Download Solving chemical problems through the application of evolutionary

Solving chemical problems through the application of
evolutionary principles
Mary M Rozenman, Brian R McNaughton and David R Liu
Molecular evolution has been widely applied in the laboratory to
generate novel biological macromolecules. The principles
underlying evolution have more recently been used to address
problems in the chemical sciences, including the discovery of
functional synthetic small molecules, catalysts, materials and
new chemical reactions. The application of these principles in
dynamic combinatorial chemistry and in efforts involving small
molecule–nucleic acid conjugates has facilitated the evaluation
of large numbers of candidate structures or reactions for
desired characteristics. These early efforts suggest the
promise of pairing evolutionary approaches with synthetic
chemistry.
Addresses
12 Oxford Street, Department of Chemistry and Chemical Biology,
Harvard University, Cambridge, MA 02138, USA
Corresponding author: Liu, David R ([email protected])
Current Opinion in Chemical Biology 2007, 11:259–268
This review comes from a themed issue on
Combinatorial chemistry and molecular diversity
Edited by Gregory A Weiss and Richard Roberts
Available online 4th June 2007
1367-5931/$ – see front matter
# 2007 Elsevier Ltd. All rights reserved.
DOI 10.1016/j.cbpa.2007.05.016
simultaneously separates functional molecules (survivors)
from uninteresting variants (unfit individuals) within
arbitrarily large libraries of different compounds
(Figure 1). Selections contrast with screens, in which
molecules are individually evaluated for desired properties in a low- or high-throughput manner. Selections can
be much more efficient than screens because the effort
needed to execute a selection generally does not scale
with library size. In addition, selections for target binding
and for bond formation are often easier to execute than
screens because selections do not require the spatial
separation of candidate molecules, do not require sophisticated equipment, typically require only tiny (subnanomole) quantities of material when nucleic acids
are involved and can be iterated to multiply their net
effectiveness. The efficiency of selections in some cases
enables researchers to conduct discovery efforts in a
broad, unbiased manner that is unconstrained by previous
hypotheses or preconceived notions of binding and reactivity. As a result, evolutionary approaches can allow
researchers to make discoveries that might have been
overlooked using other approaches.
In this review, we summarize developments in dynamic
combinatorial chemistry, tagging synthetic small molecules with DNA, translating DNA into small molecules
and DNA-based reaction discovery — four areas in which
the key evolutionary principle of selection facilitates
chemical discovery.
Introduction
Dynamic combinatorial chemistry
New functionality in Nature arises from molecules that
emerge through iterated cycles of translation, selection,
amplification and diversification of genetic material. This
process of evolution can be carried out in the laboratory by
researchers to produce molecules with specific desired
properties, rather than those needed by Nature. In recent
years, advances in molecular evolution have yielded a
broad range of functional proteins and nucleic acids,
including novel receptors, catalysts and sensors. The
application of evolutionary principles to biological molecules has been recently reviewed [1–5]. In this review,
we describe the complementary application of evolutionary principles to address chemical problems [6,7], including the discovery of functional small molecules and
new chemical reactions.
Dynamic combinatorial chemistry (DCC) enables
processes sharing important features of selections to be
applied to chemical systems, resulting in the discovery of
functional small molecules, catalysts, and materials [8].
DCC makes use of reversible reactions to generate a
mixture of product structures (a dynamic combinatorial
library, or DCL) in equilibrium [9,10]. Upon the addition
of a binding target to the system, desired molecules
capable of forming a stable complex with the target are
removed from this equilibrium (Figure 2a). The concentrations of remaining components shift in accordance with
Le Chatelier’s principle to favor the formation of
additional active molecules, resulting in their amplification at the expense of less active variants composed of the
same building blocks [11].
Evolution-based approaches to chemical discovery differ
in fundamental ways from conventional approaches. Central to evolution-based approaches is ‘selection’, a process
conceptually similar to Darwinian natural selection that
Recently, Sanders, Lam and co-workers reported
the amplification of a [2]-catenane from a DCL
generated from a single acetal-peptide-hydrazone
(1; Figure 2b) [12]. In the presence of the neurotransmitter
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Current Opinion in Chemical Biology 2007, 11:259–268
260 Combinatorial chemistry and molecular diversity
Figure 1
Evaluating molecules by screening and selection. In a screen (top), molecules are individually assayed for a desired property. In a selection (bottom),
a library of compounds is separated into active and inactive members in a single experiment. ee, enantiomeric excess; IC50, 50% inhibitory
concentration; Kd, dissociation constant.
acetylcholine, diastereomerically pure [2]-catenane was
amplified to 67% isolated yield after equilibration over 44
days, and was subsequently found to bind acetylcholine
with a dissociation constant (Kd) of 71 nM. This report
demonstrates the ability of DCC to explore diverse
chemical architectures and identify complex functional
molecules from a small number of simple starting
materials (in this case, just one starting monomer and
one target).
