Regular and Chaotic Dynamics

, Volume 23, Issue 2, pp 135–151 | Cite as

Distribution of Base Pair Alternations in a Periodic DNA Chain: Application of Pólya Counting to a Physical System

  • Malcolm Hillebrand
  • Guy Paterson-Jones
  • George Kalosakas
  • Charalampos Skokos
Article
  • 5 Downloads

Abstract

In modeling DNA chains, the number of alternations between Adenine–Thymine (AT) and Guanine–Cytosine (GC) base pairs can be considered as a measure of the heterogeneity of the chain, which in turn could affect its dynamics. A probability distribution function of the number of these alternations is derived for circular or periodic DNA. Since there are several symmetries to account for in the periodic chain, necklace counting methods are used. In particular, Pólya’s Enumeration Theorem is extended for the case of a group action that preserves partitioned necklaces. This, along with the treatment of generating functions as formal power series, allows for the direct calculation of the number of possible necklaces with a given number of AT base pairs, GC base pairs and alternations. The theoretically obtained probability distribution functions of the number of alternations are accurately reproduced by Monte Carlo simulations and fitted by Gaussians. The effect of the number of base pairs on the characteristics of these distributions is also discussed, as well as the effect of the ratios of the numbers of AT and GC base pairs.

Keywords

DNA models Pólya’s Counting Theorem heterogeneity necklace combinatorics 

Keywords

05A15 92D20 

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Copyright information

© Pleiades Publishing, Ltd. 2018

Authors and Affiliations

  • Malcolm Hillebrand
    • 1
  • Guy Paterson-Jones
    • 1
  • George Kalosakas
    • 2
  • Charalampos Skokos
    • 1
  1. 1.Department of Mathematics and Applied MathematicsUniversity of Cape TownRondebosch, Cape TownSouth Africa
  2. 2.Department of Materials ScienceUniversity of PatrasRioGreece

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