Rachel K O'Reilly1, Andrew J Turberfield2, Thomas R Wilks1. 1. Department of Chemistry, University of Warwick , Coventry CV4 7AL, United Kingdom. 2. Clarendon Laboratory, Department of Physics, University of Oxford , Parks Road, Oxford OX1 3PU, United Kingdom.
Abstract
Precise control over reactivity and molecular structure is a fundamental goal of the chemical sciences. Billions of years of evolution by natural selection have resulted in chemical systems capable of information storage, self-replication, catalysis, capture and production of light, and even cognition. In all these cases, control over molecular structure is required to achieve a particular function: without structural control, function may be impaired, unpredictable, or impossible. The search for molecules with a desired function is often achieved by synthesizing a combinatorial library, which contains many or all possible combinations of a set of chemical building blocks (BBs), and then screening this library to identify "successful" structures. The largest libraries made by conventional synthesis are currently of the order of 108 distinct molecules. To put this in context, there are 1013 ways of arranging the 21 proteinogenic amino acids in chains up to 10 units long. Given that we know that a number of these compounds have potent biological activity, it would be highly desirable to be able to search them all to identify leads for new drug molecules. Large libraries of oligonucleotides can be synthesized combinatorially and translated into peptides using systems based on biological replication such as mRNA display, with selected molecules identified by DNA sequencing; but these methods are limited to BBs that are compatible with cellular machinery. In order to search the vast tracts of chemical space beyond nucleic acids and natural peptides, an alternative approach is required. DNA-templated synthesis (DTS) could enable us to meet this challenge. DTS controls chemical product formation by using the specificity of DNA hybridization to bring selected reactants into close proximity, and is capable of the programmed synthesis of many distinct products in the same reaction vessel. By making use of dynamic, programmable DNA processes, it is possible to engineer a system that can translate instructions coded as a sequence of DNA bases into a chemical structure-a process analogous to the action of the ribosome in living organisms but with the potential to create a much more chemically diverse set of products. It is also possible to ensure that each product molecule is tagged with its identifying DNA sequence. Compound libraries synthesized in this way can be exposed to selection against suitable targets, enriching successful molecules. The encoding DNA can then be amplified using the polymerase chain reaction and decoded by DNA sequencing. More importantly, the DNA instruction sequences can be mutated and reused during multiple rounds of amplification, translation, and selection. In other words, DTS could be used as the foundation for a system of synthetic molecular evolution, which could allow us to efficiently search a vast chemical space. This has huge potential to revolutionize materials discovery-imagine being able to evolve molecules for light harvesting, or catalysts for CO2 fixation. The field of DTS has developed to the point where a wide variety of reactions can be performed on a DNA template. Complex architectures and autonomous "DNA robots" have been implemented for the controlled assembly of BBs, and these mechanisms have in turn enabled the one-pot synthesis of large combinatorial libraries. Indeed, DTS libraries are being exploited by pharmaceutical companies and have already found their way into drug lead discovery programs. This Account explores the processes involved in DTS and highlights the challenges that remain in creating a general system for molecular discovery by evolution.