Although only a small number of groups have applied
DCC to catalyst discovery, early reports describe promising results. Otto and co-workers used DCC to discover
molecules capable of catalyzing the Diels–Alder reaction
between acridizinium bromide and cyclopentadiene [13].
A series of dithiol-carboxylates was equilibrated in the
presence of the Diels–Alder product, which is structurally
similar to the transition state for the reaction. From this
library, a macrocyclic compound capable of binding the
product was amplified as a mixture of diastereomers, and
was found to increase the rate of the Diels–Alder reaction
tenfold with modest catalyst turnover.
Current Opinion in Chemical Biology 2007, 11:259–268
In addition to the identification of receptors and catalysts,
DCC has also been applied to the generation of functional
materials. Lehn and Sreenivasachary recently reported
the selection of hydrogels exhibiting enhanced stability
from an equilibrating library of monomers (Figure 2c)
[14]. Guanosine-50 -hydrazide derivative 2 (Figure 2c) was
equilibrated with different aldehydes in the presence of
potassium, generating a gelatinous mixture of potassiumcentered hydrazone G-quartets (3; Figure 2c). Because
gel formation is thermoreversible, heating this material
generated a solution containing an equal distribution of
all possible library members. Upon cooling, gelation
caused the equilibrium to shift in favor of the most stable
(highest melting temperature) hydrogel. This work
demonstrates that the DCC approach can be applied to
structures on a supramolecular scale, leading to the discovery of materials with desired bulk properties.
The analysis of DCLs has generally relied on LC/MS for
the deconvolution of complex mixtures of related compounds. This analysis strategy requires chromatographic
distinctiveness among all possible library members.
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Solving chemical problems through the application of evolutionary principles Rozenman, McNaughton and Liu 261
Figure 2
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262 Combinatorial chemistry and molecular diversity
In an effort to circumvent this limitation, Miller and
McNaughton recently developed a resin-bound DCC
method in which library building blocks are attached to
encoded polystyrene beads and equilibrated in the presence of equivalent solution-phase building blocks and
fluorescently labeled target [15]. Beads exhibiting fluorescence contain building blocks that generate the highest
affinity ligands. In this report, nine resin-linked peptidic
quinolines were mixed with solution-phase analogs, generating a 49-membered DCL. The DCL was equilibrated
by disulfide exchange in the presence of fluorescently
labeled DNA, resulting in the identification of a molecule
that binds the target DNA with moderate affinity
(Kd = 2.3 mM). Such an approach should be extendable
to libraries that are orders of magnitude larger.
provided an amplifiable record of the split-pool synthesis
history of each peptide. The peptide library was screened
for binding to an antibody by fluorescence-activated bead
sorting, and the DNA encoding each library member was
amplified by PCR and sequenced to reveal the peptides
with the highest affinities for the target antibody. This
early effort demonstrated how the information storage
capability and amplifiability of DNA could be exploited
to enable the tagging of a peptide library and the identification of minute quantities of desired library members
following screening. The resin-bound nature of the peptide library, however, precluded the use of selections. A
further limitation of this method arises from the significant
chemical constraints of co-synthesizing the synthetic
library and DNA on the same resin.
Encoding chemical libraries using DNA
A different approach that uses DNA tags to encode smallmolecule structures is encoded self-assembling chemical
libraries (ESACs), developed by Neri, Melkko and coworkers [25]. The ESAC method uses libraries of smallmolecule pharmacophores linked to DNA oligonucleotides that both identify each pharmacophore and bring
together pairs of pharmacophores non-covalently upon
base pairing (Figure 3). In a proof-of-concept experiment,
a DNA oligonucleotide linked at its 30 end to a known
ligand for one of two proteins (human serum albumin
[HSA] or carbonic anhydrase [CA]) was combined with a
library of complementary oligonucleotides linked to a
variety of small-molecule pharmacophores at their 50
ends. The resulting Watson–Crick base-paired ESAC
libraries were incubated with biotinylated target protein
and captured on streptavidin-linked sepharose. Ligand–
pharmacophore pairs surviving the binding selection were
identified by DNA sequence analysis and synthesized as
single compounds containing both the known ligand and
the selected pharmacophore now connected through linkers of variable length. Using this approach, bidentate
compounds were discovered that exhibited a 40-fold
increase in affinity over that of the known ligands alone.
