Chemistry Reference
In-Depth Information
sequence information may find applications far away from its original biological mean-
ing. But not only this feature of sequence-specific self-assembly makes DNA a highly
attractive molecule for bio-inspired technological developments. Likewise, the aforemen-
tioned understanding of - and control over - the types of double helical and higher-order
structures such as junctions and bulges that has been collected and discovered by numer-
ous scientists over the last 50 years or so sets us in the comfortable position today of being
able to create new DNA structures by design. Furthermore, oligonucleotides of lengths of
up to about 100 bases are routinely synthesized on autonomously working DNA synthe-
sizer machines based on solid-phase synthesis and the phosphoramidite protocol with
total control of the desired sequence (see Section 9.3.4) [7]. This absolutely non-biologi-
cal process of DNA synthesis starting from (commercially available) building blocks and
yielding sequences containing a programmed order of the bases A, T, G and C is fast,
reliable and comparatively cheap and is offered as a service by a number of companies
around the world today. Since automated DNA synthesis is nothing else than a sequence
of carefully developed chemical reaction steps, it opens the possibility of incorporating
artificial nucleobases inside an oligonucleotide that may either be slight modifications of
the natural bases or totally artificial structures having nothing in common with natural
bases. Although the practicality of chemical DNA synthesis is limited to the preparation
of strands of not much more than about 100 bases, systems with much longer sequences
are not out of reach when combining the aforementioned techniques with methods from
the molecular biology toolbox, such as sequence-specific strand cleavage by restriction
enzymes, strand joining by ligase enzymes and strand elongation and replication by the
polymerase chain reaction (PCR) [2,8].
These features of DNA, along with some additional properties (inherent chirality,
amphiphilic distribution of hydrophilic phosphates and hydrophobic bases) render it a
highly interesting construction material with possible applications in future nano-
technology, as we shall see in this section [9].
9.1.3 DNA Nanotechnology
As a first example for the use of chemically synthesized, yet unmodified (as compared to
natural DNA) oligonucleotides pursuing an absolutely non-biological purpose, we will
discuss the direction of nanotechnology dealing with the programmed self-assembly of
2- and 3-D structures from DNA as the building material [10].
Regarding again the experiment discussed in Section 9.1.2, we can imagine that such a
puzzle game might not only be designed in a way that strands and counterstrands specifi-
cally combine in a 1 : 1 fashion, but one long single strand can also bind a number of
shorter single strands all matching with certain stretches of the sequence along the long
strand (from now on termed the template strand). If we now further consider the possibil-
ity of implementing structural motifs such as hairpins and junctions, we might imagine
that the shorter strands not only bind the long strand once by making use of their entire
sequence, but rather bind with one end to one designated part of the template strand and
with their other end to another stretch along the sequence of the template strand, thereby
folding it into a structure that is determined by the distance and angle between the two
binding sites. We shall call these shorter strands binding the template strand twice (or
even more times) and thereby spatially arranging it “staple strands”. Figure 9.2a shows
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