January-February 2004 > Features

Polony Power

“Polonies” are tiny colonies of DNA, about one micron in diameter, grown on a glass microscope slide (the word itself is a contraction of “polymerase colony”). To create them, researchers first pour a solution containing chopped-up DNA onto the slide. Adding an enzyme called polymerase causes each piece to copy itself repeatedly, creating millions of polonies, each dot containing only copies of the original piece of DNA. The polonies are then exposed to a series of chemically-labeled probes that light up when run through a scanning machine, identifying each nucleotide base in the strand of code, much as dusting with powder allows crime-scene investigators to bring up fingerprints on a surface.

Polonies exert an aesthetic appeal. Above, a portion of a single region of the DNA nucleotide "colonies" as they are processed.

Sequencing of "microbeads," much smaller than polonies. Below, sequences from a messenger RNA molecule.

Images courtesy of George Church and the Lipper Center for Computational Genetics

A laboratory scanner can read a slide with 10 million polonies in about 20 minutes, George Church explains, making this one of the fastest sequencing methods yet devised. The resulting batches of data, however, are as disorderly as a sheaf of pages ripped from a telephone book and tossed in the air. A computer program developed by the Church research-laboratory team puts all in order by checking each page against the genetic equivalent of an intact phone directory: a reference sequence such as the one produced by the Human Genome Project. By using the technique, Church envisions that once a new personal genome is assembled, it could be checked for variations that might cause problems for that individual, or pooled with other genomes for research purposes.