Translation of DNA into a library of 13,000 synthetic small-molecule macrocycles suitable for in vitro selection.

J Am Chem Soc
Authors
Keywords
Abstract

DNA-templated organic synthesis enables the translation, selection, and amplification of DNA sequences encoding synthetic small-molecule libraries. Previously we described the DNA-templated multistep synthesis and model in vitro selection of a pilot library of 65 macrocycles. In this work, we report several key developments that enable the DNA-templated synthesis of much larger (>10,000-membered) small-molecule libraries. We developed and validated a capping-based approach to DNA-templated library synthesis that increases final product yields, simplifies the structure and preparation of reagents, and reduces the number of required manipulations. To expand the size and structural diversity of the macrocycle library, we augmented the number of building blocks in each DNA-templated step from 4 to 12, selected 8 different starting scaffolds which result in 4 macrocycle ring sizes and 2 building-block orientations, and confirmed the ability of the 36 building blocks and 8 scaffolds to generate DNA-templated macrocycle products. We computationally generated and experimentally validated an expanded set of codons sufficient to support 1728 combinations of step 1, step 2, and step 3 building blocks. Finally, we developed new high-resolution LC/MS analysis methods to assess the quality of large DNA-templated small-molecule libraries. Integrating these four developments, we executed the translation of 13,824 DNA templates into their corresponding small-molecule macrocycles. Analysis of the resulting libraries is consistent with excellent (>90%) representation of desired macrocycle products and a stringent test of sequence specificity suggests a high degree of sequence fidelity during translation. The quality and structural diversity of this expanded DNA-templated library provides a rich starting point for the discovery of functional synthetic small-molecule macrocycles.

Year of Publication
2008
Journal
J Am Chem Soc
Volume
130
Issue
46
Pages
15611-26
Date Published
2008 Nov 19
ISSN
1520-5126
DOI
10.1021/ja805649f
PubMed ID
18956864
PubMed Central ID
PMC2648815
Links
Grant list
R01GM065865 / GM / NIGMS NIH HHS / United States
R01 GM065865-03 / GM / NIGMS NIH HHS / United States
R01 GM065865-05A1 / GM / NIGMS NIH HHS / United States
R01 GM065865-02 / GM / NIGMS NIH HHS / United States
R01 GM065865-01A2 / GM / NIGMS NIH HHS / United States
R01 GM065865-06S1 / GM / NIGMS NIH HHS / United States
R01 GM065865-06 / GM / NIGMS NIH HHS / United States
Howard Hughes Medical Institute / United States
R01 GM065865 / GM / NIGMS NIH HHS / United States
R01 GM065865-04 / GM / NIGMS NIH HHS / United States