Combining NMR (Nuclear Magnetic Resonance) and Raman spectroscopy reveals structural and functional features of a new cisplatin derivative

Magdaléna Krejčíkova1,2, Konstantinos Gkionis3, Dušan Hemzal1,2, James A. Platts4, Paride Papadia5, Nicola Margiotta6, Jiří Šponer3 and Karel Kubíček1,2

1Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, CZ-611 37 Brno, Czech Republic


2Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ – 625 00 Brno, Czech Republic

3Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ - 612 00 Brno, Czech Republic

4School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom

5Dipartimento di Chimica, Universita degli Studi di Bari Aldo Moro, Via Orabona 4, I-70125 Bari, Italy

6Chimica Generale ed Inorganica, Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Universita del Salento, Prov.Le Lecce-Monteroni - Centro Ecotekne, I-73100 Lecce, Italy



Since its discovery some 40 years ago, cisplatin has evolved for its efficacy in one of the most used drugs in treatment of various cancer types. Huge effort was invested in understanding the action of cisplatin and development of more potent platinum, osmium, and ruthenium based drugs. These potential drugs target mainly neighboring purine bases of nuclear DNA forming covalent intra- or inter-strand cross-links that affect inhibition of replication and transcription, cell cycle arrest, and attempted repair of the damaged nucleotides. If such damage cannot be removed the cell dies [1].

Several structures determined by NMR or X-ray crystallography are now available in the PDB database containing 1,2d(GpG) cisplatin or oxaliplatin (e.g. 1AIO, 3LPV, 1A84). Common structural features of all these structures are: a significant roll (25-60°) of the guanine bases involved in the cross-link, bending and unwinding of the double helix at the site of cross-link and orientation towards the major groove. Also, the platinum-guanine plane angle varies between 19-54°. Although the experimental structures were often used as the starting models for molecular dynamics (MD) simulations [2,3], results of these MD still leave many questions unresolved. In our contribution, we will present an NMR study of a DNA cross-linked with a new highly potent cisplatin-based derivative. Details of the binding site have been cross-examined using complementary solution techniques used in modern structural biology, including Raman spectroscopy with DFT calculations aided interpretation of the obtained vibrational spectra. Moreover, the calculated structure of the DNA duplex was verified using SAXS (Small Angle X-ray Scattering) curve, that has been measured on an in-house bioSAXS.


1.         Lippert, B.: Cisplatin: Chemistry and Biochemistry of a Leading Anticancer drug,  Verlag Helvetica Chimica Acta, 1999

2.         Sharma, S.: Molecular Dynamic Simulations of Cisplatin- and Oxaliplatin-d(GG) Intrastand Cross-links Reveal Differences in their Conformational Dynamics, J. Mol. Biol., 5 (2007): 1123-40

3.         Elizondo-Riojas MA, Kozelka J.: Unrestrained 5 ns molecular dynamics simulation of a cisplatin-DNA 1,2-GG adduct provides a rationale for the NMR features and reveals increased conformational flexibility at the platinum binding site. J. Mol. Biol., 5 (2001):1227–1243