Suppose I have the four DNA base chemicals - thymine, adenine, cytosine, and guanine. Imagine I turn each of them into a gas, make a "cartridge" of the gas for each chemical, and then have a "pinhole" that is opened or closed by a semiconductor. When the pinhole is open, the gas will, of course, expand through the pinhole and exit the cartridge. The system must emit only one molecule at a time.
If I send a command to the semiconductor to open the pinhole, what kind of sensor can I use to detect a molecule passing through? If necessary, you can modify the base chemicals as long as it would not interfere with their chemical properties in any way other than to improve detection of those molecules, if that makes sense.
The cheaper and more compact the system, the better, of course. I was thinking about the way an inkjet printer works, with a piezoelectric crystal vibrating the ink into droplets, but even the smallest droplets (a picoliter or so) are still bigger than a single molecule, so that doesn't work. Other possible methods I've thought of include a MALDI like system, a system where a weak laser is set up with a light detector; when a molecule passes through, the beam is interrupted, using a scanning tunneling microscope (STM; no idea how that would work), or a system using fluorophores.