Exchange-Symmetric Dissipation at the DNA-RNA Polymerase Interface

Tatsuaki Tsuruyama

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arXiv · 2601.08577

Exchange-Symmetric Dissipation at the DNA-RNA Polymerase Interface

Tatsuaki Tsuruyama

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Abstract

In the DNA-RNA polymerase complex, RNA polymerase (RNAP) selectively incorporates ribonucleoside triphosphates according to the base information encoded in DNA, elongates the RNA strand, and progresses along the template. The state of the template DNA therefore conditions RNAP binding and chemical transitions. Conversely, from the viewpoint of DNA, the binding state and coordinate position of RNAP condition the local structural response of DNA. As RNAP advances, upstream DNA reanneals, downstream DNA opens, the RNA-DNA hybrid constrains the local geometry, and local bending and twisting of the DNA are updated. We introduce an interface dissipation, {\Sigma}int, that provides an exchange-symmetric measure of path irreversibility at the DNA-RNAP interface, independent of whether DNA or RNAP is assigned the role of observer or observed. Irreversibility is quantified by the path-space Kullback-Leibler (KL) divergence between the forward path measure and its time-reversed counterpart, from which the dissipation of the joint system and those of the marginal systems are defined. The non-negativity of the interface dissipation derived in this work does not rely on RNAP-specific kinetic assumptions; rather, it holds for general path processes for which the relevant KL divergences and conditional path measures are well defined. RNAP transcription is treated as a biophysical application of this general theorem to the DNA-RNAP interface.

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Tatsuaki Tsuruyama. 2026-01-13. Exchange-Symmetric Dissipation at the DNA-RNA Polymerase Interface. https://arxiv.org/abs/2601.08577

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