Foldamer R&D

• structural DNA nanotechnology
• de-novo protein engineering
• peptidomimetics like peptoids (& beta-peptides)
• spiroligomers

Some possibly relevant papers

Critical advances in structural DNA nanotechnology

Electrostatics actuation demo (fast data injection)

• Official name: "A self-assembled nanoscale robotic arm controlled by electric fields"
• Authords: "Enzo Kopperger1,*, Jonathan List1,*, Sushi Madhira2, Florian Rothfischer1, Don C. Lamb2,3,4, Friedrich C. Simmel1,4,†"
• Weblink (walled access): http://science.sciencemag.org/content/359/6373/296

Scaling of structural DNA origami to higher self-assebly convergent assembly-levels

• Official Name: "Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components"
• Authors: "Thomas Gerling, Klaus F. Wagenbauer, Andrea M. Neuner, Hendrik Dietz*"
• Places: "Physik Department, Walter Schottky Institute, Technische Universität München Am Coulombwall 4a, 85748 Garching near Munich, Germany"
• MainPublisherInfo: "Science 27 Mar 2015:
  Vol. 347, Issue 6229, pp. 1446-1452
  DOI: 10.1126/science.aaa5372"
• Weblink (walled access): http://science.sciencemag.org/content/347/6229/1446

Demonstration of atomic resolution (but very likely AP only in an statistical average yet!!)

• Official Name: "Placing molecules with Bohr radius resolution using DNA origami"
• Web (walled access): https://www.nature.com/articles/nnano.2015.240

Proof of atoimic precision (topoligical) in structural DNA origami (no atomic resolution yet)

• Official Name: "Cryo-EM structure of a 3D DNA-origami object"
• Authors: "Xiao-chen Bai a, Thomas G. Martin b, Sjors H. W. Scheres a,1, and Hendrik Dietz b,1"
• Places: "a Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; and b Physics Department, Walter Schottky Institute, Technische Universität München, 85748 Garching near Munich, Germany"
• MainPublisherInfo: "PNAS December 4, 2012 109 (49) 20012-20017; https://doi.org/10.1073/pnas.1215713109 "
• Weblink (open access): https://www.pnas.org/content/109/49/20012
• Direct link: https://www.pnas.org/content/pnas/109/49/20012.full.pdf

Advances in de-novo protein engineering

de novo protein design demo

• Official Name: "Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces."
• Authors: "Shane Gonen1,2,3,4, Frank DiMaio2,3, Tamir Gonen1,*, David Baker2,3,4,*"
• Places: (see link)
• Weblink (walled access): http://science.sciencemag.org/content/348/6241/1365.figures-only
• Open: https://cryoem.ucla.edu/uploads/image/pdfs/2015_gonen.pdf

Related

• This is part of Present-forward development as opposed to Future-backward development
• Incremental path
• Reached milestones in foldamer R&D
• Self folding
• covalent cross interlinking (increasing stiffness)
• POPs (persistant organic pollutants) -- See: "Soil pollutants"
• Microfluidics

External links

• Wikipedia: Foldamer
• Wikipedia: De_novo_protein_structure_prediction
• Wikipedia: PeptidomimeticPeptoidBeta-peptide

Video: "Clasp: Common Lisp using LLVM and C++ for Molecular Metaprogramming" [1]
Published on Jun 15, 2015 – Google Tech Talk – June 9, 2015 – Presented by Christian Schafmeister.

This video also brings up topics like:

• The importance of stiffness – double linked backbones prevent rotations making resulting structures much easier to desing and more predictable
• Iterative design of early forms of Kaehler brackets
  optimization of a stiff backbone to get functional groups as close as possible to a fixed predefined configuration (that may have been stolen from a natural protein)
• General software issues – programming language limitations, the dreaded interface problem,
  "deforresting" unnecessary computer algebra reevaluations (a problem also showing up in volumetric 3D modelling aka distance field based 3D modelling; Design levels),
  the need for derivation towers (scalar,vector,tensor) (automatic derivation - links to Conal Elliotts work)
• Going deep down the rabbit-hole to reach a far term target (in an highly non-obvious way for outsiders).
  Sidenote: That's exactly where natural evolution has severe limitations.
• Invention (and market introduction) of covalent protein crosslinking technology
• Bootstrapping of the synthesis of the fundamental spiroligomer building blocks
• The "indestructibility" of spiroligomers raise the issue of the waste problem with POPs (persistent organic pollutants) -- See: Recycling
• The suspected lignin pileup in the Carboniferous epoch of earths history.
• The talk doesn't look beyond towards gemstone based systems as far term goal. Partially brownian technology path?