Design and synthesis of pleated DNA origami nanotubes with adjustable diameters

Abstract

Supplementary Note 1 -Search algorithm for locating minimally-strained crossovers.Determination of DNA backbone coordinates. The backbone of a DNA double helix was modelled geometrically with a parametric equation for helices:where r is the radius of an ideal DNA helix (1.0 nm), g is the minor groove angle of the DNA (135°) and is positive for one strand of DNA and negative for the complementary strand, and ℎ 45 is the helical pitch of a DNA helix (3.55 nm). The coordinates of C3' carbon atoms along the helical path were defined by the helical pitch of DNA on a double helix in base pair units ( ℎ 78 = 10.5 / ) at points where = F × GH 8FIJK LM° where i is the base number and ranges from 0 to the length of the DNA helix in base pair units.Thus, a set of coordinates for C3' carbon atoms and NEMids could be determined for a DNA helix. This set of coordinates was transformed to construct an arrangement of three helices with the desired internal angle (helix α, helix β and helix α+1), (Figure 1D and 1E) and an inter-helix distance of 2.25 nm. This corresponds to a geometry where perfectly-aligned crossovers should have an ideal bond-distance. For a given internal angle and number of helices in the nanotube, the minimally strained crossover locations were determined for all combinations of q a and q b angles ( Figure 1D and E), which were sampled every 1°.Identification of crossover locations. From these geometric models, all inter-NEMid and inter-C3' carbon distances and strain scores can be determined. To reduce the number of calculations and ensure an average staple crossover density of one crossover every 1.5 turns of a DNA helix, it was useful to first approximate the location of staple crossovers. This was done as follows: Template crossovers are placed at ends of DNA helices in the nanotube. At the 'bottom' end of the nanotube, the algorithm first determines whether the template crosses over between helix α and helix β, or between helix β and helix α+1 by assessing the strain score of each. The location of the template crossover at the bottom of helix β then sets a reference point from which the location of staple crossovers that form the first length unit can be approximated. If the first template

A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results

“…Another significant application area for oxDNA has been the simulation of large structures to assess their conformation, stability and flexibility ( Fernandez-Castanon et al, 2016 ; Schreck et al, 2016 ; Sharma et al, 2017 ; Shi et al, 2017 ; Benson et al, 2018 ; Choi et al, 2018 ; Coronel et al, 2018 ; Berengut et al, 2019 ; Brady et al, 2019 ; Hoffecker et al, 2019 ; Snodin et al, 2019 ; Berengut et al, 2020 ; Chhabra et al, 2020 ; Poppleton et al, 2020 ; Tortora et al, 2020 ; Yao et al, 2020 ).…”

Stoichiometric quantification of spatially dense assemblies with qPAINT

“…52-helix pleated DNA origami nanotubes were synthesised as previously described (23). Four staple extensions (5'-CGACACCTTAAAGCCGCCGC-3') that were complementary to 20 nt Biotinylated DNA strands (5'-BIOTIN/GCGGCGGCTTTAAGGTGTCG-3) were incorporated at one end of the nanotubes to immobilise the nanotubes on streptavidin-coated surfaces.…”

“…An antiparallel-parallel-antiparallel (APA) staple was incorporated into the 4SEQ nanotubes. This created DNA staple crossovers between the inner DNA helices of the nanotube resulting in a more rigid structure where expansion from electrostatic repulsion between DNA helices was prevented (23). This allowed parallel docking strands to be closely spaced (~3 nm apart).…”

“…We, therefore, sought to address the question of whether qPAINT is a robust method for counting integer stoichiometries when docking strands are separated by small distances. We used a new DNA nanotube structure (23), which allowed us to compare dark times between four identical DNA-PAINT sites that were separated by ~15 nm and as little as 3 nm.…”

Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation

“…We assessed the in-solution properties of the PolyBrick with poly-t extension lengths of 1t, 3t and 6t, by performing molecular dynamics (MD) simulations with the oxDNA coarse-grained model. 77 The oxDNA model has been used to characterise a wide variety of DNA nanostructures [78][79][80][81] and is well suited for elucidating the structural and dynamic properties of the PolyBrick. The model provides a good description of the microscopic behaviour base-pairing interactions 82 and the mechanical properties of single and double stranded DNA, 83 as well as accurate in solution measurements on the structure and thermal fluctuations of large DNA origami structures 81,84 and DNA origami with mechanically compliant hinges.…”