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Regulation of 2D DNA Nanostructures by the Coupling of Tile Cur-Vatures and Arm Twists

submitted on 09.06.2021, 15:20 and posted on 10.06.2021, 08:30 by Chuan Jiang, Biao Lu, Wei Zhang, Yoel P. Ohayon, Caihong Ni, Feiyang Feng, Nadrian C. Seeman, Shou-Jun Xiao
DNA overwinding and underwinding between adjacent Holliday junctions have been applied in DNA origami constructs to design both left-handed and right-handed nanostructures. For a variety of DNA tubes assembled from small tiles, only an abstract concept of the intrinsic tile curvature was previously used to explain their formation. Details regarding the quantitative and structural descriptions of the intrinsic tile curvature and its evolution in DNA tubes by coupling with arm twists have been lacking. In this work, we designed three types of tile cores from a circular 128 nucleotide scaffold by longitudinal weaving (LW), bridging longitudinal weaving (bLW), and transverse weaving (TW) and assembled their 2D planar or tubular nanostructures via inter-tile arms with a distance of an odd or even number of DNA half-turns. The biotin/streptavidin (SA) labeling technique was applied to define the tube configuration with addressable inside and outside surfaces and thus their component tile conformation with addressable concave and convex curvatures. Both chiral tubes possessing left-handed and right-handed curvatures could be generated by finely tuning p and q in bLW-Ep/q designs (bLW tile cores joined together by inter-tile arms of even number of half-turns with the arm length of p base pairs (bp) and the sticky end length of q nucleotides (nt)). We were able to assign the chiral indices (n,m) to each specific tube from the high-resolution AFM images, and thus estimated the tile curvature angle with a regular polygon model that approximates each tube’s transverse section. We attribute the curvature evolution of bLW-Ep/q tubes composed of the same tile core to the coupling of the intrinsic tile curvature and different arm twists. A better understanding of integrated actions of different types of twisting forces on DNA tubes will be much more helpful in engineering DNA nanostructures in the future.


Grant No. 91753134, 21571100 from NSFC . Grant No. GM-29554 from NIGMS, Grant Nos. CTS1120890, CCF-1117210, EFRI-1332411, and CHE-1708776 from the NSF, Grant No. W911NF-1110024 from ARO, Grant Nos. N000141110729 and N000140911118 from ONR, DESC0007991 from DOE, and GBMF3849 from the Gordon and Betty Moore Foundation.


Email Address of Submitting Author


Nanjing University



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Declaration of Conflict of Interest

The authors declare no competing financial interest.

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