Nucleosomal embedding reshapes the dynamics of abasic sites

Abstract

Apurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a most efficient repair by the base excision pathway. The impact of losing a nucleobase on the conformation and dynamics of B-DNA is well characterized. Yet AP sites seem to present an entirely different chemistry in nucleosomal DNA, with lifetimes reduced up to 100-fold, and the much increased formation of covalent DNA-protein cross-links leading to strand breaks, refractory to repair. We report microsecond range, all-atom molecular dynamics simulations that capture the conformational dynamics of AP sites and their tetrahydrofuran analogs at two symmetrical positions within a nucleosome core particle, starting from a recent crystal structure. Different behaviours between the deoxyribo-based and tetrahydrofuran-type abasic sites are evidenced. The two solvent-exposed lesion sites present contrasted extrahelicities, revealing the crucial role of the position of a defect around the histone core. Our all-atom simulations also identify and quantify the frequency of several spontaneous, non-covalent interactions between AP and positively-charged residues from the histones H2A and H2B tails that prefigure DNA-protein cross-links. Such an in silico mapping of DNA-protein cross-links gives important insights for further experimental studies involving mutagenesis and truncation of histone tails to unravel mechanisms of DPCs formation.

Recognition of a Tandem Lesion by DNA Glycosylases Explored Combining Molecular Dynamics and Machine Learning

“…The parameters for 8-oxoG and Ap site have been generated with a standard antechamber procedure embedded in Amber 18 47 , as described in previous references [51][52][53] and in agreement to the literature. Four 10,000 steps minimization runs were carried out on the initial MutM:DNA complex, imposing restraints on the amino and nucleic acids, that were gradually decreased from 20 to 0 kcal/mol/Å 2 along the four runs.…”

A dynamic view of histone tails interaction with clustered abasic sites in a nucleosome core particle

“…In order to further quantify the changes in flexibility induced by the presence of the clustered Ap sites, we relied on a machine learning protocol that we recently applied for studying isolated abasic sites in N-DNA. 18 Probing the contribution of each residue to the overall dynamics of the NCP highlights the increased flexibility of the 12-bp portion of DNA helix that harbors the two lesions -see Figures 3 and S4. Although the abasic sites behavior is more monotonous than in naked B-DNA, the dynamics of the double helix are perturbed by the presence of the clustered lesions.…”

“…15,16 It has also been reported that isolated abasic sites can locally modify the structure and dynamics of Band N-DNA. 17,18 Yet, the impact of clustered abasic sites on a NCP structure remains elusive. Recently, Kurumizaka's group published the very first X-Ray structures of lesioncontaining N-DNA, 17,19,20 while the growing number X-Ray structures of canonical N-DNA and its variants allowed to stimulate computational studies.…”

“…Owing to a simulation protocol we successfully developed and used on isolated, clustered and tandem Ap sites in short oligonucleotides and isolated Ap-containing NCP, 15,16,18,26 we report here a mapping of the histone-DNA interactions in a NCP harboring two closely-spaced Ap sites at SHL 1.5 along four micro-seconds molecular dynamics (MD) simulations replicas. 27 Our model system, derived from the X-Ray structure of Richmond et al, 28 harbors in silico mutated Ap sites at positions 89 and 207 (SHL 1.5), which are directly related to experimental data 8,10 -see Figure 1.…”

“…We also quantified the flexibility of the NCP using a machine learning protocol as we previously did for isolated Ap sites in NCP. 18 Table 1 -DNA parameters of the 12-bp section harboring Ap89 and Ap207. Extrahelicity values of the Ap sites in N-DNA and B-DNA, 15 and averaged total bend angle and standard deviation values for the four MD replicas (MD1-4) and the two control MD of undamaged systems (Control 1 and Control 2).…”