DNA compaction enhances the sensitivity of fluorescence-based nucleic acid assays: a game changer in point of care sensors?

• Published in: Analyst (London) 2023-05, Vol.148 (1), p.2295-237
• Main Authors: Sudarsan, Sujesh, Prabhu, Anusha, Prasad, Dinesh, Mani, Naresh Kumar
• Format: Article
• Language: English
• Subjects: Acids; Amplification; Assaying; Cetrimonium; DNA - chemistry; DNA - genetics; Emission; Fluorescence; Genetic testing; Nucleic Acids; Point-of-Care Systems; Sensitivity enhancement
• ISSN: 0003-2654; 1364-5528
• DOI: 10.1039/d3an00102d

Fluorescence-based nucleic acid assays frequently exhibit a feeble signal at low analyte concentrations, necessitating complex, expensive methods such as the development of sequence-specific oligo tags, molecular beacons, and chemical modifications to maintain high detection sensitivity. Hence, there is growing interest in accomplishing fluorescence enhancement in nucleic acid assays using robust and cost-effective strategies. The study exploits the use of two compaction agents, PEG 8000 and CTAB, to compact the ITS-2 amplicon of the fungus Candida albicans and evaluates the effect of both of these agents on the fluorescence intensity of SYTO-9 labelled nucleic acids. Conventional fluorometric measurements showed that both CTAB and PEG 8000 enhanced the emission intensity by ∼1.2- and 2-fold, respectively. Furthermore, we leveraged paper-based spot tests and distance-based assays to validate the effect of DNA compaction for enhancing sensitivity in the point-of-care context. The spot assay performed on paper with compacted samples showed an increase in the emission intensity of SYTO-9 and this was manifested by an elevated G channel intensity in the order of PEG 8000 compacted > CTAB compacted > amplified. Moreover, in the distance-based assay, the PEG 8000 compacted sample was found to migrate farther compared to CTAB compacted and amplified DNA samples at amplicon concentrations, 15 μg ml −1 and 39.65 μg ml −1 . The limit of detection (LOD) for PEG 8000 and CTAB compacted samples on both paper-spot and distance-based assays were found to be 0.4 μg ml −1 and 0.5 μg ml −1 , respectively. Hence our work provides an overview of employing DNA compaction as an approach for enhancing the sensitivity of fluorescence-based point-of-care nucleic acid assays without the need for cumbersome sensitivity enhancement methods. Enhancement in the fluorescence signal through compaction by the cationic surfactant CTAB and neutral polymer PEG 8000 in bulk and paper-based assays.