DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study.

In eukaryotes, DNA achieves a highly compact structure primarily due to its winding around the histone cores. The nature wrapping of DNA around histone core form a 1.7 left-handed superhelical turns, contributing to negative supercoiling in chromatin. During transcription, negative supercoils generated behind the polymerase during transcription may play a role in triggering nucleosome reassembly. To elucidate how supercoils influence the dynamics of wrapping of DNA around the histone cores, we developed a novel model to simulate the intricate interplay between DNA and histone. Our simulations reveal that both positively and negatively supercoiled DNAs are capable of wrapping around histone cores to adopt the nucleosome conformation. Notably, our findings confirm a strong preference for negative supercoiled DNA during nucleosome wrapping, and reveal that the both of the negative writhe and twist are beneficial to the formation of the DNA wrapping around histone. Additionally, the simulations of the multiple nucleosomes on the same DNA template indicate that the nucleosome tends to assemble in proximity to the original nucleosome. This advancement in understanding the spontaneous formation of nucleosomes may offer insights into the complex dynamics of chromatin assembly and the fundamental mechanisms governing the structure and function of chromatin. Author summary: The compacted organization of DNA within chromatin is primarily attributed to its intricate winding around histone cores. This winding process involves 1.7 left-handed superhelical turns around the histone core, contributing to the negative supercoiling within chromatin fibers. To gain deeper insights into how DNA supercoiling impacts the dynamics of DNA wrapping around histone cores, we first devised a novel computational model that simulates the intricate interplay between DNA and histone cores. The simulations reveal that both of the positively and negatively supercoiled DNA can spontaneously adopt the nucleosome conformation upon wrapping around the histone core, and demonstrated a strong preference for negative supercoiling during nucleosome wrapping. Additionally, the simulations of multiple nucleosomes assembling show that the nucleosome tends to assemble near original nucleosome. Finally, we examined that both the negative writhe and twist components are advantageous for the formation of the nucleosome. The studies shed light on the intricate dynamics underlying chromatin assembly and its functional implications. [ABSTRACT FROM AUTHOR]