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arXiv · 1606.08629

Weak Nanoscale Chaos And Anomalous Relaxation in DNA

Alexey K. Mazur
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Abstract

Anomalous non-exponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian chaos, with parameters similar to experimental data. Here, the relationship is studied between this motion and spectroscopic signals measured in DNA with a small molecular photoprobe inserted into the base-pair stack. To this end, the earlier computational approach in combination with an analytical theory is applied to the experimental DNA fragment. It is found that the intensity of breathing dynamics is strongly increased in the internal base pairs that flank the photoprobe, with anomalous relaxation quantitatively close to that in terminal base pairs. A physical mechanism is proposed to explain the coupling between the relaxation of base-pair breathing and the experimental response signal. It is concluded that the algebraic relaxation observed experimentally is very likely a manifestation of weakly chaotic dynamics of hydrogen-bond breathing in the base pairs stacked to the photoprobe, and that the weak nanoscale chaos can represent an ubiquitous hidden source of non-exponential relaxation in ultrafast spectroscopy.

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Alexey K. Mazur. 2017-06-23. Weak Nanoscale Chaos And Anomalous Relaxation in DNA. https://doi.org/10.1103/physreve.95.062417

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