Precise control over reactivity and molecular structure is a fundamental goal of the chemical sciences. Billions of years of evolution by natural selection have resulted in chemical systems capable of information storage, self-replication, catalysis, capture and production of light, and even cognition. In all these cases, control over molecular structure is required to achieve a particular function: without structural control, function may be impaired, unpredictable, or impossible. The search for molecules with a desired function is often achieved by synthesizing a combinatorial library, which contains many or all possible combinations of a set of chemical building blocks (BBs), and then screening this library to identify "successful" structures. The largest libraries made by conventional synthesis are currently of the order of 108 distinct molecules. To put this in context, there are 1013 ways of arranging the 21 proteinogenic amino acids in chains up to 10 units long. Given that we know that a number of these compounds have potent biological activity, it would be highly desirable to be able to search them all to identify leads for new drug molecules. Large libraries of oligonucleotides can be synthesized combinatorially and translated into peptides using systems based on biological replication such as mRNA display, with selected molecules identified by DNA sequencing; but these methods are limited to BBs that are compatible with cellular machinery. In order to search the vast tracts of chemical space beyond nucleic acids and natural peptides, an alternative approach is required. DNA-templated synthesis (DTS) could enable us to meet this challenge. DTS controls chemical product formation by using the specificity of DNA hybridization to bring selected reactants into close proximity, and is capable of the programmed synthesis of many distinct products in the same reaction vessel. By making use of dynamic, programmable DNA processes, it is possible to engineer a system that can translate instructions coded as a sequence of DNA bases into a chemical structure-a process analogous to the action of the ribosome in living organisms but with the potential to create a much more chemically diverse set of products. It is also possible to ensure that each product molecule is tagged with its identifying DNA sequence. Compound libraries synthesized in this way can be exposed to selection against suitable targets, enriching successful molecules. The encoding DNA can then be amplified using the polymerase chain reaction and decoded by DNA sequencing. More importantly, the DNA instruction sequences can be mutated and reused during multiple rounds of amplification, translation, and selection. In other words, DTS could be used as the foundation for a system of synthetic molecular evolution, which could allow us to efficiently search a vast chemical space. This has huge potential to revolutionize materials discovery-imagine being able to evolve molecules for light harvesting, or catalysts for CO2 fixation. The field of DTS has developed to the point where a wide variety of reactions can be performed on a DNA template. Complex architectures and autonomous "DNA robots" have been implemented for the controlled assembly of BBs, and these mechanisms have in turn enabled the one-pot synthesis of large combinatorial libraries. Indeed, DTS libraries are being exploited by pharmaceutical companies and have already found their way into drug lead discovery programs. This Account explores the processes involved in DTS and highlights the challenges that remain in creating a general system for molecular discovery by evolution.
Two centuries of research has furnished
chemists with the ability
to synthesize a huge variety of molecular architectures based on organic
and inorganic components and to create materials with new functions
ranging from therapeutics to solar cells. While the majority of new
molecules with precisely defined structures are “small”
(i.e., <1000 Da), solid-phase synthesis techniques have made it
possible to produce monodisperse macromolecules such as DNA, peptides
and their analogues,[1,2] and advances in sequence-controlled
polymerization continue.[3] While much work
remains to be done, we now have access to a very large chemical space.
Searching this space for new molecules capable of meeting challenges
in human health, energy, and security is of vital importance. However,
even the largest combinatorial libraries are many orders of magnitude
too small to search even the most synthetically accessible regions
of chemical space effectively.[4]A
system capable of tackling the above challenge would need to
(1) operate in parallel rather than in series, drastically reducing
synthesis time; (2) use extremely small amounts of material, in order
to bring costs down and render synthesis of very large libraries of
compounds practical, while still allowing product selection and identification
(typically below the detection limit of common analytical techniques
such as mass spectrometry); (3) enable molecular evolution. Evolution
is perhaps the most important innovation as it allows a very large
chemical space to be sampled without the requirement to synthesize
all possible molecules within that space. Sequential rounds of selection,
mutation and resynthesis can allow for the identification of functional
molecules that were not present in the initial compound library (Figure ). While criterion
(1) may be addressed by improvements in synthetic methods/technology,
it is extremely difficult, if not impossible, to envisage how conventional
combinatorial synthesis could address points (2) and (3).
Figure 1
Molecular evolution
allows large chemical spaces to be searched
efficiently. A library of instructions is translated into the corresponding
library of molecular products, which are then selected for target
properties (Round 1). The instructions for the enriched products are
then amplified, mutated and translated again to generate a library
of new products (some or all of which may not have been present in
the original product library) which can be selected against to identify
products with improved properties (Round 2). Repeated cycles of translation,
selection, amplification, and mutation can enable the system to identify
on an optimized product (Round N) without the need
for every possible library member to be synthesized.
