Physics of Biology

A Model and Genomic Evidence of Imprinting DNA Sequence on Water Structure

Authors: Ivan V. Savelev, Michael M. Rempel, Alexandr V. Vikhorev, Oksana O. Polesskaya, Alexandr V. Vetcher, Richard Alan Miller, Max V. Myakishev-Rempel
Comments: 36 Pages.

A novel model is presented of DNA-water interactions within the cell nucleus, proposing a mechanism for continuous self-reorganization of water structures around DNA. The model suggests that DNA sequences may imprint information onto water through shifting layered structures, facilitating sequence-specific chromatin folding. A key feature of this model is the homologous sequence-specific adhesion of repetitive DNA elements, particularly transposons. In this process, two identical double-helical DNA sequences stick to each other in head to head orientation via transverse water layers, without unwinding or separating their strands. This adhesion is proposed to drive perpetual, dynamic chromatin refolding by pairing identical transposons to form large DNA loops and helices to form 30nm fibers and higher-order chromatin structures. The model postulates the existence of a chromatin code based on the positions of transposons in introns and intergenic sequences, offering a new perspective on the functional significance of these often overlooked genomic regions. Predictions based on this structural model were tested using genome sequence data, revealing specific patterns in purine sequence distribution and nucleotide homology that provide preliminary support for the model. This framework suggests novel functions for repetitive DNA sequences and proposes that sequence-specific chromatin refolding may serve as a mechanism for cellular sequence-guided information processing and self-regulation. While largely theoretical, the model generates testable predictions and suggests new directions for research. Several experimental approaches to validate the model are proposed, emphasizing the importance of in vivo studies or experiments closely mimicking nucleoplasm conditions. This work may have significant implications for understanding gene regulation, developmental biology and physiology, with potential applications in fields such as regenerative medicine and cancer research.
Category: Physics of Biology