In biotechnology, DNA methylation is best known as a gene silencing method. Each cell in an organism carries the entire genome in it. But a specific cell will never need most of its genetic code, and even those genes it needs must be expressed only at specific times to prevent a chaotic molecular free-for-all.

Methylation of specific DNA sequences by enzymes called DNA methyltransferases shuts off genes when they are not needed. DNA methyltransferases choreograph embryonic development, and several companies are targeting DNA methyltransferases for therapeutic use, since the methylation of tumor suppressors plays a role in the development of some cancers. (See BioWorld Today, July 14, 2004.)

But most methyltransferases have a less glamorous role. They simply prevent bacterial restriction endonucleases from chewing up their own DNA.

"By far, the most known DNA methyltransferases are part of restriction-modification systems," Elmar Weinhold, professor of chemistry at the Rheinisch-Westfaelische Technische Hochschule (RWTH) in Aachen, Germany, told BioWorld Today. Pairs of methyltransferases and restriction endonucleases recognize the same DNA sequence, and methylation of the recognition sequence by the methyltransferase protects the bacterial DNA against attack by the restriction endonuclease.

While it might seem a strange molecular setup for a cell to have a restriction endonuclease to chop up DNA and a methyltransferase to prevent the restriction endonuclease from doing its job, this buddy system allows cells to distinguish their own, methylated DNA from the unmethylated DNA of invading viruses, promptly destroying the latter while leaving the former undisturbed. Weinhold likened it to a "primitive immune system" for bacteria.

Now, DNA methyltransferases may also join restriction endonucleases as workhorses in biotech labs. In the Nov. 27, 2005, early online edition of Nature Chemical Biology, scientists from the RWTH's Institute for Organic Chemistry and the Institute of Biotechnology in Vilnius, Lithuania, reported on sidetracking the cell's methylation machinery to add other chemical groups than methyl to the DNA sequences.

Methyltransferases usually transfer methyl groups to DNA from the molecule S-Adenosyl-L-methionine, or SAM. In the research published in Nature Chemical Biology, the scientists were able to synthesize analogs that had larger carbon side chains, but were still transferred by the DNA methyltransferases. They achieved their goal by stabilizing other bonds within the donor molecule.

With the stabilized SAM analog, the researchers were able to transfer chains of up to five carbon atoms onto the DNA. The sequence specificity of the transfer was preserved; control experiments showed that the DNA methyltransferases used the same catalytic mechanism to transfer longer carbon chains as they do to transfer methyl groups. The reaction was a true catalytic one; that is, the enzyme itself is not destroyed during the reaction, but can repeatedly catalyze the same transfer. The scientists determined that the methyltransferases take slightly less than two minutes to catalyze reactions with SAM analogs, making the technique, in the words of the authors, "suitable for routine laboratory use."

More than 800 methyltransferases exist that between them recognize roughly 200 distinct DNA sequences. That sequence specificity gives the new approach its major advantage: Genes can be labeled at specific locations within their sequence.

Weinhold put the fourfold redundance in sequence specificity down to parallel evolution: "It just happened in nature that different bacteria acquired different restriction-modification systems, which have the same sequence specificities," he said.

The findings could have applications in molecular medicine. The attachment of peptides at defined places in their sequence might improve the delivery of plasmids into the cell nucleus for gene therapy, though Weinhold cautioned that how the SAM analogs will behave inside a living cell "is hard to predict at the moment." Additionally, attaching larger groups than methyl will probably affect the way the modified DNA sequences interact with cellular proteins: "I would expect that the methyl-binding proteins will not be able to bind to DNA with bulky groups and thus no gene silencing should occur," Weinhold said.

Still, the findings open up plenty of possibilities for manipulating DNA. Additional applications include the ability to modify DNA for the medical diagnosis of methylation patterns, and nanobiotechnological applications such as the targeted structuring of nanoobjects on DNA. Since RNA and proteins also are labeled with SAM-derived methyl groups, the scientists believe that their method will be applicable to them as well.

"These enzymes could serve as formidable molecular tools," Weinhold said. And to make them even more so, the researchers next plan to synthesize further SAM analogs to expand the collection of chemical groups that can be transferred to DNA by methyltransferases.