Molecular evolution
allows large chemical spaces to be searched
efficiently. A library of instructions is translated into the corresponding
library of molecular products, which are then selected for target
properties (Round 1). The instructions for the enriched products are
then amplified, mutated and translated again to generate a library
of new products (some or all of which may not have been present in
the original product library) which can be selected against to identify
products with improved properties (Round 2). Repeated cycles of translation,
selection, amplification, and mutation can enable the system to identify
on an optimized product (Round N) without the need
for every possible library member to be synthesized.One method that has been developed to allow functional
evolution
is messenger RNA (mRNA) display[5,6] (Figure ). Here, a combinatorial library of DNA sequences
is converted by reverse transcription into the corresponding mRNA
library. Each mRNA strand is then modified by ligation of a puromycin-modified
DNA strand to its 3′ end and translated into the corresponding
peptide by in vitro ribosomal peptide synthesis (RPS). When a ribosome
reaches the RNA/DNA junction at the end of a mRNA template it stalls:
at this point the terminal puromycin, a peptidyl acceptor antibiotic,
can enter the active site causing the peptide product to be transferred
to it. The resulting library of peptide products can comprise as many
as 1013 unique members, each of which is attached to its
encoding mRNA sequence. After subjecting the library to selection,
the mRNA attached to successful products can be reverse transcribed
to the corresponding DNA sequences and amplified using the polymerase
chain reaction (PCR). Mutation can be achieved by cutting members
of the DNA library using restriction enzymes and then randomly recombining
the fragments, or by error-prone PCR. Multiple rounds of selection,
mutation, and amplification allow many more peptide sequences, not
present in the original library, to be explored. Eventually, a peptide
that is highly optimized for a particular function can be identified.[7] mRNA display, the related techniques of ribosome[8] and phage[9] display,
and DNA aptamer libraries[10] provide a solution
to the selection and evolution problems identified above. However,
techniques involving RPS are limited to peptides incorporating proteinogenic
amino acids. Expanding the library of BBs to include non-natural amino
acids is possible but difficult as it involves engineering the translation
machinery of cells—a nontrivial undertaking.[11] In order to truly revolutionize the way that we search
chemical space, we need a system with the capacity of mRNA display
for directed evolution but with fewer constraints on the chemical
structures of the products. The purpose of this Account is to chart
the development of just such a technology: DNA-Templated Synthesis
(DTS).[12]
Figure 2
Molecular evolution using mRNA display.
aatRNA = aminoacyl tRNA.
Molecular evolution using mRNA display.
aatRNA = aminoacyl tRNA.The basic principle of DTS is illustrated in Figure . Reactive BBs are conjugated
to short adapter
strands of DNA. At suitably low concentrations (nM), reaction rates
between BBs are negligible in the absence of DNA–DNA interactions.[13] However, if two of the DNA adapters hybridize
to form a duplex their attached BBs are brought into close proximity,
greatly increasing their effective local concentration and hence the
rate of reaction. This mechanism allows for the selective activation
of reactions in the presence of many reactive species in the same
mixture–a feat not ordinarily possible in conventional synthetic
chemistry. The use of a nucleic acid template to control synthesis
has a precedent in RPS (Figure c)[14] in which peptide bond formation
is directed by base-pairing between aminoacyl transfer RNAs (aatRNAs)
and an mRNA template. Its ability to direct multiple reactions in
parallel means that DTS is capable of addressing criterion (1), a
key challenge in combinatorial synthesis.
Figure 3
“Traditional”
synthetic chemistry compared with DTS
and RPS. a) The traditional approach requires separate synthesis of
each distinct compound. DTS (b) and RPS (c) allow defined products
to be synthesized in parallel within complex mixtures by using sequence-specific
nucleic acid hybridization to control the proximity of reactive reactive
building blocks, BBs.
