Biomedical Engineering Reference
In-Depth Information
Fig. 5.2
Examples of DNA
lattices form by periodic
assembly of (
a
) four-arm
junctions and (
b
) bulged
three-arm junctions
a
b
a
b
c
d
e
f
Fig. 5.3
Crossover tiles: (
a
) with one crossing point, (
b
)DAE,(
c
)DAO,(
d
)PX,and(
e
)JX
2
.(
f
)
TectoRNA
base sequences at the end of the helical arms allow self-assembly to other structures
by chemical or enzymatic coupling.
For example, when four four-armed junctions assemble the resulting rhomboidal
structure looks like in Fig.
5.2
a, the acute angle is about 60
ı
. The junctions cross
orthogonally only in the presence of the RuvA protein. Similarly, bulged three-
armed junctions create a triangular motif as that in Fig.
5.2
b, the angles between
helical arms being determined by the lengths of the edges.
Rigid regular superstructures that act as building blocks for complex architec-
tures are called crossover tiles. A DNA crossover molecule consists of two dsDNA
molecules, which interchange a single strand at a single crossover point, as shown in
Fig.
5.3
a; more than one crossing points can exist. For example, a double crossover
tile, DX, forms by single-strand interchange between two dsDNA at two crossover
points. From the five possible DX structural motifs, only two are stable enough:
DAE and DAO, characterized, respectively, by an even and odd number of helical
half-turns between the crossover points. In these structures, illustrated in Fig.
5.3
b, c,
the Coulomb repulsion between antiparallel strands is minimized since the minor
groove of one helix sits in the major groove of the other. In fact, DX tiles are
four-armed junctions linked by neighboring arms, in which branch migration is
inhibited by a proper design of base sequences. Analogously, triple crossover tiles,
TX, contain three helices that interchange single strands at three crossover points,
and so on.
Other DNA motifs encountered in nanodevices based on strand replacement
are the paranemic crossover molecules, PX, which form crossovers between two
parallel helices at every possible point, and its topoisomerase structure, JX
2
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