Oligo-origami: DNA directed multi-dimensional self-assembly growth for nanoarchitectures
DNA is currently being recognized as a generic material, beyond its genetic information-conveying nature, for material sciences. DNA-based self-assembly is of particular interest which can be utilized for bottom-up system based fabrication of unique bio-nano-constructs for structural DNA nanotechnology. DNA sequences of guanine (G)-rich tracts are specially high-lighted due to their potential to form G-quadruplex.
In addition to their remarkable biological roles in vivo, their tendency for self-aggregation towards higher-ordered supramolecular structures has rendered them possible candidates for autonomous construction of bio-nano-architectures. However, the knowledge on how to control versatile aggregations is yet not clear, which is vital in the programmed assembly of novel biomaterials.
We are investigating ‘single-stranded DNA origami’ and looking for the general mechanism to describe quadruplex-based self-assembling by finding novel G-rich oligonucleotides sequences. We have reported a single-base substitution effect on self-assembling nature of G-rich dodecanucleotides shown by gel-electrophoresis, circular dichorism, molecular dynamics and AFM. The extremely interesting images
which are showing the assembly in 3-D plane with the average heights of aggregates four times or more of the measured height of double-stranded B-DNA, making these candidates very distinct from the aggregation products of other reported G-rich sequences (see Fig below).
Fig. AFM images of G-lego aggregates generated by d(G11T),12nt long oligodeoxyribonucleotides. Higher-order self assembly of d(G11T) was appeared as networks-like structure with more braches, bends and kinks. The average height was measured of 3.7±1.2 nm with a maximum height of 8.8 nm. The width was measured of 37±11nm and lengths range from 200 to >1000nm. Scale: x and y axis = 0 to 500 nm and z axis = 0 to 10 nm.
Based on the facts thus revealed, we proposing a model, ‘G-lego’, for their versatility to act as biocatalysts for the self-assembling phenomenon inspired by the Diels-Alder cycloaddition reaction. G-lego is successively kissing of a unitary G-quartet block through a switching of intramolecular or intermolecular pairing (see Fig below). We termed this phenomenon as “Oligo-origami”. Our model introduces an evolutionary concept of a systematic reforming of molecular connections by flipping (‘Right turn!’), leading to a 3D architecture. DNA quadruplex-based oligo-origami and their versatility to breakthroughs in nanobiotechnology and will open the doors for DNA-based applications in nanobiotechnology.
References:
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Manish Biyani and Koichi Nishigaki (2005) Structural characterization of ultra-stable higher-
ordered aggregates generated by novel guanine-rich DNA sequences. Gene 364, 130-138.
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Manish Biyani, Yoshihiro Kikkawa, Masahiro Fujita and Koichi Nishigaki (2009) DNA
directed
multi-dimensional self-assembly growth for nanoarchitectures: model and evidences. Nature
Materials (to be submitted)
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