One limitation of DCC is that increasing library size
results in the presence of large numbers of unfit molecules
that negatively effect selection efficiency by competing
with desired compounds for target binding. Although
recent computational efforts suggest that appreciable
amplification can be observed in libraries containing 106
members [16], published DCLs remain modest in size.
Also limiting is the necessary reliance on reversible chemical reactions for the construction of library members.
Recent efforts to apply cycles of translation, selection
and amplification to synthetic libraries have yielded
new approaches to overcoming these limitations. Nucleic
acids are ideally suited to be foundational components of
translation, selection and amplification because of their
ability to be replicated, their high information density,
their chemical stability and their ease of manipulation.
These features make DNA, in particular, an attractive
molecule for interfacing evolutionary approaches with
problems that involve synthetic molecules.
The laboratory evolution of proteins is made possible by
linking proteins with their encoding nucleic acids using
phage display [17], ribosome display and mRNA display
[18], in vitro compartmentalization methods [19] and
other approaches [20,21]. The idea that DNA can be
used as a tag to encode members of a small-molecule
library and facilitate the identification of active compounds was described over a decade ago by Brenner
and Lerner [22]. In an early example, Needels, Dower,
Gallop and co-workers reported the synthesis and
screening of a DNA-encoded library of 106 synthetic
heptapeptides [23]. The peptide library was synthesized
on amino-functionalized resin by standard split-pool peptide synthesis [24]. DNA tags were installed by following
each amino acid coupling step with two cycles of DNA
synthesis on the same resin. The resulting oligonucleotide
In ESAC technology, selective pressure is applied to noncovalent assemblies of small-molecule pharmacophores.
The conversion of sequences surviving selection into
active, discrete compounds can be challenging because
the precise nature by which pharmacophores are linked
together can strongly affect the binding properties of the
resulting unified structures. Indeed, Neri, Melkko and coworkers found linker length to play a significant role in
determining the target binding affinities of the single
compounds containing the joined fragments. The magnitude of the chelate effect that underlies the ESAC
system was recently studied by Neri and co-workers
[26]. This technology is promising in light of continued
(Figure 2 Legend) Dynamic combinatorial chemistry (DCC). (a) Synthesis and amplification of a molecule with target binding affinity from a
dynamic combinatorial library. (b) Amplification of a diastereomerically pure catenane receptor from a single peptidic hydrazine-acetal.
(c) Gelation-driven formation of a thermostable hydrogel from a dynamic combinatorial library of G-quartet hydrazones.
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Solving chemical problems through the application of evolutionary principles Rozenman, McNaughton and Liu 263
Figure 3
Encoded self-assembling combinatorial libraries (ESACs) use base pairing to bring together components of a DNA-tagged pharmacophore library.
Selection for target binding and analysis of encoding sequences reveals functional pharmacophore combinations.
interest in the area of multivalent interactions and bifunctional molecules [27].
DNA display
Halpin and Harbury recently developed DNA display, a
method in which DNA is used not only to identify DNAlinked small molecules, but also to route DNA-linked
starting materials to appropriate reagents during splitpool small-molecule library synthesis (Figure 4) [28–
30]. As a result, DNA display enables genetic information
to be translated into a molecular structure, a necessary
component of molecular evolution. In this method, DNA
sequences containing multiple 20-base ‘zip codes’
flanked by 20-base non-coding regions route DNA-linked
starting materials to columns containing beads coated
with an oligonucleotide complementary to each unique
coding region. After DNA hybridization captures library
members at appropriate columns defined by their DNA
sequences, the library members are eluted onto DEAE
sepharose, exposed to a unique set of reaction conditions
that correspond to each zip code and then re-pooled
before the next routing step. The process of DNA-programmed split-pool synthesis is continued until each
codon in the DNA support has been translated into an
encoded small molecule.
