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Bioinformatics Vol. 15 no. 12 1999
Pages 957-964
© 1999 Oxford University Press

Polymer chromosome models and Monte Carlo simulations of radiation breaking DNA

A. L.Ponomarev 1 and R. K.Sachs 1

1 Department of Mathematics, University of California, Berkeley, CA 94720, USA

Motivation: Chromatin breakage by ionizing radiation is relevant to studies of carcinogenesis, tumor radiotherapy, biodosimetry and molecular biology. This article focuses on computer analysis of chromosome irradiation in mammalian cells.

Methods: Polymer physics and Monte Carlo numerical methods are used to develop a coarse-grained computational approach. Chromatin is modeled as a random walk on a cubic lattice, and the radiation tracks hitting the chromatin are modeled as straight lines hitting lattice sites. Each track can make a cluster of DSBs on a chromosome.

Results: The results obtained replace conjectured DNA fragment-size distribution functions in the recently developed RLC formalism by more mechanistically motivated distributions. The discrete lattice algorithm reproduces features of current radiation experiments relevant to chromatin on large scales. It approximates the continuous formalism and experimental data with adequate precision. It was also found that assuming either fixed chromatin with correlations among different clusters of DSBs or moving chromatin with no such correlations gives virtually identical numerical predictions.

Availability: This set of subroutines comprises the DNABreak package available at the UC Berkeley mathematical radiobiology site: http://math.berkeley.edu/~sachs/ponomarev/artem.index.html

Contact: alp17{at}math.berkeley.edu

Abbreviations: Mbp, megabasepair; DSB, DNA double strand break; RLC, randomly-located-clusters Sachs et al. (1999);PBC, periodic boundary conditions Binder (1995); RW, random walk Sokal (1995); size, genomic content in Mbp.

Received on February 17, 1999 ; revised on June 15, 1999 ; accepted on June 17, 1999

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