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arXiv · 1206.2070

Entromics -- thermodynamics of sequence dependent base incorporation into DNA reveals novel long-distance genome organization

Petr Pancoska·Zdenek Moravek·Uday Kiran Para·Jaroslav Nesetril
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Abstract

Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously uncharacterized physical property of DNA, the incorporation reaction chemical potential Δμ. We use the combination of graph theory and statistical thermodynamics to derive entromics - a series of results providing the thermodynamic model of Δμ. We also show that Δμi is quantitatively characterized as incorporation entropy. We present formulae for computing Δμ from the genome DNA sequence. We then derive important restrictions on DNA properties and genome assembly that follow from thermodynamic properties of Δμ. Finally, we show how these genome assembly restrictions lead directly to the evolution of detectable coherences in incorporation entropy along the entire genome. Examples of entromic applications, demonstrating functional and biological importance are shown.

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Petr Pancoska, Zdenek Moravek, Uday Kiran Para, Jaroslav Nesetril. 2012-03-06. Entromics -- thermodynamics of sequence dependent base incorporation into DNA reveals novel long-distance genome organization. https://arxiv.org/abs/1206.2070

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