To validate the method, Halpin and Harbury [28] applied
DNA display to the synthesis of 106 unnatural acylated
pentapeptides, including [Leu]enkephalin, a known
7.1 nM binder for the 3-E7 antibody. Impressively, after
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only two rounds of translation, selection and amplification, the library converged on a group of sequences
encoding [Leu]enkephalin or close variants. The DNA
display method represents an important step towards the
evolution (iterative translation, selection, amplification
and diversification) of synthetic small molecules.
Although the reported chemistry interfaced with DNA
display has thus far been limited to peptide bond formation and the use of long (200-base) DNA sequences
may complicate binding selections, this method
represents a very promising approach to the creation of
large synthetic libraries that can be subjected to iterated
translation, selection and amplification.
DNA-templated synthesis
DNA-templated synthesis (DTS), first studied by Orgel,
Gilham and their respective co-workers as a model system for the prebiotic replication of nucleic acids [31–33],
has recently been developed as a general approach for the
translation of DNA sequences into corresponding synthetic small molecules [34]. Liu, Gartner and co-workers
discovered that DNA duplex formation exerts remarkable control over the effective molarity of DNA-linked
reactants and can direct chemical reactions to generate
products unrelated in structure to DNA [35,36]. In this
approach, Watson–Crick base pairing between two
complementary DNA oligonucleotides, each of which
is covalently linked to a synthetic reactant, elevates the
effective molarity of otherwise highly dilute reactants by
several orders of magnitude, inducing their efficient
Current Opinion in Chemical Biology 2007, 11:259–268
264 Combinatorial chemistry and molecular diversity
Figure 4
DNA display. Libraries of DNA-linked small molecules are routed (split and pooled in a sequence-specific manner) to achieve the stepwise
synthesis of encoded library members. DNA-displayed small-molecule libraries can then be subjected to functional selections.
Figure 5
DNA-templated organic synthesis (DTS). Base pairing between two DNA-linked small-molecule reactants elevates their effective molarity,
inducing their reaction in a sequence-programmed manner. Libraries of DNA templates can thus be translated into corresponding libraries of
small molecules, then selected for functional properties.
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Solving chemical problems through the application of evolutionary principles Rozenman, McNaughton and Liu 265
Figure 6
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Current Opinion in Chemical Biology 2007, 11:259–268
266 Combinatorial chemistry and molecular diversity
chemical reaction. As reactivity is controlled by DNA
annealing and spatial separation is not required to
prevent undesired cross-reactions, DTS enables libraries
of DNA templates in a single solution to be translated
into corresponding libraries of complex synthetic small
molecules [37,38]. The resulting small molecules are
each tethered to the DNA sequence that has directed
its synthesis (Figure 5).
In a proof-of-concept effort, Gartner and Liu achieved the
first DTS and in vitro selection of a pilot library of
synthetic small-molecule macrocycles [38]. A single
solution containing 65 DNA templates was translated
using multistep DTS into a solution containing 65 corresponding synthetic macrocycles. A minute quantity
(100 fmol) of the resulting library was subjected to two
rounds of selection for binding affinity to CA. The species
surviving the selection predominantly consisted of a
single DNA-linked macrocycle containing a phenyl sulfonamide group with known CA affinity.
The surprisingly broad range of chemistry that can be
accessed in a DNA-templated format [34,39] suggests
that DTS is a promising means of applying translation,
selection and amplification methods to small-molecule
discovery. Although recent efforts have expanded the
chemical scope of DTS to include heterocycle syntheses
[40], functional group transformations [41], ordered multistep synthesis in a single solution [35] and access to
reactions in organic solvent [42], realizing the full potential of this approach will require its application to the
creation and selection of larger and more diverse libraries
of synthetic compounds.
Reaction discovery
The evolutionary principles harnessed in the above
efforts to discover functional small molecules have also
been applied to the discovery of new chemical reactions
[43]. Reaction discovery traditionally focuses on one
particular transformation; a specific set of substrates is
chosen based on their predicted ability to serve as precursors for a target structure and reaction conditions are
evaluated for their ability to effect formation of the
desired product. This focused approach can be complemented by selection-based methods that enable the
broad exploration of chemical reactivity in a manner that
does not rely on predicted patterns of reactivity.
