Piggybacking DNA

The biomolecule, DNA, that twists throughout the cell nucleus

By piggybacking small organic molecules onto short strands of DNA, chemists at Harvard University have developed an innovative new method of using DNA as a blueprint not for proteins but for collections of complex synthetic molecules. The researchers will report on the prolific technique, dubbed "DNA-templated library synthesis," in the journal Science.

"The basic structures of proteins and nucleic acids seem limited when compared with the structures that can be created using modern synthetic chemistry, and yet this very modest set of protein and nucleic acid building blocks has given rise to the incredible complexity and diversity of living systems," says David R. Liu, associate professor of chemistry and chemical biology at Harvard. "We’re interested in marrying fundamental features of biomolecules with synthetic organic chemistry in order to apply techniques such as translation, selection, and amplification to molecules beyond those found in cells and organisms."

Liu and his colleagues attached organic molecules to single DNA strands, each containing 10 DNA bases (A, C, G, or T). When two DNA strands with complementary sequences (A matches T, G matches C) spontaneously bond together, their associated organic molecules undergo a chemical reaction to generate a product. As a result, the DNA strands essentially serve as a miniature, sequence-programmable assembly line for products of chemical synthesis.

Miller Experiment
The Miller-Urey experiment generated electric sparks — meant to model lightning — in a mixture of gases thought to resemble Earth’s early atmosphere.
Credit: AccessExcellence.org

Because the resulting synthetic compounds are linked to DNA, techniques long used to screen and amplify the genetic mainstay can now be applied. Molecules can be "selected" for desired functional properties, and the survivors of these selections can then be copied using the polymerase chain reaction (PCR).

The application of DNA-templated synthesis has enabled a collection of DNA strands to be transformed into a corresponding collection of sequence-programmed small macrocyclic molecules with potentially interesting chemical and biological properties. A single member of the collection survived a selection on the basis of its ability to bind to a protein target, and the DNA encoding the survivor was amplified by PCR and sequenced to reveal its identity.

Liu’s team found that small molecules bound to DNA can react to form larger products even when the DNA bases used to zip together the small molecules are far apart on a DNA template. This means that a template strand of 30 DNA bases, complementary to Liu’s DNA codes for three different organic molecules, can encode three separate chemical reactions, leading to the multistep DNA-programmed synthesis of relatively complex cyclic products.

Chemical synthesis occurs very differently in laboratories and in cells. Chemists typically work with molecules that react to form products when they randomly collide at high concentrations. By contrast, biomolecules are found within cells at concentrations that are often a million times lower than the concentrations of molecules in laboratory reactors. In nature, the reactions between these highly dilute molecules are directed by enzymes that selectively bring certain biological reactants together. Liu and his colleagues are now using DNA as a similar type of intermediary to bring together synthetic small molecules that are otherwise too dilute to react, allowing minute quantities of sparse molecules to behave as denser mixtures when assembled together by DNA base pairing.

RNA model
Ribose sugars and phosphate backbones combine with base pairs in the familiar helix.
Credit: Darryl Leja/Access Excellence.

"We recognized that in order to apply such an approach to as many synthetic molecules as possible, we’d have to use a different type of template than an enzyme," Liu says. "The natural and robust zipping up of complementary DNA strands is a simple way to bring molecules at low concentrations together without having to develop an entirely new class of enzymes for each different type of molecule."

The 10-base DNA strands used by Liu’s team are large enough to be stable at room temperature and in theory can encode thousands of individual small organic molecules.





Liu’s co-authors are Zev J. Gartner, Brian N. Tse, Rozalina Grubina, Jeffrey B. Doyon, and Thomas M. Snyder, all of Harvard’s Department of Chemistry and Chemical Biology. Their work was funded by the National Institute of General Medical Sciences at the National Institutes of Health, the Office of Naval Research, the Arnold and Mabel Beckman Foundation, the Searle Scholars Foundation, the Alfred P. Sloan Foundation, and fellowships from Bristol-Myers Squibb and the National Science Foundation.

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