A Genetic Code for Organic Chemistry

A new technique called DNA display makes it possible to use short DNA sequences to direct the synthesis of large collections (libraries) of small organic molecules.

The method provides a new option for creating and screening libraries of small molecules to discover agents with desired properties for a range of research and drug discovery applications. It's like a genetic code for organic chemistry, say its developers, graduate student David R. Halpin, assistant professor of biochemistry Pehr A. B. Harbury, and coworkers at Stanford University [PLoS Biol., published online June 22, http://dx.doi.org/10.1371/journal.pbio.0020173, -74, and -75].

In DNA display, small molecules are assembled on the ends of DNA oligomers in a split-pool reaction network--a system of reactions designed to create a large number of diverse compounds in a small number of steps. First, one constructs a library of DNA oligomers, each containing a series of coding sequences. Each coding sequence directs the DNA oligomer to one of several possible sites in a split-pool reaction network by hybridizing with a complementary DNA sequence at the site.

A chemical subunit is then added to the end of the DNA oligomer at each site, and a small organic compound is built up on the oligomer as it visits a series of sites in the network. The result is a large library of small molecules attached to the ends of the oligomers that encoded their synthesis.

Such attachment makes iterative screening possible. Harbury and coworkers demonstrated the technique by using it to carry out two cycles of in vitro selection (screening for binding or activity) on a library of 1 million nonnatural peptides, yielding a high-affinity protein ligand.

DNA display has the same goal as DNA-templated synthesis (DTS), a technique developed by David R. Liu, an associate professor of chemistry and chemical biology at Harvard University, and coworkers. In DTS, organic reagents bound to complementary DNA strands are brought into close proximity when the strands hybridize with each other, inducing the reagents to react in a sequence-programmed manner. "DTS and DNA display are the first methods that enable DNA to be translated into synthetic molecules, including structures not necessarily resembling proteins," Liu explains.

Each of the two techniques will most likely prove useful for different types of syntheses, but both can be used to identify functional agents. This is done by using the techniques in iterative procedures--in which large libraries of organic compounds are synthesized, active compounds from those libraries are identified by in vitro selection, and the encoding DNA that remains associated with selected compounds is then amplified for reintroduction into the cycle.

A key goal is to also use the techniques to carry out "molecular evolution," in which encoding DNA for selected compounds is also modified in an effort to create novel agents with even better activity. "While researchers have previously found great success applying evolution-based approaches to the discovery of proteins, RNAs, and DNAs with new or improved functional properties," Liu says, the advent of DTS and DNA display opens up the possibility of evolving small-molecule organic compounds as well.

DTS and DNA display "are the types of techniques that will be needed to manage the big numbers [of compounds] we hoped for in the early days of combinatorial chemistry," comments Gerald F. Joyce, professor of chemistry and molecular biology at Scripps Research Institute. They are "complementary approaches that will enable the evolution of small organic molecules," he says.