Abstract: The invention provides a set of highly orthogonal six-code universal sequences for use in bDNA singleplex and multiplex nucleic acid hybridization assays. The six-code orthogonal sequences do not cross-hybridize and thus, minimize or eliminate the 3-mer cross-hybridization inherent in the second and third generation bDNA assays. The highly orthogonal universal sequences may be used in singleplex or multiplex bDNA assays quantitatively and qualitatively to determine mRNA levels in a sample; to screen for and genotype targets, such as viruses, that are present in low volumes in a sample; to screen for and genotype SNPs; and to measure changes in the amount of a gene in a sample such as when gene amplifications or deletions occur. The highly orthogonal universal sequences may also be used as universal capture probes to selectively bind assay components in a way that facilitates their further analysis.

Abstract: The invention provides a set of highly orthogonal six-code universal sequences for use in bDNA singleplex and multiplex nucleic acid hybridization assays. The six-code orthogonal sequences do not cross-hybridize and thus, minimize or eliminate the 3-mer cross-hybridization inherent in the second and third generation bDNA assays. The highly orthogonal universal sequences may be used in singleplex or multiplex bDNA assays quantitatively and qualitatively to determine mRNA levels in a sample; to screen for and genotype targets, such as viruses, that are present in low volumes in a sample; to screen for and genotype SNPs; and to measure changes in the amount of a gene in a sample such as when gene amplifications or deletions occur. The highly orthogonal universal sequences may also be used as universal capture probes to selectively bind assay components in a way that facilitates their further analysis.