DNA as a stiff zipper
DNA consists of two strands that are held together by hydrogen bonds between the individual building blocks adenine and tyrosine, or cytosine and guanine. Using microtechniques, scientists have measured the forces of attraction. They believe that a more refined method can even be used to roughly sequence the DNA. If you find it difficult to unzip your coat while wearing mittens, you should try tearing the double-stranded DNA apart. Now, for the first time, scientists have succeeded in separating a DNA molecule using a type of molecular tweezers (Proceedings of the National Academy of Sciences of October 28, 1997). Hidden genes in unknown DNA could potentially be detected more quickly with this method.
Two years ago, biophysicists managed to measure the force exerted by a single molecule of RNA polymerase as it moves down a strand of DNA and reads the genetic code (Science 8 December 1995). This inspired physicist François Heslot and his colleagues at the École Normale Supérieure in Paris to develop a method to measure the force required by a polymerase to separate the DNA double helix into two strands.
The researchers attached small proteins to a 30 micrometer long piece of DNA at two suitable points. One end of the DNA was bound to a specially coated glass slide via one of the proteins. They broke the DNA roughly in the middle and attached the second protein to the loose end of the cut strand. This protein firmly attached to a floating, coated microbead. When the researchers touched the sticky bead with a microneedle and slowly pushed the glass slide away, the tension ripped the DNA strands apart.
The tension on the needle could be measured by the strength of its bend. It roughly corresponded to the mixture of base pairs whose bonds hold the helix together. There are only two bonds between tyrosine and adenine, while there are three bonds between cytosine and guanine. The DNA should therefore tear apart more easily in regions with a lot of adenosine and tyrosine than in regions with more cytosine-guanine pairs. Because the beginnings of many gene sequences are rich in cytosine and guanine, Heslot believes that measuring subtle changes in the tension of the needle could be a promising method for the rapid discovery of genes in unknown regions of DNA. Currently, differences between different compositions can only be detected with Heslot's microneedle if they extend over several hundred base pairs. But his team believes it can improve resolution to 20 base pairs at a time. This would allow researchers to "get a very quick sense" of the sequence, Heslot says, so they could focus on smaller stretches of interest. This would save time and money associated with base-by-base sequencing.
Biophysicists may also be able to use this technique to study how DNA is translated into RNA. "Basically, all molecular genetics is about unpicking strands, reading strands, and putting strands back together," says John Marko of the University of Illinois. Now we are able to separate double helix strands in the test tube under very controlled conditions.