Article

Modular probes for enriching and detecting complex nucleic acid sequences

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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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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.).

Author information

Author notes

    • Juexiao Sherry Wang
    •  & Yan Helen Yan

    These authors contributed equally to this work.

Affiliations

  1. Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77030, USA

    • Juexiao Sherry Wang
    • , Yan Helen Yan
    •  & David Yu Zhang
  2. Department of Bioengineering, Rice University, Houston, Texas 77030, USA

    • Juexiao Sherry Wang
    • , Yan Helen Yan
    •  & David Yu Zhang

Authors

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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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to David Yu Zhang.

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