Transcription pauses reveal DNA sequence

Biophysicists have exploited pauses in the transcription of DNA by an RNA polymerase enzyme to determine the sequence of DNA (Science 2006, 313, 801). Steven M. Block and William J. Greenleaf of Stanford University use a method originally developed to track transcription by a single RNA polymerase molecule. Two polystyrene beads-one attached to RNA polymerase, and the other attached to the far end of the DNA template-are levitated in an optical trap. The motion of the enzyme along the template changes the length of the DNA tether between the beads, which can be measured with angstrom-level precision. They do the transcriptional assay four times, with a different rate-limiting nucleotide each time. Whenever the RNA polymerase pauses, they know that it's looking for that rate-limiting nucleotide. By aligning the readouts from the four reactions, they can determine the sequence of the DNA. In preliminary work, they were able to correctly identify 30 out of 32 bases in a target region of DNA in less than three minutes.