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Modeling of Radiation Damage of Various Plasmid Loop Conformations

M Sefl1,2*, K Stefanova2 , K Pachnerova Brabcova1 , V Stepan1 , (1) Nuclear Physics Institute of the Czech Academy of Sciences, Prague, (2) Czech Technical University in Prague, Prague


(Sunday, 7/29/2018) 3:00 PM - 6:00 PM

Room: Exhibit Hall

Purpose: Plasmid DNA is often used as a simple model for radiobiological studies of the initial effects of ionizing radiation on DNA. Plasmid loop DNA can exist in various conformations; this may affect the radiation damage of plasmid.

Methods: 200 plasmid loop skeletons were prepared using the algorithm described in Huang J., et al. (PNAS 2001. 98, 968-973) and smoothed according to Kümmerle, E. A. and Pomplun E. (Eur Biophys J. 2005. 34: 13–18). The generated curves were then used to build atomic level model of the plasmid in PDB format. Resulting structure respects the base sequence of the plasmid and will be used for further simulation of radiation damage using Geant4-DNA or RADAMOL codes. RADAMOL was developed to model the pre-chemical and chemical stage of the ionizing radiation action on biomolecules in an aqueous environment. Two inputs are required – event-by-event track data from TRIOL or Geant4-DNA, and a description of the target molecule.

Results: This work presents extension of the target molecule model from simple linear oligomer to a full plasmid DNA loop. The difference between the DNA damage yields calculated for various plasmid conformations and a set of radiation qualities will be presented and discussed.

Conclusion: Radiation damage of 200 pBR322 plasmid loop conformations was studied and compared for a set of radiation qualities. Further study is required to draw a general conclusion on the effect of the plasmid conformation.

Funding Support, Disclosures, and Conflict of Interest: This project was supported by Czech Science Foundation, project No. 1 7-03403Y.


Modeling, Radiobiology, Radiosensitivity


TH- Radiobiology(RBio)/Biology(Bio): RBio- general

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