For convenience and for PCR products that are challenging to purify with high efficiency (e.g., chemically modified DNAs), it is often desirable to quantitate synthesized DNA directly from a PCR reaction. Here we describe the use of a high-sensitivity Quant-iT™ PicoGreen® dye-based fluorescence assay to quantitate PCR-synthesized, double-stranded, low molecular weight, 5’-modified DNA probes in the presence of single-stranded primers and deoxyribonucleotides.1