Field: Math/Applied Math/Informatics
Session Topic:
DNA-Based Nanosystems
Speaker:
Satoshi Murata/Tokyo Institute of Technology
1. Introduction
DNA nanotechnology is one of the emerging nanotechnologies utilizes physical and
biological properties of DNA molecules. As building material of nanostructure, DNA
molecules have advantages such as chemical stability, easiness of mass production
and specific hybridization between complementary base sequences. The last property
is especially important for programmable assembly of nanostructure. Using the
complementary strands of DNA as molecular connectors, various systems such as
molecular computer, intelligent medicine and molecular memory can be realized.
Various kinds of DNA motifs have been proposed as building blocks of
nanostructure. Among them, one of the most popular and powerful motifs is called a
DNA tile. The DNA tile is a rigid supermolecule composed of two interwoven DNA
double helices. It has four “sticky ends” at the ends of the double helices. It is proven
that DNA tiles have capability of computation. Recently, ability of DNA tiles to
self-assemble two-dimensional nanostructure has been experimentally examined. It is
possible to make programmed periodic or aperiodic patterns on a lattice made of DNA
tiles.
2. Error Suppression of DNA tile self-assembly
Suppression of assembly errors is essentially important to reap the benefits of the
nanostructure. We have to cope with several kinds of errors accompanied by
self-assembly process. These errors are mainly caused by mismatch of the sticky ends
of non-complementary strands (Fig.1).
Fig. 1 Three type of
error in DNA tile
self-assembly
(a) mismatch error
(b) facet error
(c)random aggregation
We propose two models for error
suppression: the Protected Tile Model (PTM)
and the Layered Tile Model (LTM). We
propose that these can suppress nucleation
errors as well as growth and facet errors. In
these models, we alter the implementation of
the DNA tiles by introducing new structural
motifs called protection strands and protection
tiles. These molecules cover (protect) the
exposed sticky ends of the DNA tile to
minimize spurious interactions involving
monomers, while the growth front of proper
assemblies become de-protected, and thus
favored for growth.
Fig.2 Error suppression mechanism of
Layered Tile Model
3. DNA tile self-assembly in micro-fluidic device
The assembly process is strongly affected by the concentration of the DNA tile and the
temperature of the water solution. We have proposed a microfluidic device for DNA
self-assembly. Key ideas of this microfluidic device are as follows: 1) Single-strand
DNAs are immobilized on a
surface of reaction chamber.
This gives scaffolds to initiate
the self-assembly process, while
anchoring
the
assembled
structure against the flow. 2)
Monomer
DNA
tiles
are
supplied by flow in the
microchannel.
Constant
concentration
around
the
crystal can easily be realized by
a constant flow.
Fig. 3 Micro-fluidic device for DNA tile self-assembly
4. Conclusion
DNA based-nanosystem is one of the emerging technology of nano-tech. It is still in
a primitive stage, however several basic methodologies to build up large-scale complex
nano-systems are already arising. DNA tile is one of them, which is a building block of
algorithmic self-assembly. DNA origami, which is another important method to build
programmed structure will be fundamental tool to make middle size (~100nm)
nano-structure. Many kinds of DNA logics and DNA actuators are also proposed and
examined in laboratory level. These technologies will be combined and integrated to
open new field of applications such as molecular computation, intelligent drug and
bio-material with new functions.