Programming DNA Self-Assembly by Geometry

Abstract

This manuscript introduces geometry as a means to program the tile-based DNA self-assembly in two and three dimensions. This strategy complements the sequence-focused programmable assembly. DNA crystal assembly critically relies on intermotif, sticky-end cohesion, which requires complementarity not only in sequence but also in geometry. For DNA motifs to assemble into crystals, they must be associated with each other in the proper geometry and orientation to ensure that geometric hindrance does not prevent sticky ends from associating. For DNA motifs with exactly the same pair of sticky-end sequences, by adjusting the length (thus, helical twisting phase) of the motif branches, it is possible to program the assembly of these distinct motifs to either mix with one another, to self-sort and consequently separate from one another, or to be alternatingly arranged. We demonstrate the ability to program homogeneous crystals, DNA “alloy” crystals, and definable grain boundaries through self-assembly. We believe that the integration of this strategy and conventional sequence-focused assembly strategy could further expand the programming versatility of DNA self-assembly.

Design of Orthogonal DNA Sticky-End Cohesion Based on Configuration-Specific Molecular Recognition

“…The tolerance difference against the disruption of perfect B-form DNA conformation can be attributed to the balance between bond strength of base pairing and internal strain. When the base pairing is much stronger than the strain, the desired structure holds with internal structure deformations. , Notably, as shown in a very recent study, the geometry of sticky-end cohesion interface can be engineered to enable a specific bonding orientation . In our strategy on the other hand, when relatively weak base pairing fails to counter the internal strain induced by a constrained configuration, the desired structure would only form under configuration-specific cohesions.…”

“…3,35 Notably, as shown in a very recent study, the geometry of sticky-end cohesion interface can be engineered to enable a specific bonding orientation. 42 In our strategy on the other hand, when relatively weak base pairing fails to counter the internal strain induced by a constrained configuration, the desired structure would only form under configuration-specific cohesions. As a result, the configuration specificity of our molecular recognition strategy has led to a level of extreme precision where configurational deviation of even a single base pair can result in structure failure.…”

Assembly of Two‐Dimensional DNA Arrays Could Influence the Formation of Their Component Tiles

“…Individual DNA single strands first assemble into well‐defined structural tiles, which, then, further associate with each other into final nanostructures. This strategy has allowed assembly of a wide range of DNA nanostructures from discrete objects to extended arrays [13–23] . In the tile‐based DNA assembly, the final structures can be precisely predicted from the tile structures and the tile structures have no change during the final structure formation [8] .…”

“…This strategy has allowed assembly of a wide range of DNA nanostructures from discrete objects to extended arrays. [13][14][15][16][17][18][19][20][21][22][23] In the tile-based DNA assembly, the final structures can be precisely predicted from the tile structures and the tile structures have no change during the final structure formation. [8] Here, we report a case study that the final DNA structures impact on the tile formation.…”

Self‐Assembled Micro‐Sized Hexagons Built from Short DNA in a Crowded Environment

“…The control of self‐assembled liquid crystalline composed of biological building blocks has also attracted attention from a molecular engineering perspective [14–16] . In recent years, various DNA crystals self‐assembled through base pairing have been developed [17–22] …”