Recently it has been revealed that the equilibrium hydrogen-bond breathing dynamics of terminal base pairs in short DNA exhibit a power-law relaxation similar to that in the time-resolved Stokes shift experiments with an intercalated coumarin probe. Herea simple theory is proposed that relates the Stokes shift signal to the statistics of Poincar\'e recurrences in the base-pair breathing. This theory can explain the origin of the observed slow non-exponential relaxation in time-resolved Stokes shift data for DNA as well as other complex systems. It turns out that an intercalated coumarin greatly increases the breathing fluctuations in the neighboring base pairs . This motion is qualitatively similar to that in terminal residues, with the same exponent in the power-law relaxation decay. The breathing dynamics is transmitted to the photoprobe by direct contacts between aromatic \pi orbitals of stacked bases .
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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Recently it has been revealed that the equilibrium
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
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dynamics of terminal base pairs in short DNA exhibit a
of terminal DNA base pairs exhibits a slow
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similar to that in the time-resolved Stokes shift experiments with an intercalated coumarin probe. Herea simple theory is proposed that relates the Stokes shift signal to the statistics of Poincar\'e recurrences in
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
R
breathing. This theory can explain the origin of the observed slow non-exponential relaxation in time-resolved Stokes shift data for DNA as well as other complex systems. It turns out that an intercalated coumarin greatly increases the breathing fluctuations in the neighboring base pairs . This motion is qualitatively similar
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
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residues, with the same exponent in the power-law relaxation decay. The breathing dynamics is transmitted
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
R
by direct contacts between aromatic \pi orbitals of stacked bases
, and that the weak nanoscale chaos can represent an ubiquitous hidden source of non-exponential relaxation in ultrafast spectroscopy