Base-Pair Level Analysis of DNA Four-Way Junction Structure and Dynamics

Immobile four-way junctions (4WJs) form a core structural motif of structured DNA assemblies. Understanding the sequence-level impact of four-way junctions on their structure, stability, and flexibility plays an important role in achieving Angstrom-level spatial control over nucleic acid nanodevices. 4WJs may exist in one of two stacked conformational isomers that are preferentially adopted when free in solution but forced into one or the other configuration in programmed multi-junction assemblies. It has been shown experimentally that the base sequences around the sites of strand crossover in these junctions have a significant impact on the conformational preferences of the two isomers.1,2 In particular, some sequences exhibit significant bias for one isomeric state, whereas others have equal preference between the two isomers. Here, we use explicit solvent and counterion molecular dynamics simulations to explore the base-pair level interactions that give rise to 4WJ conformational states using the classic Seeman J1 junction3 system as a point of reference. A pseudo-alchemical path approach is used to investigate how nicks placed at the site of the strand crossovers impact B-form DNA and crossover geometry and stability, and their dependence on core 4WJ sequence. Free energy calculations and analysis of the base-pair level degrees of freedom4 for each step along this path reveal the structural origin of the significant impact of base sequence on local structure, and suggest how these in turn impact global junction behaviour.References:1. Hyeon, C. et al. (2012) Nature Chemistry, 4, 907-914.2. Miick, S. M. et al. (1997) PNAS, 94, 9080-9084.3. Kallenbach, N. R. et al. (1983) Nature, 305, 829-831.4. Lavery, R. et al. (2009) NAR, 37, 5917-29.