Difference between revisions of "Foldamer R&D"

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(→‎External links: elaborated by adding: "indestructibility" of spiroligomers)
(→‎Related)
 
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* spiroligomers
 
* spiroligomers
  
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== Related ==
+
= 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"
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* 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"
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* MainPublisherInfo: "Science  27 Mar 2015: <br> Vol. 347, Issue 6229, pp. 1446-1452 <br> DOI: 10.1126/science.aaa5372"
 +
*Weblink (walled access): http://science.sciencemag.org/content/347/6229/1446
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 +
'''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"
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* Web (walled access): https://www.nature.com/articles/nnano.2015.240
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'''Proof of atoimic precision (topoligical) in structural DNA origami (no atomic resolution yet)'''
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*Official Name: "Cryo-EM structure of a 3D DNA-origami object"
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*Authors: "Xiao-chen Bai a, Thomas G. Martin b, Sjors H. W. Scheres a,1, and Hendrik Dietz b,1"
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* 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"
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* MainPublisherInfo: "PNAS December 4, 2012 109 (49) 20012-20017; https://doi.org/10.1073/pnas.1215713109 "
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* Weblink (open access): https://www.pnas.org/content/109/49/20012
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* 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,*"
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* Places: (see link)
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* Weblink (walled access): http://science.sciencemag.org/content/348/6241/1365.figures-only
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* Open: https://cryoem.ucla.edu/uploads/image/pdfs/2015_gonen.pdf
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= Related =
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* This is part of [[Present-forward development]] as opposed to [[Future-backward development]]
 
* [[Incremental path]]
 
* [[Incremental path]]
 
* [[Reached milestones in foldamer R&D]]
 
* [[Reached milestones in foldamer R&D]]
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* Microfluidics
 
* Microfluidics
  
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== External links ==
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= External links =
  
 
* Wikipedia: [https://en.wikipedia.org/wiki/Foldamer Foldamer]
 
* Wikipedia: [https://en.wikipedia.org/wiki/Foldamer Foldamer]
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* Bootstrapping of the synthesis of the fundamental spiroligomer building blocks
 
* 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 "indestructibility" of spiroligomers raise the issue of the waste problem with POPs (persistent organic pollutants) -- See: [[Recycling]]  
−
* The lignin pileup in the [https://en.wikipedia.org/wiki/Carboniferous Carboniferous] epoch of earths history.
+
* The suspected lignin pileup in the [https://en.wikipedia.org/wiki/Carboniferous Carboniferous] epoch of earths history.
 
* The talk doesn't look beyond towards gemstone based systems as far term goal. Partially [[brownian technology path]]?
 
* The talk doesn't look beyond towards gemstone based systems as far term goal. Partially [[brownian technology path]]?

Latest revision as of 12:33, 13 March 2021

This article is a stub. It needs to be expanded.

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!!)

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

Advances in de-novo protein engineering

de novo protein design demo

Related

External links

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?
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