Molecular Dynamics Investigation of Immobile DNA Four-Way Junctions

Abstract

Immobile four-way junctions (4WJs) are the core structural motif employed in structural nucleic acid nanotechnology to constrain interconnected duplexes. While it is well known that 36 sequence designs form immobile four-way junctions that may exist in one of two stacked conformational isomers, the molecular basis for their stability and stacking interactions remains obscure. For example, experiment indicates that several core sequence motifs exhibit a strong bias for one isomeric state, whereas both isomeric states are preferred equally by others. Molecular dynamics (MD) offers atomic-level insight into the structural and chemical basis for 4WJ interactions leading to preferential stability of one over the other isomeric state. To investigate 4WJ stability, we employed all-atom MD including explicit solvent and experimental ionic conditions to examine the dynamics of the canonical Seeman J1 4WJ that strongly prefers one of its two isomeric states, and compared it with several alternative sequence designs. Analysis of base-pair level duplex and crossover degrees of freedom reveals base stacking and pairing interactions that may impact overall junction stability.