Deoxynucleotides can replace dideoxynucleotides in minisequencing by arrayed primer extension

Abstract

Scientific literature describing arrayed primer extension and other array-based minisequencing technologies consistently cite the requirement for four fluorescent dideoxynucleotides (with concomitant absence/inactivation of deoxynucleotides) to ensure single-base extension and thus sequence-specific intensity data that can be interpreted as a base call or genotype. We present compelling evidence thatfluorescent deoxynucleotides can reliably be used in microarray minisequencing experiments, generating fluorescent sequence extension intensity profiles that are homologous to the single-base extensions obtained with terminator dideoxynucleotides. Due to the almost 10-fold higher costs (and limited fluorophore choice) of many commercially available fluorescent dideoxynucleotides, compared to fluorescent deoxynucleotides, as well as other potentially constraining intellectual property and licensing issues, this hitherto dismissed microarray chemistry represents an important reevaluation in the field of array-based genotyping and related enzymology.