Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model

Abstract

As detailed structural characterizations of large complex DNA nanostructures are hard to obtain experimentally, particularly if they have substantial flexibility, coarse-grained modeling can potentially provide an important complementary role. Such modeling can provide a detailed view of both the average structure and the structural fluctuations, as well as providing insight into how the nanostructure's design determines its structural properties. Here, we present a case study of jointed DNA nanostructures using the oxDNA model. In particular, we consider archetypal hinge and sliding joints, as well as more complex structures involving a number of such coupled joints. Our results highlight how the nature of the motion in these structures can sensitively depend on the precise details of the joints. Furthermore, the generally good agreement with experiments illustrates the power of this approach and suggests the use of such modeling to prescreen the properties of putative designs.

TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami

“…DNA origami are all‐DNA mesoscopic objects that possess well‐defined structures and can be assembled with high fidelity and good yield, finding applications in materials science, DNA nanotechnology, biomedicine, and more . Mesoscale simulations can be used to investigate their assembly kinetics and mechanics, as well as to aid the design of origami with tailored properties . More detailed ( e.g .…”

“…[19] Mesoscale simulations can be used to investigate their assembly kinetics [21] and mechanics, [44] as well as to aid the design of origami with tailored properties. [62] More detailed (e.g. all-atom) simulations can instead be used to look more closely at the behavior of specific portions of DNA structures, such as junctions [63,64] or, with the use of considerable computational Figure 4.…”

Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure

“…Afterwards, we measured the cleavage percentage as ic1+ic2 iun+ic1+ic2 . For site 4, where the third band has an intensity below the background noise, i c2 was estimated through the ratio ic2 ic1+ic2 , which is equal to the scaffold fraction (this is also true for sites 12,16,19 within an error of 15%). We assigned an error bar at 20% using as reference the difference in estimations for the intensities considering or not the background noise.…”

“…As an example, DNA origami objects are comprised of a long single-stranded (ss)DNA (scaffold) , folded into programmed 2D or 3D shapes by the pairing with multiple short DNA strands (staples), forming defined patterns of double-stranded (ds) domains [11][12][13][14]. In turn, patterns of soft (ss) and stiff (ds) domains can be generated with single nucleotide accuracy within nanostructures that are able to adopt interchangeable conformations [15][16][17][18].…”

Design, optimization, and analysis of large DNA and RNA nanostructures through interactive visualization, editing, and molecular simulation

“…To remedy this, several coarsegrained models have been developed [28][29][30][31][32][33][34][35][36] , each of which with a unique focus on a specific part of the DNA nanostructural design and characterization pipeline. In particular, the oxDNA/oxRNA models have grown in popularity in recent years and have been used for studying DNA/RNA nanostructures and devices 23,32,[37][38][39] as well as RNA/DNA biophysics 30,40,41 . The models represent each nucleotide as a single rigid body, where the interactions between nucleotides are empirically parameterized to reproduce basic structural, mechanical and thermodynamic properties of DNA and RNA FIG.…”