Microscale Chaotic Advection Enables Robust Convective DNA Replication

Abstract

The ability of chaotic advection under microscale confinement to direct chemical processes along accelerated kinetic pathways has been recognized for some time. However, practical applications have been slow to emerge because optimal results are often counterintuitively achieved in flows that appear to possess undesirably high disorder. Here we present a 3D time-resolved analysis of polymerase chain reaction (PCR)-mediated DNA replication across a broad ensemble of geometric states. The resulting parametric map reveals an unexpectedly wide operating regime where reaction rates remain constant over 2 orders of magnitude of the Rayleigh number, encompassing virtually any realistic PCR condition (temperature, volume, gravitational alignment), a level of robustness previously thought unattainable in the convective format.

Synchronized chaotic targeting and acceleration of surface chemistry in prebiotic hydrothermal microenvironments

“…Recent studies have explored the combined action of laminar (2D) thermal convection and thermophoresis as a physical enrichment mechanism, albeit in hairline-sized fissures (diameter d ≤ 100 μm) under steep thermal gradients (100-1,000°C/mm) (12)(13)(14)(15). In contrast, surprisingly complex 3D flows characterized by chaotic thermal convection (16,17) emerge over a broader pore size range [millimeters to centimeters, consistent with porosities in young active carbonate chimneys (18)] and under moderate temperature gradients (0.1-10°C/mm) (19,20) (Fig. 1A and SI Appendix).…”

Convective PCR Thermocycling with Smartphone-Based Detection: A Versatile Platform for Rapid, Inexpensive, and Robust Mobile Diagnostics

“…The model yields predictions of the DNA replication rate in terms of a characteristic doubling time (the concept of a "cycle time" in convective PCR differs from conventional thermocycling because all reagents do not follow identical flow paths through the temperature gradient). The efficiency of convective PCR in different reactor geometries can then be quantified in terms of a generation rate (i.e., number of doubling events per hour) [9]. This analysis leads to counterintuitive design rules for selection of reactor geometries optimally suited for PCR.…”

“…and shape (h/d ) of the cylinder yield flows displaying periodic, quasi-periodic, and chaotic trajectories. (b) A strong transverse "crossflow" component in small aspect ratio cylinders gives rise to more disordered flow trajectories as compared with high h/d [9]. (c) Microscale chaotic advection enables rapid DNA replication to be robustly achieved.…”

“…Greatly improved performance is therefore achievable because the time and energy required to heat and cool additional inactive instrument components is eliminated. Implementations of this simple yet effective concept have been reported by establishing vertical temperature gradients (i.e., RayleighBénard convection) [6,[9][10][11] (Fig. 3.1b), horizontal temperature gradients [7,12,13] (Fig.…”

“…When coupled with fluorescence detection using a standard smartphone camera, convective PCR lays a foundation to deliver a versatile DNA analysis platform that is ideally suited for portable for point-of-care applications. Rayleigh-Bénard systems execute thermocycling in a cylindrical reactor geometry by imposing a vertical temperature gradient between the top and bottom surfaces [6,9]. (c) Focused infrared heating generates a horizontal thermal gradient circulating reagents radially outward from the hot center region to the cold periphery [7].…”