Sprecher
Beschreibung
Several software have been developed for the design of curved DNA origami structures, including DNAxiS [[1]] and MagicDNA 2.0 [[2]]. However, these software have limitations that result in some structures being either completely outside their design space or only realizable with low design accuracy.
In this work, we present a general solution for finding the length differences between helices of a curved design and translating them to a pattern of insertions and deletions, as well as a set of optimal crossover positions, in a caDNAno [[3]] file. This solution is formulated in terms of arc length differences between parametric curves that represent the desired locations of helical axes. We introduce novel software, called AutoMod, that implements the aforementioned solution. AutoMod aims to complement the previous design software by achieving high-accuracy curvature in the cases where previous software either cannot be applied or produce structures whose equilibrium conformation notably deviates from the desired target shape.
We demonstrate the functionality of AutoMod by designing several curved DNA origami structures and showcase significant improvements in design accuracy by comparing oxDNA [[4]] simulation results for structures designed with AutoMod and other methods.
[[1]] D. Fu et al., "Automated design of 3D DNA origami with non-rasterized 2D curvature," Science Advances, 8(51), eade4455, 2022. doi: 10.1126/sciadv.ade4455
[[2]] W. G. Pfeifer et al., "Versatile computer-aided design of free-form DNA nanostructures and assemblies," Science Advances, 9(30), eadi0697, 2023. doi: 10.1126/sciadv.adi0697
[[3]] S. M. Douglas et al., "Rapid prototyping of 3D DNA-origami shapes with caDNAno," Nucleic Acids Research, 37(15), pp. 5001-5006, 2009. doi: 10.1093/nar/gkp436
[[4]] E. Poppleton et al., "oxDNA: coarse-grained simulations of nucleic acids made simple," Journal of Open Source Software, 8(81), 4693, 2023. doi: 10.21105/joss.04693
