Patent ID: 7892731

Claim:
A method of masking the identity of a detection sequence on a nucleic acid molecule comprising: (a) obtaining a detection nucleic acid molecule comprising a known detection sequence that hybridizes to a target nucleic acid sequence of interest in a sample during a hybridization assay; (b) designing and making a first masking nucleic acid molecule comprising a first masking sequence, wherein the first masking nucleic acid molecule is the same length as the detection nucleic acid molecule and does not hybridize to a nucleic acid sequence in the sample during the hybridization assay, and wherein the masking sequence varies from the detection sequence at at least half of its nucleic acid positions, (c) masking the identity of the detection sequence on the detection nucleic acid molecule by combining the detection nucleic acid molecule and the first masking nucleic acid molecule on the same solid support or in the same solution if the detection nucleic acid molecule and the first masking nucleic acid molecule are not immobilized on solid supports, whereby upon nucleic acid sequence analysis the presence of both the detection nucleic acid molecule and the first masking nucleic acid molecule produce a nonsensical nucleotide sequence at at least half of the nucleic acid positions in the detection sequence.