PCR in a Rayleigh-Bénard Convection Cell

Abstract

Rayleigh-Benard convection is caused by buoyancy-driven instability in a confined fluid layer heated from below (1). The dimensionless Rayleigh number Ra = ga(T -T)h3/VK expresses the interplay between buoyant forces driving the instability and diffusive restoring forces acting in opposition. Here, a is the coefficient of thermal expansion of the fluid, g is the acceleration due to gravity, T, and T2 are the temperatures of the top and bottom surfaces of the cavity, respectively, h is the height of the cavity, v is the kinematic viscosity, and K is the thermal diffusivity.The inherent structure of Rayleigh-Benard convection-steady circulatory flow between surfaces maintained at two fixed temperaturesis ideally suited for performing thermally activated chemical reactions that require temperature cycling. We have developed a device that uses Rayleigh-Benard convection to perform polymerase chain reaction (PCR) amplification of DNA inside a 35-p1l cylindrical cavity. Instead of the external temperature control of conventional thermocyclers, temperature cycling is achieved as the flow field continually shuttles fluid packets vertically through the temperature zones associated with denaturation (-95?C) and annealing/extension (60? to 70?C). The steady circulatory flow field must engage the entire reaction volume yet be slow enough to allow the reaction within each temperature zone to reach completion. The parameters available to control the fluid motion are the Rayleigh number and the aspect ratio hid, where d is the diameter of the cavity. In the case of PCR, the required reaction efficiency constrains the reaction solution and the temperature difference; thus, Ra can only be changed by varying the height of the cavity, leaving geometry as the primary flow control parameter.

Thermostability of model protocell membranes

“…Another attractive possibility for an environment that would subject primitive cells to large thermal fluctuations is provided by the possibility of convection cells near or within surface hot springs or hydrothermal vents. Rayleigh-Bernard convection cells have been shown, in the laboratory, to allow for the rapid cycling of DNA molecules between moderate and high temperatures, leading to amplification by PCR (19,20). On the early earth, such convection cells might subject an adjacent fluid reservoir containing a population of replicating protocells to brief periods of high temperature, sufficient for strand separation and enhanced nutrient uptake separated by long and random interludes at lower temperatures.…”

Extreme accumulation of nucleotides in simulated hydrothermal pore systems

“…Their catalytic surfaces might generate nucleic acid multimers by thermally triggered periodic condensation (4) and unbinding reactions. In this context, we note that, in a comparable thermal convection setting, DNA was shown to replicate exponentially by using the, albeit protein-catalyzed, PCR (33,41).…”

Development of an artificial cell, from self-organization to computation and self-reproduction

“…PCR has been carried out successfully in phospholipid vesicles (97). Natural processes such as thermal convection can also drive PCR because steady circular flow occurs between hot and cold regions, and DNA is exposed to thermal cycling (98,99). DNA replication by PCR, however, cannot be used for a synthetic cell because thermal cycling at high temperature would denature the proteins making the transcription and translation machineries.…”