Advanced
Everything covered so far is mandatory for generating any nanoframes. In this section, we will cover additional properties that one can specify for each synthesized nanoframe.
Edge Types
By default, the helices that pass through a face of the polyhedron are single-bundle. While this saves on how much DNA is used to synthesize an object of some dimensions, it also makes the structure inherently flexible. We provide the option of choosing between single-helix, double-helix, and six-helix bundles for edges of any nanoframe.
Exterior and Interior Extensions
A unique property of nanoframes is their ability to self-assemble into larger organized structures and also trap particles within. These features are enables by exterior and interior extensions which can be disabled if desired. The lengths can be adjusted and a sequence can be uploaded for cutomizable extension types. We recommend adding extensions caps if any subset of extensions will not be in use, this will reduce the probability of aggregation. Extension caps are specialized staples that fit perpendicularly to an extension opening at the edge corners of the nanoframe.
Bond Types
Two bond types exist in nanoframes - Zip Bonds and Arm Bonds. Zip Bonds fold on the second base pair and act like zippers. These bond types have two unpaired (TT) nucleotides for flexibility. Arm bond types on the other hand attached to each other in an anti-parallel fashion, and do not have spare nucleotides for flexibility.
Bridge Length
A key property of nanoframes is their ability to open under thermal control. For this to occur, an optimal set of boundary edges is computed, and the staples that fall on these edges are ligated and nicked accordingly. An intersection is defined as the region where the primary movement domain shift from one axis to another. For instance, if the scaffold is moving in the x direction and then makes a turn to the y, this is called an intersection. The bridge distance is then how many nucleotides are left above equilibrium point.
Reflection Buffer Length
Recall the defition of intersection point. A 90 degree turn is often not an equilibrium point, so to reduce the stress on the strucutre, we include buffer bases that do not bind to any domain. These buffer length are reflected in the staples and not the scaffold.
Color Palette
We have provided an option to toggle the color palletes used for nanoframes. These are only for aesthetic purposes, and can be changed later.