Non-linear longitudinal compression effect on dynamics of the transcription bubble in DNA

Ideas and methods of nonlinear mathematics and theoretical physics in DNA science: the McLaughlin-Scott equation and its application to study the DNA open state dynamics

The review is devoted to a new and rapidly developing area related to the application of ideas and methods of nonlinear mathematics and theoretical physics to study the internal dynamics of DNA and, in particular, the behavior of the open states of DNA. There are two main competing approaches to this research. The first approach is based on the molecular dynamics method, which takes into account the motions of all structural elements of the DNA molecule and all interactions between them. The second approach is based on prior selection of the main (dominant) motions and their mathematical description using a small number of model equations. This review describes the results of the study of the open states of DNA performed within the framework of the second approach using the McLaughlin-Scott equation. We present the results obtained both in the case of homogeneous sequences: poly (A), poly (T), poly (G) and poly (C), and in the inhomogeneous case when the McLaughlin-Scott equation has been used for studying the dynamics of open states activated in the promoters A1, A2 and A3 of the bacteriophage T7 genome, in the genes IFNA17, ADRB2, NOS1 and IL-5, in the pBR322 and pTTQ18 plasmids. Particular attention is paid to the results concerning the effect of various external fields on the behavior of open states. In the concluding part of the review, new possibilities and prospects for the development of the considered approach and especially of the McLaughlin-Scott equation are discussed.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12551-021-00801-0.

The influence of the DNA torque on the dynamics of transcription bubbles in plasmid PTTQ18

In this work, we study numerically the influence of the DNA torque on the movement of transcription bubbles in the potential field formed by the sequence of plasmid PTTQ18. To imitate the movement, we apply a modified sine-Gordon equation with the two additional terms that describe the effects of dissipation and the action of the DNA torsion torque, and with the coefficients that depend on the sequence of bases. We obtain the trajectories of the transcription bubbles and investigate the dependence of the trajectories on the initial bubble velocity and the DNA torsion torque. It is shown that not the initial bubble velocity but the DNA torsion torque governs the trajectories of the transcription bubbles.

First-principles calculations of Raman vibrational modes in the fingerprint region for connective tissue

Vibrational spectroscopy has been widely employed to unravel the physical-chemical properties of biological systems. Due to its high sensitivity to monitoring real time "in situ" changes, Raman spectroscopy has been successfully employed, e.g., in biomedicine, metabolomics, and biomedical engineering. The interpretation of Raman spectra in these cases is based on the isolated macromolecules constituent vibrational assignment. Due to this, probing the anharmonic or the mutual interactions among specific moieties/side chains is a challenge. We present a complete vibrational modes calculation for connective tissue in the fingerprint region (800 - 1800 cm^-1) using first-principles density functional theory. Our calculations accounted for the inherent complexity of the spectral features of this region and useful spectral markers for biological processes were unambiguously identified. Our results indicated that important spectral features correlated to molecular characteristics have been ignored in the current tissue spectral bands assignments. In particular, we found that the presence of confined water is mainly responsible for the observed spectral complexity.

Multireflection propagation of conformational kinks in a two-component model of DNA as the transfer mode of the transcriptional replication fork

The propagation, or movement, of a conformational kink along a linear structure can occur in capture, transfer, or multireflection modes. Here we use a model for two-component bistable polymer molecules with energetically non-equivalent stable states to model the propagation of the DNA transcription bubble via movement of a non-linear longitudinal stretching region along the DNA chain. We show that under certain conditions the longitudinal excitation can act as a reflector for a conformational kink and, furthermore, that conformational switching may propagate in a multireflection mode alongside conformational kink transition and conformational kink trapping.