Hypothesis Functionalized nanoparticles (NPs) offer diverse biomedical applications, but their synthesis is complex, costly, and labour-intensive, particularly when providing for additional functionalization requirements which are a key feature of biomedical applications. Pulsed laser ablation in liquids (PLAL) has previously allowed for the synthesis of metal and metal oxide nanoparticles using metal targets, which can then be surface functionalized during synthesis by the surrounding liquid species. Therefore, it should be possible to achieve biomolecule functionalization by ablating in biomolecular solutions. We explore a novel controlled recirculation PLAL scheme which should increase functionalization and productivity of functionalized nanoparticles. Experiments Traditional PLAL was performed by ablating a silicon target in a DNA solution. We have extended beyond traditional approaches by ablating the silicon target under novel flow conditions in a controlled recirculating loop of DNA solution. Findings Ablating in a DNA solution allows for high efficiency binding of DNA to silicon nanoparticles (SiNPs) in a single step process. By using SiNPs we are significantly reducing the overall cost of the process, when compared with the more traditional use of gold or silver; as well as, using a biocompatible material with an affinity for protein and nucleic acid binding. Reducing the laser shielding effects of particles and debris by removing them from the ablation site produces higher volumes and concentrations of functionalized colloid. Recirculating this liquid over the target has resulted in a 50% relative increase in binding efficiency, compared with static and single-pass flow conditions processing, achieving an average maximum binding efficiency of 78% in flow compared to 52% under static conditions. Furthermore, by reducing the initial DNA concentration, we were able to achieve 100% binding efficiency, which we believe to be the highest reported in literature to date.