DNA-Templated Organic Synthesis (DTS)

Generality of DTS

We recently discovered that DNA duplex formation exerts remarkable control over the effective molarity of DNA-linked reactants without requiring structural mimicry of the DNA backbone. As a result, DNA-templated organic synthesis (DTS) is a surprisingly general phenomenon that can direct a wide range of chemical reactions including carbon-carbon bond forming reactions and organometallic coupling reactions, even if the structures of the reactants or products do not resemble the DNA backbone. For many DNA-templated reactions, products form efficiently even when reactive groups are separated by large distances on the template ("distance-independent synthesis"). DTS is sufficiently sequence-specific that a single DNA-linked template can react primarily with its sequence-programmed partner reagent in a single solution containing a 1,000-fold excess of non-partner, sequence-mismatched reagents.

Since our initial findings, we have developed a suite of linker and purification strategies that have enabled DNA templates to be translated into small-molecule products of multistep DNA-templated syntheses. For example, a 5'-amine-terminated DNA template was sequence-specifically translated into a non-natural tripeptide or a branched thioether product through three DNA-templated steps, with each step encoded by a different region of a 30-base DNA template. More recently, we translated DNA templates into N-acyloxazolidines and macrocyclic N-acyloxazolidines using multistep DTS. To date multistep DTS has been used to create more than a dozen classes of surprisingly diverse small-molecule structures.

 

New Modes of Controlling Reactivity

In addition to exploring and expanding the synthetic capabilities of DTS, we have also shown that DNA-templated synthesis enables new modes of controlling reactivity that are not possible using current synthetic approaches. For example, in a DNA-templated format many starting materials can undergo multiple otherwise incompatible reaction types in a single solution to generate exclusively a set of sequence-programmed products, while the analogous experiment in a traditional reaction format would generate an uncontrolled mixture of all possible products.

This reaction mode has been used to diversify synthetic small molecule libraries using iterated branching reaction pathways in a single solution in contrast to the more common diversification approach of using different building blocks in one type of reaction.

In addition, we have also found that DTS enables heterocoupling reactions to take place efficiently between reactants that preferentially homocouple in a conventional synthesis format, and also allows multistep ordered small-molecule synthesis to take place in one pot between multiple reactants of comparable reactivity. For example, an orchestrated series of changes in template secondary structure was used to synthesize an ordered triolefin or an ordered tripeptide in a single solution in which all reactants are initially present. If combined under conventional synthesis conditions, these reactants would instead generate a vast mixture of predominantly non-ordered products.

 

Architectures and Stereoselectivity

Our other advances in this area include the development of two new template architectures that expand the synthetic capabilities of DTS by (i) allowing virtually any DNA-templated reaction to be encoded by any region of a DNA template, and (ii) by enabling two reactions to take place on a single DNA template in one step. The use of both of these architectures together with more recently developed DNA-templated synthetic reactions proved crucial in the DNA-templated N-acyloxazolidines syntheses mentioned above.

In addition, we discovered the ability of a DNA template to induce stereoselectivity in a DNA-templated reaction that generates products unrelated to the DNA backbone, and have traced the origins of this stereoselectivity to the macromolecular conformation of the templates. We used this stereoselectivity as a sensitive measure of the conditions under which the DNA templates can directly influence a reaction beyond simple modulation of the effective molarity of the reactants, and found that even a small number of rotatable bonds abrogates observed template-induced effects.

In some cases it may not be possible or convenient to link reactants to oligonucleotides. To develop an alternative strategy for DNA-programmed synthesis that enables the participation of non-DNA-linked reagents, we developed DNA-templated functional group transformations that convert azide groups into amines, thiols, or carboxylic acids in a sequence-specific manner. These functional group transformations were used in conjunction with four non-DNA-tethered electrophilic reactants to convert four template-linked azides in a single solution into four sequence-programmed sulfonamide, carbamate, urea, and thiourea products.

 

DNA-Templated Library Synthesis and Selections

We have also developed highly sensitive in vitro selections for DNA-linked synthetic small molecules (such as the products of DNA-templated library synthesis) with protein binding affinity and specificity. These selections can be iterated to achieve enormous enrichments for functional DNA-linked synthetic small molecules.

