* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Molecular characterization of individual DNA double strand breaks
Survey
Document related concepts
DNA sequencing wikipedia , lookup
DNA barcoding wikipedia , lookup
Comparative genomic hybridization wikipedia , lookup
Agarose gel electrophoresis wikipedia , lookup
Holliday junction wikipedia , lookup
Maurice Wilkins wikipedia , lookup
Community fingerprinting wikipedia , lookup
Bisulfite sequencing wikipedia , lookup
DNA vaccination wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Molecular evolution wikipedia , lookup
Transformation (genetics) wikipedia , lookup
Non-coding DNA wikipedia , lookup
Gel electrophoresis of nucleic acids wikipedia , lookup
Molecular cloning wikipedia , lookup
Nucleic acid analogue wikipedia , lookup
Transcript
CODECS 2013 Workshop. San Lorenzo de El Escorial, Madrid, 18th –22nd April, 2013 Molecular characterization of individual DNA double strand breaks with Tip Enhanced Raman Scattering (TERS) supported by QM/MM model Ewelina Lipieca, Jakub Bieleckib, Bayden R. Woodc, Wojciech M. Kwiateka a The Henryk Niewodniczanski Institute of Nuclear Physics, PAN, 31-342 Kraków, Poland Swierk Computing Centre Project, National Centre for Nuclear Research, Sołtana 7, 05400 Otwock-Swierk, Poland b c Centre for Biospectroscopy, School of Chemistry, Monash University, 3800, Victoria, Australia; DNA double strand breaks (DSBs) are deadly lesions that can lead to genetic defects and cell apoptosis1. Techniques to directly image DSBs in isolated DNA include scanning electron microscopy2, Atomic Force Microscopy (AFM) and single molecule fluorescence microscopy3. While these techniques can be used to identify DSBs they provide no information on the molecular events occurring at the break. Tip Enhancement Raman Scattering (TERS) can provide molecular information from DNA at the nano-scale and in combination with AFM provides a new way to visualize and characterize DSBs. In experimental part of this study pUC18 plasmid DNA was fixed onto mica surface and the susceptibility of various kinds of DNA backbone bonds to UV-C radiation was investigated. Obtained results were compared with calculated spectra. Computations of Raman activity for untreated and radiation-induce damaged (double strand break within O-C bond region) DNA structures have been carried out using GAUSSIAN 09 software package in the framework of hybrid QM/MM method (ONIOM model) with Density Functional Theory formalism with B3LYP hybrid exchange-correlation functional using 6311++G(d,p) basis functions set for a guanine-cytosine pair and Universal Force Field model for the rest of the system (additional 6 pairs). Initial positions of atoms were taken form Nucleic Acid Database. Phosphate groups atoms positions were fixed during optimization due to interaction with divalet cations Mg2+ present on the mica surface. Then, Raman activities were calculated basing on the optimized geometries. The appearance of P-O-H motions and CH2, CH3 bending and wagging modes are observable in experimental and calculated spectra of damaged DNA, what confirmed that broken DNA fragments are cleaved at the 5’- bonds upon exposure to UV-C radiation. References 1. M. Norval, Photochem. Photobiol. Sci. 10, 199-225 (2011). 2. M. Brezeanu J. Biol. Phys. 35, 163-174 (2009). 3. E. M. Filippova, Biophys. J. 84, 1281–1290 (2003).