Liu, Kanan, and co-workers recently integrated DTS and
in vitro selection into an alternative approach for the
discovery of bond-forming reactions (Figure 6a). The
researchers linked 24 different small-molecule substrates
to DNA oligonucleotides encoding their identities. The
DNA sequences were designed such that the 24 DNAlinked substrates self-assembled into 168 substrate pairs
in a single solution (Figure 6b). Bond formation between
the two substrates within any of these pairs results in the
transfer of a biotin group to the oligonucleotide encoding
the identity of the two substrates. Following exposure to a
chosen set of reaction conditions and selection for binding
to immobilized streptavidin, the DNA sequences encoding the bond-forming substrate combinations are amplified by PCR and identified by DNA microarray analysis
(Figure 6a). This selection-based approach isolates those
substrate pairs capable of forming a covalent bond under a
given set of reaction conditions in a single experiment
that consumes only picomole quantities of substrates and
takes place in a total reaction volume of 12 mL.
Kanan, Liu and co-workers applied the system to the
exploration of transition-metal-mediated chemistry in
aqueous solvents. Selection in the presence of Pd(II)
revealed reactions including the coupling of a terminal
alkene and a terminal alkyne (Figure 6c), which was
characterized as an efficient oxidative coupling that
generated a macrocyclic trans-enone under very mild
conditions. This initial discovery was further developed
by Liu, Momiyama and Kanan into an efficient, mild and
selective method for the synthesis of acyclic a,b-unsaturated ketones through the Pd(II)-catalyzed reaction of
alkynamides and alkenes [44].
The above reaction discovery system is significantly
limited by the requirement that discovered reactions
must take place under conditions that support DNA
hybridization (aqueous solvent, high cation concentration, moderate temperature and moderate pH). The
development of a system capable of supporting reaction
discovery in a broad range of solvent and temperature
conditions would significantly increase the potential
impact of this application of translation, selection and
amplification principles to a central problem in the chemical sciences.
Conclusions
The application of fundamental biological principles to
synthetic molecules has a rich foundation, including early
influential work in biomimetic chemistry [45,46], templated assembly [47] and molecular replication [48]. More
recently, researchers have begun to address chemical
problems by harnessing another defining feature of living
systems — their ability to evolve through cycles of
translation, selection, amplification and mutation. Efforts
in DCC and the use of DNA-encoded molecules have
(Figure 6 Legend) Reaction discovery enabled by DNA-templated synthesis and in vitro selection. (a) A general one-pot selection and analysis
strategy for the detection of bond-forming reactions between DNA-linked substrates. (b) Two pools of DNA-linked small molecules self-assemble
into 168 substrate pairs, each identified by a unique DNA sequence. (c) Array-based analysis of DNA sequences surviving selection for bond
formation led to the discovery of a novel alkene–alkyne oxidative coupling reaction.
Current Opinion in Chemical Biology 2007, 11:259–268
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Solving chemical problems through the application of evolutionary principles Rozenman, McNaughton and Liu 267
taken advantage of selection principles to identify
functional molecules more efficiently. Taking a further
step towards small-molecule evolution, DNA display and
DTS enable DNA sequences not only to encode smallmolecule structures, but also to direct their syntheses.
These systems are amenable to multiple rounds of translation, selection and amplification crucial to realizing the
full potential of evolution in small-molecule discovery. In
a further example, DTS and in vitro selection have been
used to discover new chemical reactions. Collectively,
these developments highlight the potential of integrating
fundamental features of living systems with chemistries
only available in the laboratory.
Conflict of interest statement
DRL is the scientific founder of Ensemble Discovery,
Inc, a Cambridge, MA company that applies DNAtemplated synthesis.
Acknowledgements
This work was supported by the National Institutes of Health/NIGMS
(R01 GM065865) and by the Howard Hughes Medical Institute. MMR
gratefully acknowledges a National Science Foundation Graduate
Research Fellowship.
1.
Arnold FH: Design by directed evolution. Acc Chem Res 1998,
31:125-131.
2.
Jaeger KE, Reetz MT: Directed evolution of enantioselective
enzymes for organic chemistry. Curr Opin Chem Biol 2000,
4:68-73.
3.
Lin H, Cornish VW: Screening and selection methods for
large-scale analysis of protein function. Angew Chem Int Ed
Engl 2002, 41:4402-4425.
4.
