Theory of phase segregation in DNA assemblies containing two different base-pair sequence types

Dominic J. Lee, Aaron Wynveen, Alexei A. Kornyshev

Research output: Contribution to journalArticlepeer-review

Abstract

Spontaneous pairing of homologous DNA sequences - a challenging subject in molecular biophysics, often referred to as 'homology recognition' - has been observed in vitro for several DNA systems. One of these experiments involved liquid crystalline quasi-columnar phases formed by a mixture of two kinds of double stranded DNA oligomer. Both oligomer types were of the same length and identical stoichiometric base-pair composition, but the base-pairs followed a different order. Phase segregation of the two DNA types was observed in the experiments, with the formation of boundaries between domains rich in molecules of one type (order) of base pair sequence. We formulate here a modified 'X-Y model' for phase segregation in such assemblies, obtain approximate solutions of the model, compare analytical results to Monte Carlo simulations, and rationalise past experimental observations. This study, furthermore, reveals the factors that affect the degree of segregation. Such information could be used in planning new versions of similar segregation experiments, needed for deepening our understanding of forces that might be involved, e.g., in gene-gene recognition.

Original languageEnglish (US)
Article number015014
JournalNew Journal of Physics
Volume19
Issue number1
DOIs
StatePublished - Jan 2017

Bibliographical note

Funding Information:
AAK is grateful to Japanese Society for promotion of Science (JSPS) for short term award and Prof KYoshikawa, his host at Doshisha University, where this work has been started. Discussions with him and Professor Takashi Ohyama are greatly appreciated. AW acknowledges the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported within this paper.

Keywords

  • DNA
  • DNAassemblies
  • homology recognition
  • phase segregation
  • statistical mechanics

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