Evolving new molecular function

Abstract

Nature evolves biological molecules such as proteins through iterated rounds of diversification, selection, and amplification. The present invention provides methods, compositions, and systems for synthesizing, selecting, amplifying, and evolving non-natural molecules based on nucleic acid templates. The sequence of a nucleic acid template is used to direct the synthesis of non-natural molecules such as unnatural polymers and small molecules. Using this method combinatorial libraries of these molecules can be prepared and screened. Upon selection of a molecule, its encoding nucleic acid template may be amplified and / or evolved to yield the same molecule or related molecules for re-screening. The inventive methods and compositions of the present invention allow for the amplification and evolution of non-natural molecules in a manner analogous to the amplification of natural biopolymer such as polynucleotides and protein.

Description

PRIORITY INFORMATION [0001] This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional patent applications 60 / 277,081, filed Mar. 19, 2001, entitled “Nucleic Acid Directed Synthesis of Chemical Compounds”; 60 / 277,094, filed Mar. 19, 2001, entitled “Approaches to Generating New Molecular Function”; and 60 / 306,691, filed Jul. 20, 2001, entitled “Approaches to Generating New Molecular Function”, and the entire contents of each of these applications are hereby incorporated by reference.BACKGROUND OF THE INVENTION [0002] The classic “chemical approach” to generating molecules with new functions has been used extensively over the last century in applications ranging from drug discovery to synthetic methodology to materials science. In this approach (FIG. 1, black), researchers synthesize or isolate candidate molecules, assay these candidates for desired properties, determine the structures of active compounds if unknown, formulate structure-activity relationships based ...

AI Technical Summary

Benefits of technology

[0008] It will be appreciated that libraries synthesized in this manner (i.e., having been encoded by a nucleic acid) have the advantage of being amplifiable and evolvable. Once a molecule is identified, its nucleic acid template besides acting as a tag used to identify the attached compound can also be amplified using standard DNA techniques such as the polymerase chain reaction (PCR). The amplified nucleic acid can then be used to synthesize more of the desired compound. In certain embodiments, during the amplification step mutations are introduced into the nucleic acid in order to generate a population of chemical compounds that are related to the parent compound but are modified at one or more sites. The mutated nucleic acids can then be used to synthesize a new library of related compounds. In this way, the library being screened can be evolved to contain more compounds with the desired activity or to contain compounds with a higher degree of activity.

Problems solved by technology

Several factors limit the effectiveness of the chemical approach to generating molecular function.

First, our ability to accurately predict the structural changes that will lead to new function is often inadequate due to subtle conformational rearrangements of molecules, unforeseen solvent interactions, or unknown stereochemical requirements of binding or reaction events.

The resulting complexity of structure-activity relationships frequently limits the success of rational ligand or catalyst design, including those efforts conducted in a high-throughput manner.

Second, the need to assay or screen, rather than select, each member of a collection of candidates limits the number of molecules that can be searched in each experiment.

Finally, the lack of a way to amplify synthetic molecules places requirements on the minimum amount of material that must be produced for characterization, screening, and structure elucidation.

As a result, it can be difficult to generate libraries of more than roughly 106 different synthetic compounds.

Despite nature's efficient approach to generating function, nature's molecular evolution is limited to two types of “natural” molecules—proteins and nucleic acids—because thus far the information in DNA can only be translated into proteins or into other nucleic acids.

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