The relationship between periodic dinucleotides and the nucleosomal DNA deformation revealed by normal mode analysis

Abstract

Nucleosomes, which contain DNA and proteins, are the basic unit of eukaryotic chromatins. Polymers such as DNA and proteins are dynamic, and their conformational changes can lead to functional changes. Periodic dinucleotide patterns exist in nucleosomal DNA chains and play an important role in the nucleosome structure. In this paper, we use normal mode analysis to detect significant structural deformations of nucleosomal DNA and investigate the relationship between periodic dinucleotides and DNA motions. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing that they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently.

Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae

“…A dinucleotide refers to the pairing of two nucleotides along the DNA sequence. The observed transitions of dinucleotides can be correlated with the thermodynamic, geometrical, and structural properties of DNA sequences [103].…”

“…Our analysis suggests that the occurrence of specific dinucleotides in the PsgM02F and PsgM04F phage genomes is intricately related to DNA flexibility to a certain degree. Numerous studies have established the impact of dinucleotides and their spatial arrangement within the genome on contributing to a more flexible DNA structure [103,108,116,117]. It is crucial to note, however, that the role of certain dinucleotides in DNA flexibility or rigidity is context-dependent, indicating that their influence is not universally defined and can vary.…”

Transcriptional Protein-Protein Cooperativity in POU/HMG/DNA Complexes Revealed by Normal Mode Analysis

“…Cooperativity, in protein-DNA [ 25 ] and protein-protein [ 26 ] interactions, is an important feature in biomolecular interactions. In our work, we carried out a series of studies on the cooperative manner of Oct and Sox at their enhancer binding sites, which are important elements in the transcriptional regulation of embryonic stem cells.…”