Building Programmable Jigsaw Puzzles with RNA

  title={Building Programmable Jigsaw Puzzles with RNA},
  author={Arkadiusz Chworos and Isil Severcan and Alexey Y. Koyfman and Patrick Weinkam and Emin Oroudjev and Helen Greenwood Hansma and Luc Jaeger},
  pages={2068 - 2072}
One challenge in supramolecular chemistry is the design of versatile, self-assembling building blocks to attain total control of arrangement of matter at a molecular level. We have achieved reliable prediction and design of the three-dimensional structure of artificial RNA building blocks to generate molecular jigsaw puzzle units called tectosquares. They can be programmed with control over their geometry, topology, directionality, and addressability to algorithmically self-assemble into a… 

A polyhedron made of tRNAs

This work demonstrates that a remarkable degree of structural control can be achieved with RNA structural motifs to build thermostable 3D nano-architectures that do not rely on helix bundles or tensegrity.

Composing RNA Nanostructures from a Syntax of RNA Structural Modules.

This work defined an extended structural syntax of RNA modules for programming RNA strands to assemble into complex, responsive nanostructures under both thermodynamic and kinetic control of helical struts to form larger self-folding domains.

Self-assembling RNA square

The programmed self-assembly of RNA squares from complex mixtures of corner units are demonstrated and a concept to exploit the RNA square as a combinatorial nanoscale platform is established.

Defining the syntax for self-assembling RNA tertiary architectures.

  • L. Jaeger
  • Biology
    Nucleic acids symposium series
  • 2009
RNA architectonics refers to the deciphering of a proto-language of RNA and its use to build new functional RNA shapes with self-assembly properties for potential applications in nanotechnology, synthetic biology and medicine.

Controlling RNA self-assembly to form filaments

The three-dimensional design of tectoRNAs incorporating modular 4-way junction motifs, hairpin loops and their cognate loop–receptors to create extended, programmable interaction interfaces are reported, emphasizing the potential of RNA as a scaffold for designing and engineering new controllable biomaterials mimicking modern cytoskeletal proteins.

Design and Crystallography of Self-Assembling RNA Nanostructures.

Methods for the design and X-ray crystallographic structure analysis of an RNA square and two different triangles, which self-assemble from short oligonucleotides and serve as a platform for building functional nano-sized nucleic acid architectures are described.

Rational design of DNA nanoarchitectures.

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

Squaring theory with practice in RNA design.

RNA self-assembly and RNA nanotechnology.

The next step in synthetic RNA design will involve new ways to implement these same types of dynamic and responsive architectures into nanostructures functioning as real nanomachines in and outside the cell.



TectoRNA: modular assembly units for the construction of RNA nano-objects.

Structural information on complex biological RNA molecules can be exploited to design tectoRNAs or artificial modular RNA units that can self-assemble through tertiary interactions thereby forming

Design and self-assembly of two-dimensional DNA crystals

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.

Circuits and programmable self-assembling DNA structures

  • A. CarboneN. Seeman
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2002
This work investigates how basic ideas on tiling can be applied to the assembly and evaluation of circuits, and suggests that these procedures can be realized on the molecular scale through the medium of self-assembled DNA tiles.

TectoRNA and ‘kissing‐loop’ RNA: atomic force microscopy of self‐assembling RNA structures

AFM imaging is presented for two different RNA molecules able to self‐assemble into complex supramolecular architectures, one of which is a molecular dimer of a 230‐nt RNA fragment coming from the RNA genome of a murine leukaemia virus and a large supramolescular fibre formed of artificial self‐assembling RNA molecular units called tectoRNA.

Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices

The construction of an aperiodic patterned DNA lattice (barcode lattice) by a self-assembly process of directed nucleation of DNA tiles around a scaffold DNA strand, a step toward implementation of a visual readout system capable of converting information encoded on a 1D DNA strand into a 2D form readable by advanced microscopic techniques.

Two-dimensional supramolecular chemistry with molecular Tinkertoys

After some initial experiments with point (4) connectors, which function by forming bonds from a central atom to the termini of several rods, the development of a “molecular construction kit,” analogous to the children's Tinkertoy construction set, was worked on.

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

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.

A nanomechanical device based on the B–Z transition of DNA

This work has constructed a supramolecular device consisting of two rigid DNA ‘double-crossover’ (DX) molecules connected by 4.5 double-helical turns, using the transition between the B and Z, forms of DNA to effect switchable motion.