TECHNICAL NOTE: Theoretical considerations for counting nucleic acid molecules in microdevices

Abstract

We describe the theoretical design of a microchip for the amplification, detection and counting of individual nucleic acid molecules in an ensemble of non-specific molecules. The device permits access to individual molecules through the transformation of a three-dimensional amplification reaction volume into a two-dimensional area or a one-dimensional line. The nucleic acid molecules in the amplification solution can be spatially separated along a one-dimensional line or across a two-dimensional area. The arrangement of the molecules is governed by the geometry of the microreactor in a manner analogous to the concept of ‘limiting dilution’ in a volume of fluid. When PCR amplification is allowed to proceed, the target sequences on individual molecules are amplified and diffuse outward. At the end of the amplification process, the zones of concentrated DNA surrounding the individual molecules can be detected as spatially resolved signals through the use of DNA binding dyes or fluorescence resonance energy transfer (FRET) probes. These amplification peaks would serve to establish a count of the number of target molecules in a sample with a much higher accuracy than that of traditional quantification using real-time PCR. The theoretical accuracy of this technique is only limited by the Poisson statistics of sampling.