Detection and sizing of telomeric and other simple repeats by dideoxy-PRINS

The protocol is suited for the quantitative and qualitative detection of simple repeat target DNA composed of three or fewer of the four bases A, C, G, and T. A consequence of the lacking base(s) is that such DNA can be synthesized from nucleotide mixtures containing the particular bases as dideoxynucleotides. Most genomic DNA contains all four bases and can therefore not be synthesized from such a nucleotide mixture. The combined effects of probe specificity and selective DNA synthesis from the nucleotide mixture improves the signal-to-noise ratio for such targets approximately an order of magnitude, enabling the detection of exceedingly small hybridization targets (e.g., variant telomeric repeat variants embedded in, or situated next to, the main repeat), provided that they present enough template for the DNA synthesis.