Integrating many of the above concepts, we recently translated a library of 65 DNA templates into a pilot library of complex synthetic small-molecule macrocycles using a "genetic code" that dictates which reactants are recruited by each 10-base coding sequence. The resulting library of DNA-linked macrocycles was selected for binding to a target protein, and the DNA templates encoding macrocycles with target protein affinity were amplified by PCR and characterized by DNA sequencing. A single template of the pilot library that encodes a synthetic macrocycle with affinity for the target protein was successfully enriched in this manner. This work represents the translation, selection, and amplification of a library of DNA sequences that encode synthetic small molecules, rather than proteins. Encouraged by these developments, we and others are currently applying this approach to small molecule synthesis and discovery on libraries of much larger complexities and structural diversities. For example, we are currently characterizing a DNA-templated library of 1,000 N-acyloxazolidine heterocycles for use in functional selections.

 

Synthetic Polymers

We have begun to apply these principles to synthetic polymers in addition to small molecules. Based on the distance dependence of DNA-templated reductive amination and on the previous findings of David Lynn and co-workers, we have translated DNA templates into synthetic sequence-defined peptide nucleic acid (PNA) polymers using DNA-templated polymerization of PNA aldehydes. This polymerization proceeds with remarkable efficiency, excellent sequence-specificity, and can generate synthetic polymers of length similar to that of proteins and nucleic acids known to possess functional binding or catalytic properties. These findings are the basis of our ongoing efforts to evolve sequence-defined synthetic heteropolymers through processes of translation, selection, amplification, and diversification previously available only to natural biopolymers.

 

This novel approach to creating and discovering functional molecules offers significant advantages compared with existing methods. DNA-templated libraries of synthetic molecules can be subjected to true in vitro selections (as opposed to screens) for desired binding or catalytic activities, obviating the need to spatially separate each library member or to spend effort characterizing uninteresting molecules. Only minute quantities of material (~1,000 molecules of each different library member) are required for these selections because the information that directs each member's synthesis can be amplified by PCR; indeed the syntheses and selections described above were typically executed on a nanomole to subfemtomole scale. The small amount of material required coupled with the suitability of these molecules to undergo selection in theory enables libraries of unprecedented complexity (much larger than the current total size of the CAS synthetic structure database) to be generated and evaluated using this approach. In addition, the new modes of controlling reactivity enabled by DNA-templated synthesis may allow diverse regions of structure space to be explored in a manner more effective than what is possible using existing library creation strategies. Finally, the infrastructure requirements to perform library synthesis and evaluation in this format are modest compared with those of conventional approaches.

 

A New Approach to Reaction Discovery

Unique features of DNA-templated organic synthesis have also led to a new approach for the discovery of bond-forming chemical reactions. In contrast with traditional reaction discovery methods, our approach does not focus on a specific combination of substrates or on the formation of one type of product structure. Instead, we combine pools of many DNA-linked substrates in one solution and select all possible pairwise combinations of substrates simultaneously for bond-forming combinations in a single experiment. The identity of bond-forming reactant pairs is revealed by exposing DNA sequences that survive the in vitro selection to DNA microarrays containing sequences that represent every possible combination of substrates. Because the results of this reaction discovery selection can be amplified by PCR, we perform this process on a femtomole scale that is unprecedented for reaction discovery.

We validated this approach to reaction discovery by "rediscovering" several known reactions mediated by transition metals or organic reagents. We have since used this system in a 96-and 168-reaction matrix format to discover several new transition metal-catalyzed bond-forming reactions that have been confirmed in a DNA-templated format. One of the discovered reactions, a carbon-carbon bond-forming macrocyclization between a simple alkyne and alkene mediated by catalytic quantities of Pd(II) in neutral water or mixed organic solvent at room temperature to form a macrocyclic trans-enone in high yield, has also been confirmed by extensive characterization in a non-DNA-templated, conventional synthesis format. Our exploration of this discovered enone-forming reaction has recently led to its successful use in an intermolecular (rather than macrocyclization) format. This approach enables a broad and unbiased search of functional group space for new reactions at a rate of thousands of combinations of reactants and reaction conditions per two-day experiment. The development of these new areas lies at the heart of merging the creativity of the chemist with the powerful principles underlying the evolution of living systems.