A DNA structure that tags genetic junk?

Although DNA holds the instructions for making proteins, a sizable fraction of these sacred codes appears to contain nonsense. Indeed, after an RNA copy ol DNA is made, an elaborate splicing system removes the genetic junk, sequences called introns. The substantive information in the remaining codes, called exons, can be patched together and translated into an enzyme or other useful protein. So why do introns exist at all?

A report in the June 22 BIOCHEMISTRY may provide a clue. Using a chemical probe, two chemists at the California Institute of Technology in Pasadena have discovered a structural landmark that appears to flag introns.

"Here we have what I think is a first indication that introns are structurally delineated at the DNA level," says Jacqueline K. Barton, one of the Caltech researchers.

A regularly occurring structure on DNA should play some important role, she says. Thus, the finding contradicts the view that introns are evolutionary relics that are removed because they serve no purpose

The work supports the exon shuffling theory, which contends that introns act as spacers where breaks for genetic recombination occur. Under this scenario, exons -- which usually contain instructions for building a protein subunit - remain intact when shuffled during recombination, In this way, proteins with new functional repertoires can evolve.

Barton and co-worker Inho Lee were searching vital DNA for unusual structures, which often prove to be biologi ically interesting. They used a chemical probe containing rhodium, which Barton describes as a "funny-looking metal complex which recognizes funny-looking structures."

The probe, it turns out, bound to specific structures on DNA introns The researchers shone a light on the DNA to trigger a break at the sites of each of these structures and then determined their locations by studying the cleavage patterns. The structures appeared to occur near the ends of introns, says Barton. The same results emerged for each ol the two different viral DNAs they studied.

The new structures may be signposts marking where an intron ends and an exon begins, Barton says The two chemists are planning additional studies that will compare the cleavage patterns of DNA introns and their RNA analogs. They hope eventually to look for hints 01 how these structures function. By fishing out which cellular or nuclear components bind to the structures, Barton says, they may be able to deduce the structures' physiological role.