Biomedical Engineering Reference
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transfer from the first to the second adapter. Then the remover strand is added to
initiate strand exchange, displacing the first strand as a waste product. This working
cycle is repeated with different DNA adapters to achieve sequential synthesis. The
final product can be isolated from the reaction mixture by using a biotin-tagged
remover strand. The group of Liu developed the sequential strand displacement
deriving DNA-templated coupling reactions by adopting a “toehold displacement”
strategy [
81
]. The multistep synthesis mediated a six-step DNA template reaction
that proceeded in 35% overall yield.
A different but more impressive example is the autonomous synthesis of
oligomer through DNA walking device by the group of Liu [
82
]. The DNA walker
is designed similar to that reported by Mao's research group [
62
], which can move
along the track autonomously and processively from station to station by cleaving
the DNA-RNA stators and subsequently dissociating DNA fragments. The system
is indicated in Fig.
11.13
b. Three substrates (S1-S3) and an initiator (S0) assemble
on a single-stranded DNA track (T). Each substrate has an amino acid NHS ester
at its 5
0
end and two ribonucleotides in the middle of its DNA sequence. The DNA
walker (W) contains a 3
0
amine group and an RNA-cleaving DNAzyme that could
cleave the ribonucleotide in the substrates. The initiator W tends to hybridize with
the nearest stator S1 and induces DNA-templated acylation of the walker's amine
group with the NHS ester of S1, resulting in the transfer of the first amino acid
building block from S1 to W. The loop of the DNAzyme in the walker cleaves
the ribonucleotide linkage in S1, allowing the 5
0
fragment of S1 to dissociate.
Two subsequent cycles of translocation, amine acylation, cleavage, and dissociation
produce the final reaction product, a triamide containing three amino acid building
blocks in a specific T-programmed order, covalently linked to the walking strand.
Because each step of this cycle occurs spontaneously under identical conditions, the
entire three-step reaction sequence proceeds autonomously, requiring intervention
from the environment. Moreover, the automated mechanical system enables the
efficient generation of target product, since each activated amino acid could only
react with the adjacent product and any of possible undesired reactions between
reactants could be eliminated.
Templated organic reactions were also performed on addressable DNA tweezers
array, reported by Yan and coworkers [
83
]. Three tweezers, each bearing two
coupling reactants, are self-assembled on a linear DNA track. A fourth tweezer
floating freely in solution can be bound to any one of the tweezers and close them
by the addition of a unique pair of “fuel” DNA strands. The coupling reactions
happen when the tweezers are closed, and this can be controlled sequentially from
one tweezers to another (Fig.
11.13
c).
11.4.3
Switchable Carriers
Structural DNA nanotechnology has been enabled to construct scaffolds with
potential ability of being the carriers. The advantages about DNA nanostructures,
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