Evaluation of alternative safe nucleic acid staining dyes for DNA quantification with a qubit Fluorometer

Some of the common dyes used for DNA visualization are known for their potential to cause teratogenic and mutagenic effects. Although safer alternatives are widely available, cost-effective, eco-friendly DNA quantification techniques remain underutilized in some biolabs. This study evaluated nine safe staining dyes for DNA quantification using the common Qubit fluorometer to reduce costs in an environmentally friendly DNA assay. We investigated the effects of dye concentration on sensitivity and the dynamic range for various amounts of DNA. Two quantification assays were developed that were high-sensitivity or broad-range for DNA quantification. With the optimized dyes and protocols, the developed methods achieved sensitivity levels comparable to the Qubit dsDNA BR (Broad Range, 2–1000 ng) Assay Kit and the Qubit dsDNA HS (High Sensitivity, 0.2–100 ng) Assay Kit at reduced cost. The results presented here provide an alternative, low-cost fluorometric assay for DNA quantification using available fluorometers. With a cost per sample of less than a cent, this approach is highly advantageous for resource-limited settings and low-budget laboratories. • Evaluated nine eco-friendly nucleic acid dyes as non-mutagenic substitutes for hazardous DNA stains. • Established broad-range (2–1000 ng) and high-sensitivity (0.2–100 ng) detection methods. • Achieved sensitivity comparable to Qubit dsDNA BR/HS assay kits. • Reduced cost per test to <US$0.01, ideal for resource-constrained laboratories.