The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

Abstract

The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context.

Mesojunction-Based Design Paradigm of Structural DNA Nanotechnology

“…Specifically, regular junctions are geometrically driven by stacking interactions between opposing helices . Alteration of the junction sequence can be exploited by careful study to drive crossing angles with high precision, but inaccuracies can lead to torsion, bundling, or junction disruption in unanticipated ways . Presumably, the mesojunction design universe of DNA nanotechnology would be less dependent on stacking.…”

Molecular dynamics simulations of cyanine dimers attached to DNA Holliday junctions

“…Furthermore, MD simulations of Holliday junctions have also been performed. 44,[57][58][59] Mathur et al has showed that MD simulations of dyes attached to the Holliday junctions of large DNA bundles can yield dye orientations in agreement with experimental uorescence data. 44 Wheatley et al found that isolated, four-arm Holliday junctions initialized in an open conformation stabilize in a stacked conguration at both high and low salt concentrations, indicating that MD is able to capture the conformational transitions of the Holliday junction.…”

“…Typical Holliday junction IDAs and twist angles fall in the range of ∼60° and ∼40–60°, respectively. 57–59,82 It should be noted that these values are for Holliday junctions without dyes attached to the DNA backbone – the dyes in our study act as an additional base or spacer in the DNA sequence, which may affect the DNA dynamics and conformations. This could lead to discrepancies observed between pure DNA Holliday junctions and Holliday junctions with dyes.…”

“…MD simulations were performed to determine the orientations of the dye dimers and interactions of the dyes with the DNA. The OL15 forceeld, 58,61,62 which had been tested for base ipping in DNA and TNA duplexes, 63,64 was used with non-bonded modi-cations for the DNA phosphate-ion interactions. 65 Similar to previous studies, 45,53 the general Amber forceeld (also known as GAFF) was used for dye bonded and van der Waals parameters 66 that were generated using the ANTECHAMBER soware.…”

“… 57 Simmons et al successfully used MD simulations to explore ion binding sites in isolated Holliday junctions. 58 Adendorff et al utilized MD to study the structure and dynamics of four-arm isolated Holliday junctions to understand the impact of base sequences on the junction structure. 59 However, the role of the DNA Holliday junction conformations and the interactions between the DNA and dyes that affect dye orientations and resultant excitonic properties are not fully understood.…”