Abstract
We used coarse-grained molecular dynamics simulations to characterize the global and local mechanical properties of a DNA origami triangle nanostructure. The structure presents two metastable conformations separated by a free energy barrier that is lowered upon omission of four specific DNA staples (defect). In contrast, only one stable conformation is present upon removing eight staples. The metastability is explained in terms of the intrinsic conformations of the three trapezoidal substructures. We computationally modeled the local accessibility to endonucleases, to predict the reactivity of twenty sites, and found good agreement with the experimental data. We showed that global fluctuations affect local reactivity: the removal of the DNA staples increased the computed accessibility to a restriction enzyme, at sites as distant as 40 nm, due to an increase in global fluctuation. These results raise the intriguing possibility of the rational engineering of allosterically modulated DNA origami.
Highlights
DNA origami are 2D or 3D nanostructures, resulting from the assembly of hundreds of single-strandedDNA molecules with a long ssDNA [1,2,3,4,5]
We showed that REases act in a binary fashion, as certain sites cannot be cut even at extended reaction times, or, for HhaI REase recognition sites in particular, become reactive following the introduction of a distant structural defect in the triangle
We performed extensive Langevin molecular dynamics simulations to determine the conformational dynamics of three triangles that differ in staple composition, and of the isolated trapezoid substructure too
Summary
DNA origami are 2D or 3D nanostructures, resulting from the assembly of hundreds of single-stranded (ss)DNA molecules (staples) with a long ssDNA (scaffold) [1,2,3,4,5]. Studies have demonstrated control of nanostructures behavior through buffer conditions [16,17,18], enzyme action with particular attention to endonuclease reactivity [19,20,21,22,23], and electric fields [24,25,26,27]. We investigated the action of several sequence-specific, DNA-cutting enzymes (restriction endonucleases or REases) towards their recognition sites present in the M13 scaffold sequence. We showed that REases act in a binary fashion, as certain sites cannot be cut even at extended reaction times, or, for HhaI REase recognition sites in particular, become reactive following the introduction of a distant structural defect in the triangle (i.e. by omitting, in the self-assembly process, four staples at a distance of ∼40 nm from the REase site)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
