Nanoscience

Regulation of 2D DNA Nanostructures by the Coupling of Intrinsic Tile Curvature and Arm Twist

Authors

Abstract

The overwinding and underwinding of duplex segments between junctions have been used in designing both left-handed and right-handed DNA origami nanostructures. For a variety of DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the DNA tile (specified as the intrinsic tile curvature) has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile curvature and its evolution in DNA tubes by the coupling of the twist of the inter-tile arm (specified as the arm twist) have never been addressed. In this work, we designed three types of tile cores built around a circular 128 nucleotide scaffold by using longitudinal weaving (LW), bridged longitudinal weaving (bLW) and transverse weaving (TW). Joining the tiles with inter-tile arms having the length of an odd number of DNA half-turns (termed O-tiling) almost resulted into planar 2D lattices, whereas joining the tiles with the arms having the length of an even number of DNA half-turns (termed E-tiling) nearly generated tubes. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the E-tiling tubes and thereby the conformations of their component tiles with addressable concave and convex curvatures. When the arms have the normal winding at the relaxed B-form of DNA, the intrinsic tile curvature deter-mines the chirality of the E-tiling tubes. By regulating the arm length and the sticky end length of the bLW-Ep/q (E-tiling of the bLW cores with the arm length of p-bp and the sticky end length of q-nt) assemblies, the arm can be overwound, resulting in a left-handed twist, and can also be underwound, resulting in a right-handed twist. Chiral bLW-Ep/q tubes with either a right-handed curvature or a left-handed curvature can also be formed by the coupling of the intrinsic tile curvature and the arm twist. We were able to assign the chiral indices (n,m) to each tube using high-resolution AFM images, and therefore were able to estimate the tile curvature using a regular polygon model that approximated the transverse section of the tube. A deeper understanding of the integrated actions of dif-ferent types of twisting forces on the DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future.

Version notes

Main revisions as follows: 1 Redo the biotin/SA binding experiments for the bLW-E20/4 (renew Fig. S16) and bLW-E22/6 tubes and correct the assignment of the chirality of bLW-E22/6 to the left-handed curvature (renew Fig. S17). 2 Add the biotin/SA control experiments for the well-known DAE-E21/5 tubes to confirm their right-handed curvature reported previously (new Fig. S23). 3 Add the analysis results of perimeter distributions for bLW-E22/6, bLW-E31/5, both “large” and “giant” bLW-E32/6, and TW-E21/5 tubes (new Tables S3-7). 4 Rewrite and re-organize the manuscript, including the abstract, introduction, results, and discussion.

Content

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Supplementary material

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Regulation of 2D DNA nanostructures by the coupling of intrinsic tile curvature and arm twist
Supporting information available: experimental methods, a discussion about the theoretical estimation of lattice linear and angular constants, a discussion about the tube parameters calculated from the chiral indices (n,m), a discussion about the assignment of the chiral indices (n,m) to a specific tube based on its high-resolution AFM images, a discussion about the assignment of a cluster of the chiral indices (n,m) by numerical approximation for each design, a discussion about the saddle-like model for tile oligomers to simultaneously grow “large” and “giant” tubes, additional AFM images of each assembly with descriptions, and sequence information. These materials are available free of charge via the Internet.