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Modular probes for enriching and detecting complex nucleic acid sequences

Abstract

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.

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Figure 1: M-Probe design and demonstration.
Figure 2: Sequence variation tolerance.
Figure 3: Combinatorial construction of M-Probes for VDJ recombination detection.
Figure 4: M-Probe detection of single nucleotide variants within 560 nt targeting regions.
Figure 5: Profiling triplet repeat number using M-Probes.

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Acknowledgements

The authors thank A. Pinto for discussions. This work was funded by the Cancer Prevention Research Institute of Texas (grant RP140132 to D.Y.Z.) and by the National Human Genome Research Institute (grant R01HG008752 to D.Y.Z.).

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Contributions

J.S.W., Y.H.Y. and D.Y.Z. conceived the project. J.S.W. and Y.H.Y. performed experiments and data analysis. J.S.W., Y.H.Y. and D.Y.Z. wrote the manuscript. J.S.W. and Y.H.Y. contributed equally to this work.

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Correspondence to David Yu Zhang.

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The authors declare no competing financial interests.

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Wang, J., Yan, Y. & Zhang, D. Modular probes for enriching and detecting complex nucleic acid sequences. Nature Chem 9, 1222–1228 (2017). https://doi.org/10.1038/nchem.2820

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