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which store their information in the form of single-stranded oligonucleotides: certain
types of viruses. Based on how these viruses replicate their genome, researchers found a
way to obtain long, single-stranded DNA using techniques from molecular biology that
will not be further discussed here. Most appealingly, this direction of DNA nano-
technology has been termed DNA origami by its founders [12].
Now it should be a simple task for us to imagine porting this building principle from
the second to the third dimension in order to create objects such as the cube depicted
in Figure 9.2b. Following this seminal work of DNA-based 3-D nanoconstruction by See-
man, others subsequently described the self-assembly of even larger and more complex 3-D
shapes such as boxes with a controllable lid to open and close constructed of only DNA [13].
Figure 9.2c shows an example of how artificial structures such as 1,1
0
:3
0
,1
00
-terphenyl
moieties can be incorporated into large circular DNA single strands in order to preorgan-
ize them in the shape of a triangle. Subsequently, three matching single strands, compris-
ing overhangs on both ends, wrap around the preformed triangle and thereby equip it with
six single-stranded studs, two each protruding from every corner in opposite directions.
After another strand has been added, these overhangs are joined together and long
polymeric tubes of triangular cross-section are formed which again can be visualized on
surfaces by techniques such as AFM [14]. It was further shown that guest compounds
such as gold nanoparticles can be loaded and released from the prism-shaped compart-
ments of the polymeric structure, which might give new perspectives for DNA-based
drug delivery [15].
Although the sense of playing puzzle games with DNA on the nanoscale might be
questioned, a couple of systems may serve as examples for possible future applications:
(1) the precise molecular positioning of reaction partners on top of DNA origami tiles
allows the elucidation of reaction mechanisms on the single molecule scale, indepen-
dent of substrate orientation and distance [12], (2) constructs consisting of DNA and
other materials act as specific sensors for small molecules [9], (3) DNA-based molecu-
lar machines based on dynamic hybridization/dehybridization processes such as legs
walking along a track help to understand related biological systems such as kinesin
walking on microtubuli [16], (4) self-replicating systems help to gain understanding
concerning the origin of life on earth [17] and (5) the self-assembly of electron-
conducting and electronic information processing DNA structures might enable the bot-
tom-up development of computer chips based on DNA and organic molecules instead
of silicon wafers [18]. It is especially this latter idea which has spurred the investiga-
tion of electron conductance through DNA double strands. After realizing the low (but
not zero!) intrinsic conductivity of unmodified DNA duplexes [19], the focus has now
turned upon double-stranded DNA containing metal ions coordinated in the middle of
its helix structure [20].
9.1.4
Interactions of DNA with Metal Ions
Metal ions can interact with oligonucleotides in a number of ways of which several
have direct biological importance and others have therapeutic or technological relevance.
Figure 9.3 summarizes the main interactions found between oligonucleotides and metal
ions or coordination compounds. DNA is almost always associated with mono- and
divalent ions such as Na(I) and Mg(II) ions (Figure 9.3a) which are closely associated
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