“Traditional”
synthetic chemistry compared with DTS
and RPS. a) The traditional approach requires separate synthesis of
each distinct compound. DTS (b) and RPS (c) allow defined products
to be synthesized in parallel within complex mixtures by using sequence-specific
nucleic acid hybridization to control the proximity of reactive reactive
building blocks, BBs.As Gartner and Liu realized nearly 20 years ago, DTS also
has the
potential to address the more difficult questions of product identification
and molecular evolution.[13] The products
of DTS are tagged with DNA: it is possible to design ribosome-inspired
DTS systems that encode information about the order of addition of
BBs in the base sequence of this DNA tag (Figure ).[15] Following
selection against a target, DNA amplification and sequencing methods
can be applied to “read off” the reaction sequence,
from which the chemical structure of the successful product can be
inferred. It is important to note that due to the expense associated
with synthesizing BB-DNA adapters, it is usually practical to make
only very small amounts of product by DTS (usually on the order of
picomoles). However, since amplification by PCR requires, in principle,
only a single DNA molecule, product detection is still possible even
at such small reaction scales (criterion (2)). Finally, molecular
evolution could be achieved by iterated cycles of DTS, selection,
amplification and mutation[13] (for example,
by cutting or “restricting” the DNA into fragments then
randomly recombining them). Translation is key to
this process: the DNA tags attached to selected products must be capable
of directing subsequent rounds of product synthesis.
Figure 4
Principle of product
encoding and molecular evolution enabled by
DTS. The base sequence of a DNA tag directs the synthesis of a product
and defines its chemical structure. Selection against a target followed
by amplification, shuffling of the instructions encoded in the DNA
tag (restriction and recombination), and then resynthesis by another
round of DTS allows the production of new products with improved properties.
Molecular evolution is therefore possible.
Principle of product
encoding and molecular evolution enabled by
DTS. The base sequence of a DNA tag directs the synthesis of a product
and defines its chemical structure. Selection against a target followed
by amplification, shuffling of the instructions encoded in the DNA
tag (restriction and recombination), and then resynthesis by another
round of DTS allows the production of new products with improved properties.
Molecular evolution is therefore possible.DTS thus has the potential for development into a tool to
search
efficiently and quickly a vast chemical space. In this Account, we
outline the evolution of DTS toward this goal and the challenges associated
with its development.
DNA-Templated Chemistry
A simple
example of DTS is the use of a DNA template to facilitate
ligation of two DNA strands through a native phosphodiester bond[16] or a non-natural linkage,[12] as pioneered by the groups of Orgel, Liu, and many others.
Numerous examples of bond-forming and bond-breaking reactions directed
by DNA templates have been reported (Figure ),[17] including
Heck coupling, the copper-catalyzed azide–alkyne cycloaddition
“click” reaction, transition metal-mediated catalysis,
and synthesis of conductive polymers and macrocyclic drug-like molecules.
Thanks to the work of Kool, Seitz, and others, there is a well-developed
field of research into DNA/RNA probes based on fluorogenic reactions
templated by a target nucleic acid.[18]
Figure 5
Examples
of reactions that have been performed on a DNA template.
For acyl transfer X = S or N-hydroxysuccinimide.[17]
Examples
of reactions that have been performed on a DNA template.
For acyl transfer X = S or N-hydroxysuccinimide.[17]Three different architectures are commonly used to bring
BBs into
close proximity (Figure ).[19] In an “end of helix”
design, the reactants coupled to each strand are brought together
at the end of a double helix. In “cross nick”, reactions
take place across a gap between DNA adapters held on a template strand.
“Junction”-based designs template reactions in small
volumes where multiple DNA strands intersect; an example is the YoctoReactor
reported by Hansen and co-workers (see below).[20]
Figure 6
DNA architectures employed in DTS.
DNA architectures employed in DTS.For programmed, multistep synthesis, perhaps the most useful
DTS
reactions are transfer reactions in which bond formation
is coordinated with cleavage from one of the DNA adapters (Figure , blue box). Transfer
reactions can facilitate autonomous, multistep DTS as they avoid steric
problems caused by the accumulation of DNA adapters. An exemplar from
nature is RPS (Figure c). Here, amino acid BBs are linked to transfer RNAs (tRNAs) by activated
ester bonds. As the ribosome scans from codon to codon along an mRNA,
the growing peptide chain is continually passed to the incoming tRNA
(selected by the next codon in the mRNA program) by means of an acyl
transfer reaction that coordinates peptide bond formation with cleavage
from the penultimate tRNA.Relatively few DTS transfer reactions
have been reported to date.
