Programming biomolecular self-assembly pathways

@article{Yin2008ProgrammingBS,
  title={Programming biomolecular self-assembly pathways},
  author={Peng Yin and Harry M. T. Choi and Colby R. Calvert and Niles A. Pierce},
  journal={Nature},
  year={2008},
  volume={451},
  pages={318-322}
}
In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human… 

Developmental Self-Assembly of a DNA Tetrahedron

TLDR
This work demonstrates the “developmental” self-assembly of a DNA tetrahedron, where a prescriptive molecular program orchestrates the kinetic pathways by which DNA molecules isothermally self-assemble into a well-defined three-dimensional wireframe geometry.

Kinetic Trans-Assembly of DNA Nanostructures.

TLDR
By integrating the structural and dynamic paradigms of DNA nanotechnology, this work presents a rationally designed synthetic platform that functions in an analogous manner to create complex DNA nanostructures.

Dynamic Self-Assembly: Growth and Breakage of Synthetic DNA Nano-Structures

TLDR
This work bridge dynamic and structural DNA nanotechnology and demonstrate the programmable, dynamic control of self-assembly of DNA nanotubes, a well-known class of micron-sized DNA nanostructures.

DNA Nanotechnology: From Structure to Functionality

Self-assembly, which is ubiquitous in living systems, also stimulates countless synthetic molecular self-assembling systems. Most synthetic self-assemblies are realized by passive processes, going

Developmental Self-Assembly of a DNA Ring with Stimulus-Responsive Size and Growth Direction

TLDR
It is articulate that reversible assembly steps with slow kinetics at appropriate locations in a reaction pathway could enable multiple populations of structures with stimulus-responsive properties to be simultaneously created in one developmental program.

Sequential self-assembly of DNA functionalized droplets

TLDR
The authors program the sequential self-assembly of DNA functionalized emulsions by altering the DNA grafted strands to provide time and logic control during the self- assembly process, and offers a new perspective on the synthesis of materials.

Enzyme-free nucleic acid dynamical systems

TLDR
The creation of a biochemical oscillator that requires no enzymes or evolved components, but rather is implemented through DNA molecules designed to function in strand displacement cascades is described.

Dynamic and Active Proteins: Biomolecular Motors in Engineered Nanostructures.

  • M. Vélez
  • Biology
    Advances in experimental medicine and biology
  • 2016
TLDR
This chapter summarizes some of the progress made in incorporating bio-molecular motors and dynamic self-organizing proteins into protein based functional nanostructures.

Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions.

TLDR
A DNA self-assembly system that can be tuned to form a complex target structure isothermally at any prescribed temperature or homogeneous condition within a wide range is described.

Towards Active Self-Assembly Through DNA Nanotechnology

TLDR
This review introduces progress towards, or related to, active assembly via DNA nanotechnology, and catalogue dynamic DNA assembly systems ranging from passive assembly–disassembly systems, to autonomous assembly systems to sophisticated artificial metabolism and time-clocking oscillation systems.
...

References

SHOWING 1-10 OF 41 REFERENCES

Rational design of DNA nanoarchitectures.

TLDR
This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.

Algorithmic Self-Assembly of DNA Sierpinski Triangles

TLDR
This work reports the molecular realization, using two-dimensional self-assembly of DNA tiles, of a cellular automaton whose update rule computes the binary function XOR and thus fabricates a fractal pattern—a Sierpinski triangle—as it grows.

A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron

TLDR
The design and synthesis of a 1,669-nucleotide, single-stranded DNA molecule that is readily amplified by polymerases and that, in the presence of five 40-mer synthetic oligodeoxynucleotides, folds into an octahedron structure by a simple denaturation–renaturation procedure is reported.

Catalyzed relaxation of a metastable DNA fuel.

TLDR
A metastable DNA "fuel" and a corresponding DNA "catalyst" that improve upon the original hybridization-based catalyst system and becomes a viable component enabling future DNA-based synthetic molecular machines and logic circuits.

Design and self-assembly of two-dimensional DNA crystals

TLDR
The design and observation of two-dimensional crystalline forms of DNA that self-assemble from synthetic DNA double-crossover molecules that create specific periodic patterns on the nanometre scale are reported.

A self-replicating ligase ribozyme

  • N. PaulG. F. Joyce
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 2002
TLDR
A linear dependence was observed between the initial rate of formation of new copies and the starting concentration of ribozyme, consistent with exponential growth, and further optimization of the system may lead to the sustained exponential growth of ribozymes that undergo self-replication.

A DNA-fuelled molecular machine made of DNA

TLDR
The construction of a DNA machine in which the DNA is used not only as a structural material, but also as ‘fuel’; each cycle produces a duplex DNA waste product.

A unidirectional DNA walker that moves autonomously along a track.

TLDR
DNA, with its immense information-encoding capacity and welldefinedWaston–Crick complementarity, has been explored as an excellent building material for nanoconstruction and a diverse group of DNA nanomechanical devices have also been demonstrated.

Folding DNA to create nanoscale shapes and patterns

TLDR
This work describes a simple method for folding long, single-stranded DNA molecules into arbitrary two-dimensional shapes, which can be programmed to bear complex patterns such as words and images on their surfaces.

Nucleic acid junctions and lattices.

  • N. Seeman
  • Biology
    Journal of theoretical biology
  • 1982