Idempotent Vector Design for Standard Assembly of Biobricks

Abstract

The lack of standardization in assembly techniques for DNA sequences forces each DNA assembly reaction to be both an experimental tool for addressing the current research topic, and an experiment in and of itself. One of our goals is to replace this ad hoc experimental design with a set of standard and reliable engineering mechanisms to remove much of the tedium and surprise during assembly of genetic components into larger systems. William Sellers, in a speech "On a Uniform System of Screw Threads" at the Franklin Institute in Philadelphia on April 21, 1864, remarked that "In this country, no organized attempt has as yet been made to establish any system, each manufacturer having adopted whatever his judgement may have dictated as best, or as most convenient for himself" (Surowiecki 02). He argued forcefully and successfully for the standardization of pitch, diameter, and form of screw threads, providing the infrastructure which allowed the industrial revolution to take off. The machinists of the Franklin Institute built the lathes, drills, taps, and dies necessary to make the standard a success. We anticipate advantages similar to those which accompany the standardization of screw threads in mechanical design -- the widespread ability to interchange parts, to assemble sub-components, to outsource assembly to others, and to rely extensively on previously manufactured components. Here, we present a simple sequence and assembly standard as part of an experiment to see how far this idea of standardized interface technology can be applied. The key notion in the design of our strategy is that the transformations performed on component parts during the assembly reactions are idempotent in a structural sense. That is, each reaction leaves the key structural elements of the component the same. The output of any such transformation, therefore, is a component which can be used as the input to any subsequent manipulation.