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Predicting promoter activity of DNA fragment is an important task for computational biology. Approaches using physical properties of DNA to predict bacterial promoters have recently gained a lot of attention. To select an adequate set of physical properties for training a classifier, various characteristics of DNA molecule should be taken into consideration. Here, we present a systematic approach that allows us to select less correlated properties for classification by means of both correlation and cophenetic coefficients as well as concordance matrices. To prove this concept, we have developed the first classifier that uses not only sequence and static physical properties of DNA fragment, but also dynamic properties of DNA open states. Therefore, the best performing models with accuracy values up to 90% for all types of sequences were obtained. Furthermore, we have demonstrated that the classifier can serve as a reliable tool enabling promoter DNA fragments to be distinguished from promoter islands despite the similarity of their nucleotide sequences.

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The problem of modelling the movement of a nonlinear conformational perturbation (i.e., kink) along a DNA molecule is considered taking into account the dissipation. The study of movement peculiarities is performed using a homogeneous sequence of nucleotides and a heterogeneous one consisting of two homogeneous parts separated by a boundary. Using analytic and numerical methods, it is shown that the effect of dissipation leads to a decrease of the energy of kink E, its velocity v, and the mass M. It is also shown that the consideration of the dissipation near the boundary leads to a smoothing of kink motion trajectories in the plane {z, t} in comparison with trajectories calculated without taking into account the dissipation and characterized by a sharp bend on the boundary caused by effects of reflection from the boundary or by a passage through the boundary with an increase or decrease of motion velocity.

В данной работе в рамках модели синус-Гордона рассчитываются динамические характеристики кинков и антикинков, активированных в однородных полинуклеотидных цепочках, каждая из которых содержит только один из видов оснований: аденины, тимины, гуанины или цитозины. Получены аналитические формулы и построены графики для профилей кинков и антикинков и для плотности их энергии в 2D-и 3D формате. Вычислены масса кинков и антикинков, их энергия покоя и размеры. Рассчитаны траектории движения кинков и антикинков в фазовом пространстве в 2D-и 3D-формате.