The two predominant examples in the literature are acyl transfer and
Wittig olefination. Acyl transfer is useful as it enables the creation
of peptidomimetic molecules,[21] and several
research groups have used this reaction to create oligopeptides and
for various other applications.[17] The limited
stability of the activated esterBBs in solution can cause problems,
however.[22,23] Wittig olefination results in the formation
of a carbon–carbon double bond, so allows the exploration of
a different region of chemical space. It has been used for DTS of
macrocycles[24−27] and linear oligomers (see ref (22) for a recent example). However, its broader
application is limited by the stability of the phosphoryl BBs, which
can be oxidized in water.[22] Less commonly
used transfer reactions include a modified Staudinger ligation,[28] native chemical ligation,[29] nucleophilic aromatic substitution[30] and a tetrazine-transfer reaction.[31] In
combination, these reactions could be very useful for the introduction
of specific functional groups during DTS. In our opinion, this avenue
remains underexplored. However, with the current state of the art,
multistep syntheses take around a day to complete, and the best yields
per step are around 80%, resulting in rather low overall yields. Investigation
of alternative transfer chemistries compatible with DTS conditions
should be given high priority as the discovery of a highly efficient
and versatile method for DNA-templated oligomer synthesis could make
the development of autonomous systems analogous to the ribosome much
more straightforward.
Product Encoding
The idea of encoding
the identity of a small-molecule product using
an attached DNA sequence was first proposed by Brenner and Lerner
25 years ago.[15] DNA is an ideal identifying
tag because it is straightforward to synthesize large libraries of
unique oligonucleotides which can be sequenced to identify products.
Its most useful feature, however, is its ability to be amplified by
PCR, which has a limit of detection far below conventional analysis
methods.The original proposal was that solid-phase synthesis
of a combinatorial
library of target molecules (by repeatedly pooling then splitting
support beads between different reactions) would proceed in parallel
with the construction of DNA tags on each bead to encode the sequence
of addition of BBs (Figure a). However, DNA serves only as a post hoc record of the reaction
steps: it does not program synthesis, and cannot be used to direct
the resynthesis of enriched products. As a result, this system is
not suitable for the implementation of molecular evolution. An elegant
alternative, termed “DNA routing”, was devised by Halpin
and Harbury (Figure b):[32] successive codons in a DNA “gene”
are used to route a growing oligomer between reaction vessels, determining
the sequence of BB coupling reactions and, therefore, the structure
of the final product.
Figure 7
Comparison of the reaction cycles of a) split and pool
synthesis,
b) DNA routing, and c) DTS.
Comparison of the reaction cycles of a) split and pool
synthesis,
b) DNA routing, and c) DTS.Using DNA-encoded chemical libraries (DECLs) for molecular
discovery
is advantageous because compounds can be selected from a pooled library
as opposed to serial screening, enabling a 106-fold increase
in library size.[32] Selection from DECLs
has become a well-established method and has been used by pharmaceutical
companies in drug discovery programs.[4] In
both split-and-pool and DNA-routed syntheses, each reaction occurs
in a different reaction vessel without the direct involvement of the
DNA tag. These methods are thus distinct from DTS, in which reactions
occur in the same pot and are programed by DNA interactions. For this
reason, we will not include them in our discussion below, but readers
are directed to a recent paper illustrating the potential of DNA routing
for molecular evolution.[33]DTS has
been employed in a number of ways to create products tagged
with a unique identifying DNA sequence. These approaches fall into
three categories, which we have termed “templated parallel”,
“templated sequential” and “autonomous”
(Figure ). In each
case, the use of DNA amplification and sequencing to confirm the identity
of the DNA-tagged product oligomers has been demonstrated.[20,22,34]
Figure 8
Methods for product encoding in DTS. (a)
Templated parallel: BBs
are arranged in sequence by hybridization of their adapters to the
template, concatenated in a single step then cleaved from adapters.
(b) Templated sequential: BBs attached to DNA adapters are sequentially
transferred to a reactive site on the DNA template in response to
an external stimulus; in the case illustrated, spent adapters are
displaced by addition of the following adapter. (c) Autonomous systems.
Upper: a simplified version of a DNA walker, reported by He and co-workers,[35] which steps down a track (driven by ribozyme-catalyzed
cleavage of the track anchorages) picking up BBs in a programmed order.