Yuan L, Kurek I, English J, Keenan R: Laboratory-directed
protein evolution. Microbiol Mol Biol Rev 2005, 69:373-392.
5.
Klussman S (Ed): The Aptamer Handbook. Weinheim: Wiley-VCH;
2006.
6.
Gartner ZJ: Evolutionary approaches for the discovery of
functional synthetic small molecules. Pure Appl Chem 2006,
78:1-14.
7.
Scheuermann J, Dumelin CE, Melkko S, Neri D: DNA-encoded
chemical libraries. J Biotechnol 2006, 126:568-581.
8.
Corbett PT, Leclaire J, Vial L, West KR, Wietor JL, Sanders JK,
Otto S: Dynamic combinatorial chemistry. Chem Rev 2006,
106:3652-3711.
9.
Brady PA, Bonar-Law RP, Rowan SJ, Suckling CJ, Sanders JKM:
‘‘Living’’ macrolactonization: thermodynamically-controlled
cyclization and interconversion of oligocholates. J Chem Soc
Chem Commun 1996, 3:319-320.
10. Huc I, Lehn JM: Virtual combinatorial libraries: dynamic
generation of molecular and supramolecular diversity
by self-assembly. Proc Natl Acad Sci USA 1997,
94:2106-2110.
14. Sreenivasachary N, Lehn JM: Gelation-driven component
selection in the generation of constitutional dynamic
hydrogels based on guanine-quartet formation. Proc Natl Acad
Sci USA 2005, 102:5938-5943.
15. McNaughton BR, Miller BL: Resin-bound dynamic
combinatorial chemistry. Org Lett 2006, 8:1803-1806.
16. Corbett PT, Otto S, Sanders JK: What are the limits to the size
of effective dynamic combinatorial libraries? Org Lett 2004,
6:1825-1827.
17. Smith GP, Petrenko VA: Phage display. Chem Rev 1997,
97:391-410.
18. Roberts RW: Totally in vitro protein selection using mRNAprotein fusions and ribosome display. Curr Opin Chem Biol
1999, 3:268-273.
19. Miller OJ, Bernath K, Agresti JJ, Amitai G, Kelly BT,
Mastrobattista E, Taly V, Magdassi S, Tawfik DS, Griffiths AD:
Directed evolution by in vitro compartmentalization.
Nat Methods 2006, 3:561-570.
20. Thorn SN, Daniels RG, Auditor MT, Hilvert D: Large rate
accelerations in antibody catalysis by strategic use of
haptenic charge. Nature 1995, 373:228-230.
21. Olsen MJ, Stephens D, Griffiths D, Daugherty P, Georgiou G,
Iverson BL: Function-based isolation of novel enzymes from a
large library. Nat Biotechnol 2000, 18:1071-1074.
22. Brenner S, Lerner RA: Encoded combinatorial chemistry.
Proc Natl Acad Sci USA 1992, 89:5381-5383.
23. Needels MC, Jones DG, Tate EH, Heinkel GL, Kochersperger LM,
Dower WJ, Barrett RW, Gallop MA: Generation and screening of
an oligonucleotide-encoded synthetic peptide library.
Proc Natl Acad Sci USA 1993, 90:10700-10704.
24. Lam KS, Salmon SE, Hersh EM, Hruby VJ, Kazmierski WM,
Knapp RJ: A new type of synthetic peptide library for
identifying ligand-binding activity. Nature 1991,
354:82-84.
25. Melkko S, Scheuermann J, Dumelin CE, Neri D: Encoded
self-assembling chemical libraries. Nat Biotechnol 2004,
22:568-574.
26. Melkko S, Dumelin CE, Scheuermann J, Neri D: On the magnitude
of the chelate effect for the recognition of proteins by
pharmacophores scaffolded by self-assembling
oligonucleotides. Chem Biol 2006, 13:225-231.
27. Carlson CB, Mowery P, Owen RM, Dykhuizen EC, Kiessling LL:
Selective tumor cell targeting using low-affinity, multivalent
interactions. ACS Chem Biol 2007, 2:119-127.
28. Halpin DR, Harbury PB: DNA display II. Genetic manipulation of
combinatorial chemistry libraries for small-molecule
evolution. PLoS Biol 2004, 2:E174.
29. Halpin DR, Harbury PB: DNA display I. Sequence-encoded
routing of DNA populations. PLoS Biol 2004, 2:E173.
