Biomolecular Architecture for Nanotechnology - Bionanoelectronics: Bioinquiring and Bioinspired Devices - page 154

(see Fig. 5.3 d, e). PX are more stable than DX molecules. Crossover tiles can
act as building blocks for more complex motifs and can self-assemble in planar
periodic patterns or nonplanar architectures through sticky ends, which hybridize
with complementary base sequences placed as sticky ends on other tiles.
Other motifs used in bionanotechnology and that can be assembled in larger
bidimensional structures are DNA quadruplexes, which consist of four guanine-rich
strands that form a bundle with a square cross section in the presence of monovalent
cations, and tecto-RNA structures, which contain two connected hairpin loops
positioned at a right angle, as shown in Fig. 5.3 f( Feldkamp and Niemeyer 2006 ).
A more detailed discussion on RNA architectonics can be found in Jaeger and
Chworos ( 2006 ). RNA molecules are less stable than DNA, and the Watson-
Crick base-pairing principle is less selective. Therefore, they are seldom used in
conjunction with inorganic nanotechnology.
Tubular DNA or protein structures can be considered as building blocks for three-
dimensional architectures. These nanotubes are in turn assembled from smaller
planar tiles, for example, DX tiles, designed such that a curved structure is favored
by the orientation and spacing of crossover points. Three-dimensional structures can
be obtained by joining together different types of component tiles/molecules. For
example, DNA polyhedra have duplexed DNA edges and rigid multiarm junction
molecules as vertices ( Lin et al. 2009 ). In other experiments, cubes are constructed
with edges consisting of two turns of DNA double helices and faces containing
a cyclic strand linked twice to each neighbor ( Seeman 1998 ). Tetrahedra can be
opened or closed to act as cage for smaller molecules if hairpin loops, which can
be opened by specific fuel strands and closed by corresponding antifuel strands, are
incorporated on the edges of tetrahedra. A wide variety of architectures that can be
build from DNA strands are described in detail in the review works ( Seeman 1998 ;
Feldkamp and Niemeyer 2006 ; Jaeger and Chworos 2006 ; Lin et al. 2009 ).
Nondesirable hybridization between tiles can be avoided by limiting the sim-
ilarity of base sequences of strands that must not hybridize; powerful computer
programs are used to design such sequences, which usually consist of short
overlapping subsequences. It is important to know whether the final biomolecular
pattern is symmetric or asymmetric since the number of different tiles required to
form a specific structure depends on the symmetry of the structure. For example, a
bidimensional array of N tiles with m-fold symmetry can be self-assembled using
N=m different tiles instead of N, if this ratio has an integral value, or IntŒN=m C 1
unique tiles otherwise ( Lin et al. 2009 ). The dimension of a certain structure is
controlled by replacing the sticky ends at the tiles that do not bind, i.e., on the
boundaries of the structure, by hairpin loops, or blunt ends.
Biological self-assembly of DNA junctions, lattices, or tiles, occur under certain
environmental conditions according to the structural information encoded in their
base sequence. The self-assembly process is hierarchical, in the sense that the
individual tiles form first and their association follows. Spontaneous self-assembly
is possible only when the final structure has a lower free energy than the starting
components. To synthesize DNA for example, purified oligonucleotides with a
properly designed base sequence are mixed at the stoichiometric molar ratio in