Lower: the HCR system, developed in our laboratories,[22] which coordinates programmed DNA polymerization with oligomer
assembly. Complementary “toehold” domains, whose hybridization
controls the reaction sequence, are identified by color.
Methods for product encoding in DTS. (a)
Templated parallel: BBs
are arranged in sequence by hybridization of their adapters to the
template, concatenated in a single step then cleaved from adapters.
(b) Templated sequential: BBs attached to DNA adapters are sequentially
transferred to a reactive site on the DNA template in response to
an external stimulus; in the case illustrated, spent adapters are
displaced by addition of the following adapter. (c) Autonomous systems.
Upper: a simplified version of a DNA walker, reported by He and co-workers,[35] which steps down a track (driven by ribozyme-catalyzed
cleavage of the track anchorages) picking up BBs in a programmed order.
Lower: the HCR system, developed in our laboratories,[22] which coordinates programmed DNA polymerization with oligomer
assembly. Complementary “toehold” domains, whose hybridization
controls the reaction sequence, are identified by color.In the templated parallel approach, BB-DNA adapters
are arrayed
in sequence by hybridization to a DNA template (Figure a). Template domains act as codons, each
of which uniquely specifies a single BB. The BBs are then chemically
linked to each other and released from the now-redundant adapters.
Kleiner and co-workers elegantly demonstrated this idea by connecting
BBs to peptide nucleic acid (PNA) adapters[36] via cleavable linkers. Upon completion of the synthesis, the product
was liberated while remaining tagged at one end with the templating
DNA sequence.[34] Zhu and co-workers have
also applied the templated parallel approach to produce “nylon
DNA” using amide condensation reactions.[37]The templated sequential approach provides a more
flexible but
laborious route to oligomer synthesis. As in the templated parallel
approach, the DNA template provides an ordered array of binding sites
for BB-DNA adapters. However, the assembly of the BBs on the template,
and hence the BB transfer reactions, occurs sequentially in this case–generally
at the terminus of the template–and is controlled externally
by strand-displacement reactions that bring successive reactants into
close proximity with the growing oligomer (Figure b).[38−41] Again, the product remains covalently attached to
the DNA template, which can encode its chemical structure.Finally,
autonomous systems use a DNA “program” to
control the sequential addition of BBs without the need for external
intervention. One example of this approach couples motion of a DNA
“walker” with chemical reactions between BBs (Figure c, upper scheme).[35] The walker, a single strand of DNA, moves along
a track consisting of an array of single-stranded anchorages. At each
step the walker catalyzes cleavage of the anchorage to which it is
bound, thereby initiating a strand-displacement reaction that transfers
it to the next anchorage. In a sequence programmed by the track, BBs
attached to the anchorages are transferred to the growing oligomer
attached to the walker. In principle, the final product could be ligated
to a template strand on which the track is built to enable the sequence
of BBs to be read off.We recently reported a second example
of autonomous DTS, using
a hybridization chain reaction (HCR) to bring BBs into proximity with
the growing oligomer in sequence[22] (Figure c, lower scheme).
The DNA components are hairpins formed by partially self-complementary
strands. A staggered duplex is formed by HCR between the hairpins,
in which the sequence of hairpin addition is controlled by hybridization
between complementary “toehold” domains. A set of “instruction”
hairpins programs the sequence in which “chemistry”
hairpins are incorporated and thus the sequence in which BBs coupled
to these hairpins are added. The growing oligomer is carried forward
on a strand of DNA that remains at the reactive end of the duplex.
Ligation of the “instruction” hairpins creates a DNA-encoded
record of the reaction sequence.