30. Halpin DR, Lee JA, Wrenn SJ, Harbury PB: DNA display III.
Solid-phase organic synthesis on unprotected DNA.
PLoS Biol 2004, 2:E175.
31. Sulston J, Lohrmann R, Orgel LE, Miles HT: Nonenzymatic
synthesis of oligoadenylates on a polyuridylic acid template.
Proc Natl Acad Sci USA 1968, 59:726-733.
32. Orgel LE: Evolution of the genetic apparatus. J Mol Biol 1968,
38:381-393.
11. Eliseev AV, Nelen MI: Use of molecular recognition to drive
chemical evolution: controlling the composition of an
equilibrating mixture of simple arginine receptors. J Am Chem
Soc 1997, 119:1147-1148.
33. Naylor R, Gilham PT: Studies on some interactions and
reactions of oligonucleotides in aqueous solution.
Biochemistry 1966, 5:2722-2728.
12. Lam RT, Belenguer A, Roberts SL, Naumann C, Jarrosson T,
Otto S, Sanders JK: Amplification of acetylcholine-binding
catenanes from dynamic combinatorial libraries. Science 2005,
308:667-669.
34. Li X, Liu DR: DNA-templated organic synthesis: nature’s
strategy for controlling chemical reactivity applied to
synthetic molecules. Angew Chem Int Ed Engl 2004,
43:4848-4870.
13. Brisig B, Sanders JK, Otto S: Selection and amplification of a
catalyst from a dynamic combinatorial library. Angew Chem Int
Ed Engl 2003, 42:1270-1273.
35. Gartner ZJ, Kanan MW, Liu DR: Multistep small-molecule
synthesis programmed by DNA templates. J Am Chem Soc
2002, 124:10304-10306.
www.sciencedirect.com
Current Opinion in Chemical Biology 2007, 11:259–268
268 Combinatorial chemistry and molecular diversity
36. Gartner ZJ, Liu DR: The generality of DNA-templated synthesis
as a basis for evolving non-natural small molecules.
J Am Chem Soc 2001, 123:6961-6963.
37. Calderone CT, Liu DR: Small-molecule diversification from
iterated branching reaction pathways enabled by DNAtemplated synthesis. Angew Chem Int Ed Engl 2005,
44:7383-7386.
38. Gartner ZJ, Tse BN, Grubina R, Doyon JB, Snyder TM, Liu DR:
DNA-templated organic synthesis and selection of a library of
macrocycles. Science 2004, 305:1601-1605.
39. Calderone CT, Puckett JW, Gartner ZJ, Liu DR: Directing
otherwise incompatible reactions in a single solution by using
DNA-templated organic synthesis. Angew Chem Int Ed Engl
2002, 41:4104-4108.
40. Li X, Gartner ZJ, Tse BN, Liu DR: Translation of DNA into synthetic
N-acyloxazolidines. J Am Chem Soc 2004, 126:5090-5092.
41. Sakurai K, Snyder TM, Liu DR: DNA-templated functional group
transformations enable sequence-programmed synthesis
using small-molecule reagents. J Am Chem Soc 2005,
127:1660-1661.
Current Opinion in Chemical Biology 2007, 11:259–268
42. Rozenman MM, Liu DR: DNA-templated synthesis in organic
solvents. ChemBioChem 2006, 7:253-256.
43. Kanan MW, Rozenman MM, Sakurai K, Snyder TM, Liu DR:
Reaction discovery enabled by DNA-templated synthesis and
in vitro selection. Nature 2004, 431:545-549.
44. Momiyama N, Kanan MW, Liu DR: Synthesis of acyclic
alpha,beta-unsaturated ketones via Pd(II)-catalyzed
intermolecular reaction of alkynamides and alkenes.
J Am Chem Soc 2007, 129:2230-2231.
45. Breslow R: Biomimetic chemistry and artificial enzymes:
catalysis by design. Acc Chem Res 1995, 28:146-153.
46. Breslow R: Biomimetic control of chemical reactivity.
Acc Chem Res 1980, 13:170-177.
47. Thompson MC, Busch DH: Reactions of coordinated ligands. II.
Nickel(II) complexes of some novel tetradentate ligands.
J Am Chem Soc 1962, 84:1762.
48. Rebek J: Studies in molecular replication. Acc Chem Res 1994,
27:198-203.
www.sciencedirect.com