DNA: Not just good for genes

January 14, 2016

The main job of deoxyribonucleic acid (DNA) is to encode and store our genetic information. But there is more to it: Like many proteins and ribonucleic acids (RNAs), DNA can also catalyze chemical reactions like an enzyme. A team of Göttingen researchers headed by Claudia Höbartner and Vlad Pena have now, for the first time, visualized the spatial structure of a DNA enzyme in atomic detail. The scientists thus provide evidence that also DNA folds into complex three-dimensional shapes to be catalytically active. The new findings solve a long-standing puzzle in nucleic acid chemistry and are an important step to better understand DNA enzymes as well as to utilize them as tools. (Nature, January 14, 2016)

The first three-dimensional structure of a DNA enzyme. The deoxyribozyme (blue) has fused two RNA strands (orange).

Unlike catalytic proteins and RNAs, DNA enzymes – also termed deoxyribozymes – have not been found in living cells so far. Scientists prepare them synthetically by producing a large number of individual DNA strands and then fishing out those which are able to catalyze chemical reactions. The deoxyribozymes can then serve as tools in research. They are used for example for cutting RNA molecules at a specific site or for linking two RNAs. The hope is that they can also be applied in medicine, for example to target genes involved in certain diseases.

“In order to generate more efficient variants of deoxyribozymes by rational optimization we need to know how they function,” explains Claudia Höbartner, Head of the Group Nucleic Acid Chemistry at the Göttingen Max Planck Institute (MPI) for Biophysical Chemistry and Professor at the Institute for Organic and Biomolecular Chemistry at the University of Göttingen. “To this end, it is important to learn how the DNA specifically selects only one out of many possible sites in the RNA for carrying out the reaction. This can only be explained when we understand the DNA’s three-dimensional structure.” Researchers have been trying to solve such a deoxyribozyme structure since DNA enzymes were discovered more than 20 years ago. The team headed by Claudia Höbartner and Vlad Pena has now achieved the breakthrough: They have unveiled the spatial structure of a deoxyribozyme with atomic accuracy. This provided detailed insight into how DNA enzymes work – a milestone in research on nucleic acids and structural biology.

The examined DNA enzyme catalyzes the formation of a natural chemical bond between two RNA molecules, resulting in a single strand of RNA. The structure identified by the Göttingen chemists shows the deoxyribozyme after the reaction has occured. “We saw that the DNA strand folded up to form a compact unit. Thereby, certain building blocks of the DNA juxtapose with the RNAs’ reactive ends in one spot, forming a center where the chemical reaction takes place,” explains Vlad Pena, Head of the Research Group Macromolecular Crystallography at the MPI for Biophysical Chemistry. With the first three-dimensional structure of a deoxyribozyme, the Göttingen scientists now show what has long been suspected but could not be verified so far: Just like enzymatic RNAs and proteins, DNA enzymes adopt a defined three-dimensional structure to fulfill their catalytic task. “This poses the fascinating question of whether more complex DNA structures might also play a role in Nature, similar to what is currently known only for RNAs and proteins,” Pena says.

The researchers’ findings also help to understand the exact course of the reaction and to improve DNA enzymes as tools. Thanks to the new information, they were able to modify the DNA enzyme so that it changed its preference for certain RNA substrates.

With the first structure of a deoxyribozyme, the chemists solved a long-standing puzzle of catalytically active DNA molecules: RNA enzymes are particularly good catalysts because on each individual building block they have an additional so-called hydroxyl group which plays an important role for the 3D organization and catalysis. This additional hydroxyl group is missing in DNA. So how do deoxyribozymes manage to catalyze reactions equally well as the chemically much better equipped RNA enzymes? “The structure of the deoxyribozyme shows that lack of the hydroxyl group is not a disadvantage for DNA,” reports Almudena Ponce-Salvatierra, first author of the publication. “This endows DNA with structural properties more versatile than those of RNA, enabling more possibilities to bring together its chemical building blocks for catalysis.”

In the future, Max Planck researcher Claudia Höbartner wants to find out even more about these particular nucleic acid molecules. “We will try to ‘freeze’ a deoxyribozyme not only after, but also before or during the chemical reaction to analyze its structure. This would give us additional information about the catalytic mechanism.” (ch/vp)

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