silver(I)-induced pairing of Cytosine

8. Spectroscopic evidence for an i-motif structure in C-Ag+-C
kJ/mol
Berdakin, Steinmetz, Maitre, Pino, JPCA 2014, 118, 3804

9. Low-energy tautomers of neutral cytosine
5-methylcytosine
keto/amine
enol/amine
enol/amine
Lowest at MP2 C1 C2 C3
Alkali metal ion binding stabilizes C1
Yang, Wu, Polfer, Berden, Oomens, Rodgers, JASMS 2013, 24, 1523 C6 C4 C5
keto/imine
keto/imine
keto/amine
Yang, Wu, Berden, Oomens, Rodgers, JPCB 2013, 117, 14191

10. IR spectra of monomeric Cu+-C complexes
C1N3O 0 kJ/mol
C1O kJ/mol
+9.4
mixture of 2 structures
C1N3O not previously identified
covalent interaction
B3LYP/6-311G(2df,2p) – MP2/6-311G(2df,2p)

11. IR spectra of MeCN-Cu+-C complexes
C1O 0 kJ/mol
+2.4
C1N kJ/mol
mixture of 2 structures
Cu(I) binds to O or N3
covalent interactions

12. IR spectra of C-Cu+-C complexes
C1N3C1N kJ/mol
i-motif structure
Single structure
Cu(I) binds to N3
add’l stabilization by H-bonds
covalent interactions

13. Cu+ and Ag+ induce the i-motif structure How about alkali metal ions?

14. IR spectrum of C-Na+-C complex
Na+ binds to N3 and O
No add’l H-bonds
electrostatic interactions
No i-motif structure!
C1N3OC1N3O

15. IR spectra of C-M+-C complexes
Li+
All alkali metal ions bind to N3 and O
Parallel displaced structure
No i-motif structure!
Na+ K+

16. Molecular orbitals C-Na+-C C-Cu+-C HOMO HOMO - 4 HOMO HOMO - 45

17. Computed parameters C – M+ - C complexes
Ionic radius
M+ partial charge
D(N…O)
Dissociation energy
Li+
0.90
+0.731
0.002
141
Na+
1.16
+0.839
0.003
117 K+
1.52
+0.885
1.86
104
Cu+
0.91
+0.609
1.19
260
Ag+
1.29 -
2.0
195 H+
+0.462
0.04
NPA

19. Monomeric Cu+-C complexes: two structures co-exist
Conclusions
Monomeric Cu+-C complexes: two structures co-exist
Copper and silver complexes have i-motif structure
 H-bonding preferred over Cu+-O bonding
Alkali metal ions induce parallel displaced structure
 M+-O bonding preferred over H-bonding

20. Acknowledgements Juehan Gao Giel Berden Britta Redlich Lex v.d. Meer
& FELIX staff
Dutch Astrochemistry Network
VICI
Access to SARA Supercomputer

21. Low-energy tautomers of protonated cytosine
O-protonated is lowest in energy
keto/amine
enol/amine
enol/amine
keto/imine
keto/imine
keto/amine
Yang, Wu, Berden, Oomens, Rodgers, JPCB 2013, 117, 14191

22. Cytosine: one of the four nucleobases in DNA4 5 3 6 2 1