Biomedical subjects

V Michalik

Publications and source records attributed to V Michalik.

15 recordsLinked to original sources

PubMed2001

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. The modelling procedure and the results of simulations for some representative structures (B, Z and quadruplex forms) are here described and discussed. The calculated relative probabilities of OH* radical attack to all reaction sites are compared to experimental FSB and ARB values. By a fitting procedure, the relative efficiencies of conversion of the C4' and C5'-centred radicals into FSB, epsilon (C4'): epsilon (C5'), and the relative efficiencies of base radicals- to- ARB conversion, epsilon(T) : epsilon(A) : epsilon(C) : epsilon(G), are then deduced for each DNA form. The ability of the model to account for the distribution of damages in DNA-ligand complexes is proven by its successful application to two DNA-protein systems : the lac repressor-lac operator complex and the nuclcosome core.

Bacterial Proteins↗

PubMed2000

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. The volume variations due to the intercalation of EtBr were calculated. The expected radio-modifying effect at each nucleotide site of the linear fragment was evaluated using a reported simulation procedure. RESULTS: The ssb yield in the plasmid increased for concentrations up to 0.04 drug/bp and fell back in the range 0.04-0.1 drug/bp. For the linear DNA, only a slight protective effect was observed over the whole concentration range. The effect was almost the same at all nucleotide sites. CONCLUSION: For the linear DNA fragment, radioprotection was mainly due to scavenging of OH* radicals by the intercalated drug. For the plasmid, the radio-modifying effect results mainly from the variation of its effective volume, due to the modification of superhelicity.

DNA↗

PubMed1999

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. RESULTS: Good agreement between the calculated and experimental frank strand break (FSB) probabilities is obtained using the relative efficiencies of conversion of the C4' and C5'-centred radicals into FSB determined for the quasi-random duplex (2.8:1 respectively). Efficiencies of base radicals-to-alkali-revealed breaks (ARB) conversion are determined by fitting the calculated probabilities of base attack to the previously reported experimental probabilities for ARB. The efficiency of conversion of thymine radical into an ARB is 3.4+/-0.7 times higher than for guanine radical. CONCLUSIONS: This paper supports the calculation method and allows evaluation of the relative efficiencies of thymine and guanine radicals-to-ARB conversion.

Base Sequence↗

PubMed1998

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. The corresponding initial yields at approximately 1 fs were found to be G(ion) = 4.37, G(exc) = 2.81 and G(e-sub) = 4.38. The energy spectrum of subexcitation electrons has been calculated. Autoionizations and dissociations of excited molecules, hole migration, electron thermalization, geminate recombination and the cage effect are considered at the physico-chemical stage. The mean thermalization distance of subexcitation electrons is 24.5 nm. The initial yields of e(aq)-, H+, OH, H, H2 and O are 4.89, 4.86, 5.96, 1.10, 0.15 and 0.15, respectively. The reactions between radicals and products as well as their diffusion are simulated at the chemical stage. The decay kinetics of the most important radicals is reported together with the time evolution of the most important reactions. The yields of the reactive radicals, e(aq)-, H+, OH, H and OH-, at 1 ps are 4.84, 4.85, 5.87, 1.09 and 0.0, respectively. The respective steady-state yields at 10 micros are 2.70, 3.58, 2.89, 1.17 and 0.79. The yields of molecular products, H2O2 and H2, are 0.73 and 0.47 at 10 micros. The concentration-dependent yields of e(aq)-, OH and H2O2 are calculated in three different aqueous solutions. The predictions of the model agree fairly well with experimental data.

Chemical Phenomena↗

PubMed1997

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. The probability of strand breakage was measured using sequencing gel electrophoresis. The accessibility and the probability of reaction were calculated for the energy-minimized modelled DNA fragment. A Monte-Carlo simulation was used for calculating the probabilities of H-atom abstraction by OH.. It was observed that reduced breakage occurs in sequences exhibiting low accessibility of H4' and H5'2 and low probability of H-atom abstraction by OH., due to a narrow, minor groove. This shows that the breakage probability at a given nucleotide site is not determined by the chemical nature of the nucleotide (A, T, G or C), but mainly by the local sequence-modulated intrinsic structure. Fitting the experimental results with the calculated probabilities of reaction suggests that a C4'-centered radical evolves towards a strand break three times more efficiently than the C5' one, and that half of the breaks occur via the 4'-path and half via the 5'-path.

Base Sequence↗

PubMed1996

Two types of double-strand breaks in electron and photon tracks and their relation to exchange-type chromosome aberrations.

Yields of DNA double-strand breaks (dsb), i.e. the average number of dsb, N, per relative molar mass, M(r), and dose, D, produced by electrons and photons in the energy range 50 eV-1 MeV were calculated. The experimental data of dsb induction by ultrasoft x-rays and by photons agree well with the calculated yields of dsb as a function of photon energy. The dsb are classified into simple and complex ones. Energy transfers of less than about 200 eV producing at least two ionizations generate mainly simple dsb, while low-energy electrons with an initial energy between 200 and 500 eV induce preferentially complex dsb. Assuming that dsb is the main DNA lesion leading to exchange-type chromosome aberrations (etca), three different mechanisms have to be considered: 1) complex dsb on its own; 2) interaction between two dsb induced by the same primary particle; and 3) interaction between two dsb induced by different primary particles. Mechanisms 1) and 2) produce a linear term, whereas mechanism 3) leads to a quadratic term for the yield of etca. The sum of contributions 1) and 2) to the yield of dicentrics describes fairly well the non-trivial structure of the experimental data. The results suggest that interaction between complex dsb does not contribute significantly to the formation of dicentrics via mechanism 3).

Chromosome Aberrations↗

PubMed1995

Calculation of hydroxyl radical attack on different forms of DNA.

