Revision as of 15:09, 13 May 2022

Examples of termination control:
– rotationally symmetric assembly with specifiable number of segments left out
– in self-assemlbly terminating grid of voxels (carterian, hexagonal, or whatever) where
subsets of those voxels (ideally each one individually) can be set or unset (addressed) individually.

Using the terminology of "addressing voxels" may be confusing:
There are no changes after assembly, static structural structures assumed.

Delineation from superficially impressive firatures like size and symmetry:
Infinite symmetries like a non-terminating rod, plane, or volume are considered to possess zero termination control.
Note that this also holds for full 360° rotational symmetry despite there actually being termination.
Full circle termination is considered to be not a controlled one.
Full circle termination is rather considered to be accidental by the fact that ends happen to meet up.

Limiting factors in termination control and countermeasures

de-novo proteins

• artificial de-novo proteins can only provide a small set of orthogonal interfaces.
  And it is hard to get high specificity and activity at the same time
• their otherwise desired stiffness gets in the way.
  There is no DNA like step by step unzipping process possible.
  All bond breaking energy needs to be supplied in one fell swoop.
• Internal cohesion, external intefaces and everntal other external functionality are
  three mutually competing factors on the choice of sie-chain sequences.
  Such a situation is not present in structural DNA nanotechnology.

Countermeasures:

• Squigglesebly
• Circumsembly
• integrate into more termination-control-scalable background framework
  like e.g. structural DNA nanotechnology

spiroligomers

• their otherwise desires stiffness gets in the way.
  They are less conforming and less tolearant to in variation to complementary shapes
• they still quite small molecules limiting their rreachion site choosing specificity similar to conventional chemistry

Countermeasures:

• integrate into more termination-control-scalable background framework like e.g. de-novo proteins.

Structural DNA nanotechnology

• Diffusuion time. Especially for larger 3D structures exclusively made from short strands yields drop far down.

Countermeasures:

• Using longer backbone strands shortening the finding process can help, but
  these come with tradeoffs. (wiki-TODO: refresh on that one)
• Hierarchical assembly
• Maybe tether-based / hinged-based assembly approaches

Related

• Self assembly

(TODO: look into formally quantifying the quantity of termination control)