Breaking the bond of life's most important molecule

by Sylvain Comeau

Chemistry professor Jik Chin is working to give tomorrow's clinicians a new, powerful approach to developing drugs. Since the mid '80s, Chin has concentrated on developing catalysts which can actually cleave--or cut--DNA and RNA molecules.

"A DNA molecule is like a string of beads held together by phosphodiester bonds," says Chin. "The key is the effectiveness of the catalysts in breaking these bonds."

Chin and his research team are using a variety of metals to produce the catalysts. Among other things, metals help hydroxides, which are found in water, attack the phosphodiester bonds.

"Hydroxides are negatively charged, and they are repelled by the negatively charged phosphodiester bonds. We use positively charged metal complexes as catalysts, to neutralize the negative charges, and allow the hydroxides to attack the bonds."

One potential application of the cleaving technique would be treating or curing infectious diseases, both in animals and humans. All living organisms, including viruses and bacteria, carry DNA or RNA molecules. "Catalysts that can cut DNA or RNA sequence specifically (targeting one particular phosphodiester bond) could in principle be used to attack viruses or bacteria without harming the host."

On the surface, Chin's most promising results would appear to be in the area of RNA cleavage. RNA is the chemical "messenger" of DNA, which sends the DNA code out of the cell nucleus. Compared to DNA, RNA is simply an easier nut to crack.

"In the absence of any added catalysts, the half-life of the phosphodiester bonds of RNA is billions of times shorter than those of DNA," explains Chin. Half-life is the amount of time it takes for half the bonds to break down.

Using metal catalysts, Chin's research team has cut down the RNA half-life from tens of years to about eight seconds, and the DNA half-life from tens of billions of years to about two hours. "That's fast enough for RNA, but we need to get the DNA half-life down to seconds as well."

Genetic diseases are another promising area for applications. Environmental factors notwithstanding, some people carry a predisposition to certain diseases within their DNA molecules, the body's repository of genetic information. Catalysts may one day be designed to cleave, sequence specifically, only the disease-causing gene.

Chin notes that the DNA sequences of all human beings are more than 99% identical. Thus, aside from environmental factors, human diversity--including genetic diseases--arises from variations in less than 1% of DNA. Catalysts must be able to "paste" as well as "cut"--not only cleave DNA in the cells, but actually replace a faulty, disease-causing gene with the normal version.

Some biotechnology and pharmaceutical companies are concentrating on RNA cleavage, which is likely to lead to applications more rapidly. However, says Chin, most applications would offer only band-aid solutions because the source of the disease--faulty genes in the DNA molecule--would remain unchanged as long as cleavage of RNA alone is achieved.

Chin's work, funded by NSERC and FCAR grants and interested biotechnology companies, focuses on DNA cleavage.

"Once we develop catalysts that are very efficient at cleaving DNA, we may someday be able to use the same principles to develop catalysts that can 'paste' by reversing the cleavage reaction."

Catalysts must not only be effective but non-toxic as well, for applications in drugs. "In developing the catalysts, we may initially use any metals as catalysts, including toxic ones, such as lead or mercury," explains Chin. "What we learn with the toxic metals may then be applied to non-toxic metals such as zinc, magnesium or calcium."

RNA and DNA cleavage may be used not only in treating or curing disease; there is considerable interest in manipulating plant genes for applications in agriculture.

Although the potential is enormous, Chin cautions that there are many hurdles to overcome before his work can yield direct applications. He and his current crop of graduate students--Mark Wall, Mary Jane Young, Jin Seog Seo and Dan Williams, along with postdoctoral fellow Andrea Erxleben--recognize the significance of their work, but also the need to take the long view.

"It's such a fundamental problem," says Chin. "DNA and RNA are probably the most important molecules of life. How can you put a time limit on that? I will probably work on it for the rest of my life, and then others after me will pick up where I left off."