Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics.

ABSTRACT: Immobile four-way junctions (4WJs) are core structural motifs employed in the design of programmed DNA assemblies. Understanding the impact of sequence on their equilibrium structure and flexibility is important to informing the design of complex DNA architectures. While core junction sequence is known to impact the preferences for the two possible isomeric states that junctions reside in, previous investigations have not quantified these preferences based on molecular-level interactions. Here, we use all-atom molecular dynamics simulations to investigate base-pair level structure and dynamics of four-way junctions, using the canonical Seeman J1 junction as a reference. Comparison of J1 with equivalent single-crossover topologies and isolated nicked duplexes reveal conformational impact of

SUBMITTER: Adendorff MR 

PROVIDER: S-EPMC8789063 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature