We hypothesize that a continuous-flow microfluidic PCR system utilizing surface-immobilized gold nanorod (GNR) arrays for plasmonic heating can achieve ultrafast thermal cycling (30 cycles in under 7 minutes), reducing amplification time from approximately 2 hours in conventional PCR to under 7 minutes. However, the primary barrier to successful amplification in this regime is not thermal but biochemical.

We propose that surface passivation with bovine serum albumin (BSA) will preserve the fidelity and efficiency of high-fidelity polymerases (such as Q5) by mitigating enzyme inhibition caused by direct interaction with the GNR surface. Specifically, we predict that BSA passivation will result in significantly lower error rates (<1.5 errors/kb) and higher amplification efficiency (>75%) compared to PEGylated or unpassivated GNR surfaces, thereby validating the integration of surface-immobilized plasmonics with continuous-flow for high-integrity synthetic biology applications.