Extending the Length of
Sequence-Controlled Oligomers
Extending the length of sequence-controlled
oligomers that can
be synthesized is important for two reasons. First, product diversity
increases rapidly with oligomer length. For example, a library of
1 billion trimers requires 1000 distinct BBs, while a comparable library
of decamers needs only eight. Second, sequence-controlled macromolecules
are a “holy grail” of polymer science as perfect control
may allow the discovery of synthetic polymers with well-defined folded
conformations, analogous to native proteins, with greatly enhanced
properties.The mechanism and architecture used in DTS determines
the maximum
number of BBs that can be concatenated. For example, the YoctoReactor
restricts the number of reactants that can be colocalized and thus
cannot produce products longer than tetramers.[20]By using the templated parallel approach, Niu and
co-workers were
able to synthesize long, precisely defined polymers by templating
the concatenation of up to ten BBs that were themselves oligomers
(of amino acids or ethylene glycol subunits).[34] This method therefore makes it possible to explore the structure–function
relationships of artificial polymers similar in length to proteins—this
is extremely important for the development of artificial enzymes,
for example. However, the system cannot encode variability within the oligomeric BBs, so only a fraction of possible
sequences of the subunits could be explored.Strategies for
oligomer synthesis using the templated sequential
method can be limited by the lengths of adapter and template that
it is practical to synthesize, usually around 200 nucleotides. Alternative
approaches in which the adapter length is kept constant usually result
in the reactive site at the distal end of the oligomer moving further
and further from the new BB as the synthesis proceeds, potentially
limiting yield. As a result, hexamers are currently the longest oligomers
that have been produced using these methods.[40]To prevent the DNA mechanism from imposing limits on oligomer
length
we have developed a simpler strand-displacement mechanism (Figure a).[42] Here, the growing oligomer is transferred to the incoming
BB which remains attached to its adapter, as in the ribosome. The
spent adapter is then removed by strand displacement, making way for
hybridization of the next DNA-BB adapter. Adapters are distinguished
by the unhybridized toehold domain used to drive their eventual displacement
so they can all be designed to be the same length. Using this method
we have so far been able to demonstrate the construction of decamers
which, with those synthesized using the templated parallel method
described above, are currently the longest oligomers constructed by
DTS.[43] However, control over reaction sequence
requires the sequential addition of BBs. A more sophisticated system
(Figure b) uses the
serial addition of instruction strands to control reactions within
a vessel containing a mixture of all BBs.[44] Neither method lends itself to encoding the identity of the product
in the final DNA tag, however.
Figure 9
Methods for sequential DTS of oligomers
based on DNA strand exchange.
Oligomer sequence can be determined by controlling the sequence of
addition of either (a) BBs or (b) separate instruction strands.
Methods for sequential DTS of oligomers
based on DNA strand exchange.
Oligomer sequence can be determined by controlling the sequence of
addition of either (a) BBs or (b) separate instruction strands.The autonomous systems described
above have perhaps the greatest
potential for the synthesis of long oligomers by DTS. The DNA walker[35] and HCR[22] systems
have significant potential for optimization and extension, but they
have yet to realize sequence-controlled synthesis of products longer
than tetramers.
Combinatorial Synthesis by DTS
Gartner
and Liu first demonstrated the potential of DTS for combinatorial
synthesis by templating 1025 distinct thiol–maleimide additions
in a single pot.[13] The authors expanded
this approach to produce a DNA-templated library of 65 macrocycles,[24] and later larger libraries of 13 000[26] and 160 000 similar molecules (Figure a).[45] The library size in these and similar systems
is ultimately limited by the number of orthogonal adapter sequences
required, as a unique adapter is needed to encode not only the identity
of each BB but also each possible position of that BB within the product
(as with DNA routing[33]).
