RADACK, a stochastic simulation of hydroxyl radical attack to DNA.

RADACK was conceived to simulate the radiation-induced attack to different DNA forms and complexes. It allows to separately calculate the probability of attack to each reactive atom of the sugar and of the base and takes into account the sequence-dependent structure of DNA as known from crystallographic or NMR studies or resulting from molecular modelling. The calculations are aimed to assess sequence-, structure- and ligand-dependent modulation of damages of sugar and bases, leading to single strand breaks (frank strand breaks, FSB) and alkali-labile base modifications (alkali-revealed breaks, ARB), respectively.

Monte Carlo simulation of radiolytic attack to 5'-d[T4G4]4 sequence in a unimolecular quadruplex.

Purpose: To extend to a quadruplex the stochastic model of radiolytic attack previously applied to a quasi-random duplex DNA.

Materials And Methods: The quadruplex structure is obtained from the PDB databank (first structure from 201D entry). The probabilities of OH* radical attack at all sugar and base reaction sites are calculated using a stochastic model based on the Monte Carlo method.

Effect of ethidium bromide intercalation on DNA radiosensitivity.

Purpose: To assess the influence of the intercalating drug ethidium bromide (EtBr) on the yields of single strand breaks (ssb) induced by fast neutrons in supercoiled pBR322 plasmid and in a linear DNA restriction fragment.

Materials And Methods: The yield of ssb in the plasmid was measured by agarose gel electrophoresis. The proportion of fragments bearing one ssb and the probability of breakage at each nucleotide site was determined using sequencing gel electrophoresis.

Computer-aided stochastic modeling of the radiolysis of liquid water.

A computer-aided stochastic model of the radiolysis of liquid water has been developed. It is based on Monte Carlo simulation of charged-particle tracks, a random-flight method to simulate diffusion of species and the Debye-Smoluchowski theory of reactions between radicals. The model takes into account the formation of ionizations, excitations and subexcitation electrons at the physical stage.

Sequence-dependent variations of DNA structure modulate radiation-induced strand breakage.

Using a 80 base pair DNA fragment, the sequence-dependence was compared for: (i) the probability of fast neutrons induced strand breakage, (ii) the accessibility of the H4'- and H5'-atoms to OH. attack, (iii) the width of the minor groove, and (iv) the probability of OH. reactions with H4'- or H5'-atoms.