Nanoliter array advances: miniaturized, high-speed PCR sensing & control

We have previously reported on our laboratory-on-a-chip nanoarray system based on nanoliter-capacity wells etched in silicon (Young, I.T. et al., J. Microscopy, vol.212, no.3, p.254-63, 2003; Dietrich, H.R.C. et al., Analytical Chemistry, vol.76, no.14, p.4112-17, 2004). We now describe how temperature sensing and control embedded in the floor of the nano-wells make it possible for us to cycle each well independently through the temperatures 92°C, 55°C, and 75°C. This individual temperature cycling on nanoliter wells means that the nano-array architecture is suitable for PCR applications and that the total time needed for 30 cycles of PCR amplification could be less than five minutes. Further, we describe how, by embedding photodiodes in the floor of the wells, we can track the fluorescence associated with the melting and annealing of DNA when labeled with a suitable nucleic acid stain. Measurements performed with the fluorophores Rhodamine B and SYBR Green I have demonstrated our ability to control the temperature, measure the fluorescence, and monitor the denaturation and renaturation of DNA.