Figure 10
Methods for combinatorial
synthesis using DTS based on (a) linear
templates;[25] (b) a “universal”
template;[46] (c) the YoctoReactor;[20] and (d) HCR.[22]
Methods for combinatorial
synthesis using DTS based on (a) linear
templates;[25] (b) a “universal”
template;[46] (c) the YoctoReactor;[20] and (d) HCR.[22]Li and co-workers exploited the
non-natural base deoxyinosine,
which forms base pairs almost indiscriminately with all four natural
bases, in order to simplify the design of adapters.[46] This enabled the use of a single “universal”
template for the combinatorial synthesis of a model library of 114 688
distinct products, with the identity of the products encoded in DNA
regions opposite deoxyinosine tracts (Figure b). However, the use of a universal template
means that mutation is not possible.The YoctoReactor has been
used to generate libraries comprising
more than 107 unique members.[47] This method, as well as a related approach described by Cao and
co-workers,[41] simplifies adapter design
by decoupling the DNA domain encoding BB identity from that directly
involved in DNA templating (Figure c). However, in both cases a BB requires a different
adapter for each position in the product. The preparation of all oligomers
of length n therefore requires the synthesis of n different DNA-linked versions of the same BB, making this
methodology time-consuming and limited in flexibility.Our work
on HCR goes some way toward solving issues related to
adapter sequence design and BB interchangeability, since the identity
of a BB is encoded in the base sequence of the chemistry hairpin loop
and any chemistry hairpin can be added at any point in the sequence
(Figure d). Using
the HCR approach with a branching (nondeterministic) synthesis program
we were able to demonstrate the combinatorial synthesis of a library
of 12 different products[22] and are working
toward the synthesis of larger libraries.Given that the largest
combinatorial libraries synthesized by DTS
are still at least an order of magnitude smaller than libraries generated
by mRNA display,[9] reaching libraries of
this size remains a key target.
Selection of Functional
Products
The principle of functional product selection from
DNA-tagged libraries
is illustrated in Figure . The most widely used method involves the incubation of a
library with an immobilized target followed by stringent washing to
remove any products that do not bind. The DNA tags of selected products
are then amplified by PCR and sequenced: the chemical structures of
the successful binders can be inferred from the DNA sequence. This
approach has the advantage that it may not be necessary to remove
unreacted DNA adapters/templates from the reaction mixture since these
will be removed during the washing step, simplifying library synthesis.
Figure 11
Principle
of functional selection against DNA-tagged combinatorial
libraries.
Principle
of functional selection against DNA-tagged combinatorial
libraries.Many of the compound
libraries produced by DTS have been exposed
to selection experiments, resulting in the identification of inhibitors[25,27,47] and antagonists[45] of several important biological targets including kinases
and apoptosis inhibitors. These examples demonstrate the great potential
of DTS in drug discovery, but the libraries involved remain limited
by their relatively small sizes. To our knowledge there are as yet
no therapeutics discovered using DTS libraries that have made it to
market, although both Vipergen and Ensemble Therapeutics are working
toward this end.Libraries produced by DTS are constrained by
the requirement that
product synthesis be water-compatible. In contrast, DECLs produced
by solid phase methods encounter no such limitation since BB conjugation,
DNA tag extension and hybridization reactions can be carried out in
different solvents (Figure ). Since comparable library sizes are achievable with both,
it is perhaps not surprising that the adoption of DTS by the pharmaceutical
industry has been slower, in spite of the promise shown by functional
selection experiments.[4]
Conclusions and
Future Challenges
Over the past 20 years, DTS has developed
enormously. A diverse
range of chemical reactions can now be directed by DNA templates.
Different template architectures allow the synthesis of oligomeric
and macrocyclic products. Mechanisms for autonomous DTS have been
developed, and synthesis of large combinatorial libraries containing
DNA-tagged molecules for selection against various biological targets
is now possible. However, there remains much work to be done to identify
water-stable yet reactive BBs, to develop autonomous DTS systems to
the point where they can produce large combinatorial product libraries,
and to diversify the range of targets against which selection experiments
are performed. DTS has developed to meet most of the requirements
of a system for molecular evolution—but not all. The capacity
for mutation and resynthesis is still missing from all published DTS
systems: we believe that this is a priority for those working in the
field.Some of the most exciting possibilities for DTS lie in non-natural materials discovery. The current approach to
materials chemistry can largely be characterized by “make one,
test one”—a material is made with a particular function
in mind, it is tested, and then improvements are proposed based on
the outcome. A DTS system capable of evolving molecules
to meet challenges such as light harvesting or carbon sequestration
would be truly revolutionary: this technology has the potential to
usher in a new and exciting era of materials discovery.
Authors: Wenjing Meng; Richard A Muscat; Mireya L McKee; Phillip J Milnes; Afaf H El-Sagheer; Jonathan Bath; Benjamin G Davis; Tom Brown; Rachel K O'Reilly; Andrew J Turberfield Journal: Nat Chem Date: 2016-04-11 Impact factor: 24.427