Biomedical Engineering Reference
In-Depth Information
association/dissociation cycle may allow multiple one-pot DNA-templated reactions
to take place on a single DNA-linked core structure (Figure 11.17c) [89].
Nuevolution claims to be able to build a 100-million member library in two to
three days, and today their libraries comprise over 1 billion chemical structures (see
http://www.nuevolution.com/). Although Nuevolution has disclosed several collabo-
rations with major pharmaceutical companies and to have assembled over 1 billion
chemical structures with its proprietary technology, the role of chemetic in a DNA-
encoded chemical library field and in drug discovery has yet to be demonstrated.
11.2.2.3.3 YoctoReactor
Vipergen AS is a Danish company that has recently
developed a unique DNA-directed approach for the construction of DNA-encoded
chemical libraries, termed YoctoReactor technology (yR). The key feature of yR
is the formation of a highly stable three-dimensional DNA complex called DNA
junction (Figure 11.18a) [90,91]. Such architecture allows for confining suitable
DNA-conjugate reagents within a volume on the order of a yoctoliter (10
−
24
liter,
hence the name
YoctoReactor
) [90,91].
In virtue of the proximity effect (see Section 11.2.2.3), DNA-directed reactions
take place at the center of the reactor, delivering the corresponding building blocks on
the initial reaction site (Figure 11.18a). It is worth noting that in contrast to the DPC
approach (see above) [70], in yR technology there is no structural distinction between
a reagent and a template oligonucleotide. Each DNA-conjugate compound equally
contributes to the three-dimensional structural framework of the junction, serving
simultaneously as both template and reagent for another DNA-linked reactive moiety
(Figure 11.18a).
Figure 11.18b depicts the use of Vipergen's approach to the synthesis of a three-
way DNA-encoded chemical library. Before library assembly, individual building
blocks are linked via cleavable or noncleavable linkers to distinct hairpin-shaped DNA
oligonucleotides, each containing (1) an appropriate annealing domain for three-
dimensional DNA-junction formation, as well as (2) a compound-specific coding
sequence, at the distal end of the oligonucleotide [90,91].
Reactions for library assembling are programmed to occur in stepwise fashion
following DNA-junction formation. Initially, DNA-building block conjugates
a
1-n
and
b
1-m
undergo the first DNA-directed reaction (Figure 11.18b). Following encoding
of building block
b
1-m
by ligation of the appropriate DNA extremities, cleavage of
the linker enables the irreversible delivery of the compound to the initial reaction
site (Figure 11.18b). Iteration of the process enables incorporation of additional
building blocks (i.e.,
c
1-p
) and corresponding DNA-coding tags. After completion of
the programmed reactions, the molecular reactor is dismantled (performing a single
round of PCR) and the final small-molecule library is displayed on linear double-
stranded DNA templates (Figure 11.18b) [90,91].
Like other DNA-directed approach, yR is compatible with multiple rounds of
selection and chemical translation (termed
rolling translation
by Vipergen) [48,70,
90]: PCR-amplified DNA-coding tags selected in the first round of panning serve as
yR templates for synthesis of the next-generation library in the subsequent round of
selection (Figure 11.18c).
