P 06 ISSRNS 2012: Abstracts / Synchrotron Radiation in Natural Science Vol. 11, No 1 – 2 (2012)
FIRST-PRINCIPLE APPROACH TO INTERPRETATION OF CHANGES IN IR SPECTRA OF CELLULAR DNA
J. Bielecki1∗, E. Lipiec2, and W.M. Kwiatek2
1Swierk Computing Centre Project, National Centre for Nuclear Research,´ So ltana 7, 05–400 Otwock-´Swierk, Poland
2Institute of Nuclear Physics, Polish Academy of Sciences, Radzikowskiego 152, 31–342 Krak´ow, Poland Keywords: synchrotron radiation, SR-FTIR, DFT, ab-initio, DNA
∗e-mail : jakub.bielecki@ncbj.gov.pl
The Fourier Transform Infrared Microspec- troscopy (µFTIR) has been proven to be a power- ful tool for detecting changes in biomolecules such as cellular DNA [1]. However only Synchrotron Radiation-based techniques (e.g. µSR-FTIR) pro- vide sufficient signal-to-noise ratio to conduct vi- brational analysis at the single cells level [2]. Nev- ertheless large molecules such a DNA are likely to yield IR spectra with many close lying peaks what makes a systematic analysis of the spectra quite dif- ficult. Thus an accurate first-principles-based calcu- lations are required for interpretation of the spectra changes due to radiation damage.
Development of modern high performance com- puting (HPC) systems together with the improve- ment of numerical methods as well as more common utilization of graphics processing units (GPU) for scientific calculations enables conducting large-scale computations of molecular vibrational spectra with high level of accuracy (e.g. within density functional theory (DFT) with B3LYP exchange-correlation functional and 6 − 31 + G(d) or 6 − 31 + G(d, p) basis set).
This work aims to provide a comparison of ex- perimentally obtained µSR-FTIR spectra of cellular DNA (PC-3 cells line) damaged by particle radi- ation with the calculated spectra in order to pro- vide comprehensive interpretation of damage mech- anisms. The PC-3 cells were irradiated by horizon- tal focused proton microbeam (16 µm in diameter at the irradiated spot) from the Van de Graaff acceler- ator (Single Proton Hit Facility at IFJ PAN, Krakow [3]). Irradiation process was conducted with single cells at protons energies of 1 MeV, 1.5 MeV and 2 MeV and five different doses were delivered for each energy (50, 200, 400, 2000, 4000 protons per cell). The experiment control group consisted of un- treated cells.
The influence of possible radiation damage of DNA segments such as: (i) strand breaks, (ii) base
removing from backbone, (iii) base damage on ex- perimentally obtained spectra was verified by DFT B3LYP calculations. Energy thresholds for differ- ent types the DNA damage as well as IR spectra of modified DNA structures were calculated. Develop- ment was preformed at ´Swierk Computing Centre - National Centre for Nuclear Research [4] while com- putations where carried out with the use of PL-Grid infrastructure [5].
Acknowledgments: This work is co-financed under the Operational Programme Innovative Economy 2007 – 2013 (agreement No. POIG.02.03.00–00–013/09). The experimental research leading to these results has re- ceived funding from the European Community’s Sev- enth Framework Programme (FP7/2007 – 2013) under grant agreement No. 20110351. The research was also partially supported by PL-Grid Infrastructure.
References
[1] E. Lipiec, J. Kowalska, J. Lekki, A. Wiechec, and W.M. Kwiatek, “FTIR microspectroscopy in stud- ies of DNA damage induced by proton microbeam in single PC-3 cell,” Acta Phys. Pol. A 121 (2012) 506 – 509.
[2] M. Diem, M. Romeo, C. Matthaus, M. Miljkovic, L. Miller, P. Lasch, “Comparison of Fourier transform infrared (FTIR) spectra of individual cells acquired using synchrotron and conventional sources infrared,” Infrared Phys. Technol. 45 (2004) 331 - 338.
[3] W. Polak, O. Veselov, J. Lekki, Z. Stachura, M. Zazula, R. Ugenskiene, M. Polak, J. Stycze´n,
“Irradiating single cells using Krak´ow microprobe facility,” Nucl. Instr. Meth. B 249 (2006) 743 - 746.
[4] http://www.cis.gov.pl/en.
[5] http://www.plgrid.pl/en.
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