A stochastic model of hydroxyl radical reaction with the DNA macromolecule in dilute aqueous solution is presented. It is based on the Monte Carlo method, the model of Smoluchowski, the model of the regular DNA atomic structure and the knowledge of reaction rate constants for .OH radical reaction with DNA constituents. The calculated respective overall probability of .OH radical reaction with sugar or base moiety dependents on DNA form (A, B or Z), base composition (AT/GC content) and strandedness (single and double). While for all three DNA forms studied (A, B and Z) as well as for both single- and double-stranded B-DNA, the specific probability of .OH radical attack on nucleobases is modulated by their sequence, the attack on deoxyriboses is only slightly sequence dependent (except for Z-DNA). The model predictions are compared to the experimental patterns of strand breaks and alkali revealed breaks for single and double stranded DNA in B-form and discussed in terms of molecular mechanisms of DNA damage induced by hydroxyl radical.

Base Composition↗

PubMed1994

Radiolytic signature of Z-DNA.

Ionizing radiations induce various damages in DNA via the hydroxyl radical OH. generated by the radiolysis of water. We compare here the radiosensitivity of B- and Z-DNA, by using a Z-prone stretch included in a plasmid. In the supercoiled plasmid, the stretch is in the Z-form, whereas it is in the B-form when the plasmid is relaxed. Frank strand breaks (FSB) and alkali-revealed breaks (ARB) were located and quantified using sequencing gel electrophoresis. We show that B- and Z-DNA have the same mean sensitivity towards radiolytic attack, for both FSB and ARB. Nevertheless, the guanine sites are more sensitive, and the cytosine sites less sensitive in Z- than in B-DNA, leading to a characteristic signature of the Z-form. The comparison of experiments with the outcome of a Monte Carlo simulation of OH. radical attack suggests that transfer of initial damage from a guanine base to its attached sugar or the adjacent 3' cytosine is more important in Z-DNA than in B-DNA.

Base Sequence↗

PubMed1994

Target model of nucleosome particle for track structure calculations and DNA damage modelling.

A non-homogeneous target model of nucleosome particle for track structure calculations and biophysical modelling of radiation-induced DNA damage was developed together with a sampling method for non-homogeneous targets. The model allows one to distinguish energy deposited in the histone core, primary hydration shell and nucleosome DNA. Illustrative results for low energy electrons are presented and compared with results obtained with simpler models of a nucleosome particle.

DNA Damage↗

PubMed1994

Simple and complex double-strand breaks induced by electrons.

Biophysical modelling of DNA damage based on Monte Carlo simulation of charged particle tracks allows to describe radiation induced double-strand breaks (dsb) in a quantitative and qualitative way. Experimental and calculated data suggest that in the electron energy range from 50 eV to 1 MeV dsb can be grouped in simple and complex dsb. Complex dsb are mainly produced by low energy electrons with initial energies between approximately 200 and approximately 500 eV, whereas simple dsb are preferentially induced by energy transfers < 200 eV, which produce at least two ionizations.

DNA Damage↗

PubMed1993

Estimation of double-strand break quality based on track-structure calculations.

The aim of this study was to investigate whether double-strand break (DSB) quality is related to the complexity of radiation-induced damage or to the spatial distribution of initial DSBs. The analysis was based on track structure calculations and DNA damage modelling. The results obtained indicate that the quality of DSBs is related to their initial spatial distribution rather than to their complexity.

DNA Damage↗

PubMed1993

Energy deposition clusters in nanometer regions of charged-particle tracks.

Energy deposition clusters in the nanometer scale have been investigated systematically in electron, proton, and alpha-particle tracks. The mean absolute frequency distributions of ionization clusters in nanometer sites have been computed. For locally multiply damaged sites and especially for double-strand breaks, the threshold numbers of ionizations in a site of a given diameter necessary for their induction have been estimated. At least three to six ionizations localized in sites of 1 to 4 nm diameter, respectively, are required to produce the double-strand break.

Alpha Particles↗

PubMed1992

Model of DNA damage induced by radiations of various qualities.

A theoretical model permitting estimation of yields of various DNA damages induced by radiations of varying qualities is described. It is based on the Monte-Carlo track structure simulation and DNA structure, and links physical, physicochemical and chemical stages of radiation action. Direct and indirect effects are not strictly distinguished but treated cooperatively. Good agreement between calculated and measured initial yields of double-strand breaks was observed. Other multiple and single damages of DNA are studied. When radiation quality is changed there are quantitative and qualitative transitions in the damage spectrum. The proportion of multiple damage in the damage spectrum is about 30% for low-LET radiations and increases considerably with increasing ionization density.

DNA↗

PubMed1992

Theoretical estimation of quality factor for tritium.

A theoretical calculation of the tritium quality factor is made and some of the results are presented. These results may contribute to a better dose equivalent assessment of tritium since there is some uncertainty, as is reflected in published data that are inconsistent. The results in this study support the ICRU Report 40 recommended value.

Models, Theoretical↗

PubMed1991

Particle track structure and its correlation with radiobiological endpoint.

One of the possible ways to classify track structures is application of the conventional partition techniques of analysis of multidimensional data to the track structure. Using these cluster algorithms this paper attempts to find characteristics of radiation reflecting the spatial distribution of ionizations in the primary particle track. Absolute frequency distributions of clusters giving the mean number of clusters produced by radiation per unit of deposited energy have been computed for radiation of different qualities. The results were compared with the published experimental data of cell inactivation. For particular biological objects the critical properties of radiation correlating with the cell inactivation can be found and it seems that the occurrence of a cluster of at least four ionizations formed in a domain of approximately 2-3 nm correlates with the induction of double strand break.

Ions↗