Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity

Abstract

The DNA bricks method exploits self-assembly of short DNA fragments to produce custom three-dimensional objects with subnanometer precision. In contrast to DNA origami, the DNA brick method permits a variety of different structures to be realized using the same library of DNA strands. As a consequence of their design, however, assembled DNA brick structure have fewer interhelical connections in comparison to equivalent DNA origami structures. Although the overall shape of the DNA brick objects has been characterized and found to conform to the features of the target designs, the microscopic properties of DNA brick objects remain yet to be determined. Here, we use the all-atom molecular dynamic method to directly compare the structure, mechanical properties and ionic conductivity of DNA brick and DNA origami objects different only by internal connectivity of their consistituent DNA strands. In comparison to equivalent DNA origami objects, the DNA brick objects were found to be less rigid and less dense and having a larger cross-section area normal to the DNA helix direction. At the microscopic level, the junction in the DNA brick structures are found to be right-handed, similar to the structure of individual Holliday junctions in solution, which contrasts with the left-handed structure of Holliday junctions in DNA origami. Subject to external electric field, a DNA brick plate is more leaky to ions than an equivalent DNA origami plate because of its lower density and larger cross-section area. Overall, our results indicate that the structures produced by the DNA bricks method are fairly similar in their overall appearance to those created by the DNA origami method but are more compliant when subject to external forces, which likely is a consequence of their single crossover design.Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2017-02-28 without embargo termsThe student, Scott Michael Slone, accepted the attached license on 2016-07-27 at 10:50.The student, Scott Michael Slone, submitted this Thesis for approval on 2016-07-27 at 11:00.This Thesis was approved for publication on 2016-07-28 at 09:57.DSpace SAF Submission Ingestion Package generated from Vireo submission #10091 on 2017-02-28 at 14:44:56Made available in DSpace on 2017-03-01T15:45:43Z (GMT). No. of bitstreams: 3 SLONE-THESIS-2016.pdf: 22643186 bytes, checksum: b63a7931600e5e0bde05ec624382c949 (MD5) lego_PNAS_thesisversion.zip: 57417658 bytes, checksum: 25c6ce998360377a5ce35f82f4054985 (MD5) LICENSE.txt: 4216 bytes, checksum: 6403a57017f04def6ce2d6763c16d35e (MD5) Previous issue date: 2016-07-2