The Rule of Thirds: Controlling Junction Chirality and Polarity in 3D DNA Tiles

Abstract

The successful self-assembly of tensegrity triangle DNA crystals heralded the ability to programmably construct macroscopic crystalline nanomaterials from rationally-designed, nanoscale components. This 3D DNA tile owes its "tensegrity" nature to its three rotationally stacked double helices locked together by the tensile winding of a center strand segmented into 7 base pair (bp) inter-junction regions, corresponding to two-thirds of a helical turn of DNA. All reported tensegrity triangles to date have employed <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:semantics> <mml:mrow><mml:mrow><mml:mo>(</mml:mo> <mml:mrow><mml:mi>Z</mml:mi> <mml:mo>+</mml:mo> <mml:mn>2</mml:mn> <mml:mo>/</mml:mo> <mml:mn>3</mml:mn></mml:mrow> <mml:mo>)</mml:mo></mml:mrow> </mml:mrow> <mml:annotation>\[\left( {Z{\bm{ + }}2{\bf /}3} \right)\]</mml:annotation></mml:semantics> </mml:math> turn inter-junction segments, yielding right-handed, antiparallel, "J1" junctions. Here a minimal DNA triangle motif consisting of 3-bp inter-junction segments, or one-third of a helical turn is reported. It is found that the minimal motif exhibits a reversed morphology with a left-handed tertiary structure mediated by a locally-parallel Holliday junction-the "L1" junction. This parallel junction yields a predicted helical groove matching pattern that breaks the pseudosymmetry between tile faces, and the junction morphology further suggests a folding mechanism. A Rule of Thirds by which supramolecular chirality can be programmed through inter-junction DNA segment length is identified. These results underscore the role that global topological forces play in determining local DNA architecture and ultimately point to an under-explored class of self-assembling, chiral nanomaterials for topological processes in biological systems.