Unzip Your Genes

If you think trying to unzip your coat while wearing mittens is hard, try undoing that most famous of zippered molecules, double-stranded DNA. Now, for the first time, scientists have been able to use something akin to molecular tweezers to pry apart a DNA molecule. The feat, described in the current issue of the Proceedings of the National Academy of Sciences, could lead to a faster method of finding hidden genes in unexplored DNA.

Two years ago, biophysicists succeeded in measuring the force exerted by a single molecule of RNA polymerase as it moves along a single DNA strand, reading the genetic code (Science, 8 December 1995, p. 1653). That inspired physicist François Heslot and his colleagues at the École Normale Supérieure in Paris to devise a way to measure the force required for the polymerase to unzip a DNA double helix into two strands.

The researchers designed a 30-micrometer-long stretch of DNA with two small proteins stuck on at strategic places. One protein anchored one end of the DNA to a specially coated glass slide. They also created a break in one of the two strands, halfway up the DNA, and attached the other "sticky" protein onto a loose end of the broken strand. That protein attached itself tightly to a floating, coated microbead. When the researchers touched a microneedle to the sticky bead and slowly slid the glass slide, the tension peeled apart the DNA strands.

The needle's tension, revealed by how much it bent, roughly matched the pattern of DNA base pairs whose bonds keep the helix together. The DNA would pull apart more easily in stretches dominated by adenosine and tyrosine, compared to those with more cytosine and guanine pairs, which are known to bind more tightly.

Because the beginnings of many gene sequences are rich in cytosine and guanine, measuring subtle changes in tension during DNA unzipping could be a promising method for quickly spotting genes in virgin DNA territory, according to Heslot. For now, however, Heslot's microneedle can only gauge differences in tension over several hundred base pairs, although the team thinks it can improve the resolution to every 20 base pairs. That would allow researchers to get "a very quick view" of the sequence, Heslot says, so they can concentrate on smaller sections of interest and avoid the time and cost of sequencing every base.

The technique might also help biophysicists better study how DNA is translated into the RNA that makes proteins. "Basically all of molecular genetics is based on getting strands apart, reading strands, putting strands back together," says John Marko of the University of Illinois, Chicago. "Now we can pull strands of double helix apart in the test tube under very controlled conditions."