The third technology used in SMRT is the chip used to sequence many DNA fragments in parallel.
It consists of a glass microscope cover slip with a 100 nm-thick layer of aluminum deposited on top of it.
In the aluminum is an array of cylindrical wells 70 nm–100 nm in diameter.
The aluminum is chemically treated so that polymerase molecules will stick to the glass at the bottom of each well rather than the sides of the wells.
This is important because there is no way to manipulate a polymerase molecule to deliberately place it at the bottom of a well; rather the chip must be prepared by soaking it in a solution containing polymerase molecules, which then stick to every surface they can.
The polymerase solution is very dilute, so that, on average, there is no more than one polymerase molecule per well. The cover glass at the bottom of the well permits an image of the activity of the polymerase at the bottom of each well to be projected onto a detector.