Modular probes for enriching and detecting complex nucleic acid sequences

Complex DNA sequences are difficult to detect and profile, but are important contributors to human health and disease. Existing hybridization probes lack the capability to selectively bind and enrich hypervariable, long or repetitive sequences. Here, we present a generalized strategy for constructing modular hybridization probes (M-Probes) that overcomes these challenges. We demonstrate that M-Probes can tolerate sequence variations of up to 7 nt at prescribed positions while maintaining single nucleotide sensitivity at other positions. M-Probes are also shown to be capable of sequence-selectively binding a continuous DNA sequence of more than 500 nt. Furthermore, we show that M-Probes can detect genes with triplet repeats exceeding a programmed threshold. As a demonstration of this technology, we have developed a hybrid capture method to determine the exact triplet repeat expansion number in the Huntington's gene of genomic DNA using quantitative PCR. Modular hybridization probes (M-Probes) have been developed that enable sequence-selective binding of complex nucleic acid targets. The M-probes can target sequences that: are hypervariable at prescribed loci, are long continuous sequences of over 500 nucleotides, or contain repetitive sequences. A hybrid-capture assay using the M-probes was developed that was capable of determining the exact triplet repeat expansion number in the Huntington's gene from genomic DNA.