Patent ID: 7202038

Claim:
A method for determining the number of tandem repeat units in a target oligonucleotide, comprising: selecting at least two probes, under the following selection criteria: (i) each probe has repeated sequence elements (“probe repeats”), each probe repeat being complementary to the target oligonucleotide's repeat unit (“target repeat”), but each probe having fewer probe repeats than the total number of target repeats present in the target oligonucleotide; and (ii) each probe, upon hybridizing to the target oligonucleotide under conditions permitting the formation of a duplex of at least one repeat unit, is labeled with a first color in configurations in which the probe's 3′ end is aligned in juxtaposition to a target repeat nucleotide which is not the 5′ terminal target repeat nucleotide, and labeled with a second, different color in the configuration in which the probe's 3′ end is aligned in juxtaposition to the 5′ terminal target repeat nucleotide; hybridizing said at least two probes to one target oligonucleotide, and determining, for each of said at least two probes the intensities of the respective signals of the first and second colors; analyzing the intensities of the signals resulting from the hybridization step where said intensities reflect the probability of different duplex configurations for probes and targets having respectively particular probe repeats and target repeats; and determining the number of tandem repeats in the target oligonucleotide by regression analysis.