AI Article Synopsis
- - The paper focuses on immobile four-way junctions (4WJs), which are essential components in creating programmed DNA assemblies, highlighting the importance of understanding how their sequences affect their structure and flexibility.
- - Using all-atom molecular dynamics simulations, the authors evaluate the structural dynamics of the canonical Seeman J1 junction and compare it with other configurations to assess the influence of the double-crossover motif.
- - The study finds that the base sequence significantly influences local structure, isomer preferences, and overall dynamics of 4WJs, which is crucial for designing complex DNA architectures.
Article 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 the double-crossover motif. We additionally contrast J1 with a second junction core sequence termed J24, with equal thermodynamic preference for each isomeric configuration. Analyses of the base-pair degrees of freedom for each system, free energy calculations, and reduced-coordinate sampling of the 4WJ isomers reveal the significant impact base sequence has on local structure, isomer bias, and global junction dynamics.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8789063 | PMC |
| http://dx.doi.org/10.1093/nar/gkab1246 | DOI Listing |
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