While individuals can be unpredictable, the group behaviour of a flock or herd is a little easier to determine. A similar principle has been enrolled to devise chemical clocks. The lifetime of a state in a molecular process is probabilistic so that its duration can vary widely, but summed over a large enough ensemble of molecules undergoing the same process there will be a clear peak at what is the statistical lifetime of that state. By summing over a large number of steps in a reaction process instead of a large number of molecules undergoing the process, Alexander Johnson-Buck and William M Shih at the Dana-Farber Cancer Institute and Harvard Medical School in Boston in the US have devised a way of controlling the timing of processes at the level of single molecules.

Johnson-Buck and Shih designed single-molecule clocks using DNA polymerase to control the duration of the bonding of an initiator molecule with a fluorescent primer on a template molecule. The timing function hinges on the way DNA polymerase lengthens through the addition of deoxyribonucleoside triphosphates (dNTPs) in a series of steps. The local fluorescence increases when the fluorescent primer bonds to the template molecule, but as the string of dNTPs lengthens, the fluorescent complex eventually dissociates and the fluorescence decreases. The time between bonding and dissociation can be controlled by the design of the template molecule, which determines how many dNTPs are needed before the fluorescent complex dissociates.

Although the time taken for the addition of each dNTP is stochastic and so can take a range of values, the times taken for the addition of several dNTPs follow a Gaussian distribution, and the distribution of the time taken for the addition of a series of dNTPs reduces the larger the number of added dNTPs in the series. Johnson-Buck and Shih conclude in their report of the findings, "We anticipate a variety of compelling uses for the deterministic control of kinetics at the single-molecule level."

Full details can be found in Nano Letters.