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Download Hi-Res ImageDownload to MS-PowerPointCite This:Anal. Chem. 2017, 89, 1, 728-735
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Adaptive PCR Based on Hybridization Sensing of Mirror-Image l-DNA

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†Department of Biomedical Engineering, ‡Department of Physics and Astronomy, and §Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
*Address: Biomedical Engineering, Vanderbilt University, VU Station B #351631, 2301 Vanderbilt Place, Nashville, TN 37235. Tel: (615) 322-6622. Fax: (615) 343-7919. E-mail: [email protected] (F.R.H.).
*Address: Biomedical Engineering, Vanderbilt University, VU Station B #351631, 2301 Vanderbilt Place, Nashville, TN 37235. Fax: (615) 343-7919. E-mail: [email protected] (N.M.A.).
Cite this: Anal. Chem. 2017, 89, 1, 728–735
Publication Date (Web):December 7, 2016
https://doi.org/10.1021/acs.analchem.6b03291
Copyright © 2016 American Chemical Society
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Abstract

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Polymerase chain reaction (PCR) is dependent on two key hybridization events during each cycle of amplification, primer annealing and product melting. To ensure that these hybridization events occur, current PCR approaches rely on temperature set points and reaction contents that are optimized and maintained using rigid thermal cycling programs and stringent sample preparation procedures. This report describes a fundamentally simpler and more robust PCR design that dynamically controls thermal cycling by more directly monitoring the two key hybridization events during the reaction. This is achieved by optically sensing the annealing and melting of mirror-image l-DNA analogs of the reaction’s primers and targets. Because the properties of l-DNA enantiomers parallel those of natural d-DNAs, the l-DNA reagents indicate the cycling conditions required for effective primer annealing and product melting during each cycle without interfering with the reaction. This hybridization-sensing approach adapts in real time to variations in reaction contents and conditions that impact primer annealing and product melting and eliminates the requirement for thermal calibrations and cycling programs. Adaptive PCR is demonstrated to amplify DNA targets with high efficiency and specificity under both controlled conditions and conditions that are known to cause traditional PCR to fail. The advantages of this approach promise to make PCR-based nucleic acid analysis simpler, more robust, and more accessible outside of well-controlled laboratory settings.

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The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.analchem.6b03291.

  • A list of the oligonucleotides; additional details on the thermal cycling control parameters; raw data for the Adaptive PCR experiments (PDF)

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Cited By

This article is cited by 11 publications.

  1. Min Li, Fangfei Yin, Lu Song, Xiuhai Mao, Fan Li, Chunhai Fan, Xiaolei Zuo, Qiang Xia. Nucleic Acid Tests for Clinical Translation. Chemical Reviews 2021, 121 (17) , 10469-10558. https://doi.org/10.1021/acs.chemrev.1c00241
  2. Ziqi Xu, Linli Liao, Yaqin Chai, Haijun Wang, and Ruo Yuan . Ultrasensitive Electrochemiluminescence Biosensor for MicroRNA Detection by 3D DNA Walking Machine Based Target Conversion and Distance-Controllable Signal Quenching and Enhancing. Analytical Chemistry 2017, 89 (16) , 8282-8287. https://doi.org/10.1021/acs.analchem.7b01409
  3. Fabian Rohden, Jörg D. Hoheisel, Hans-Joachim Wieden. Through the looking glass: milestones on the road towards mirroring life. Trends in Biochemical Sciences 2021, 46 (11) , 931-943. https://doi.org/10.1016/j.tibs.2021.06.006
  4. Zackary A. Zimmers, Nicholas M. Adams, Frederick R. Haselton. Addition of mirror-image L-DNA elements to DNA amplification circuits to distinguish leakage from target signal. Biosensors and Bioelectronics 2021, 188 , 113354. https://doi.org/10.1016/j.bios.2021.113354
  5. Yongxi Zhao, Xiaolei Zuo, Qian Li, Feng Chen, Yan-Ru Chen, Jinqi Deng, Da Han, Changlong Hao, Fujian Huang, Yanyi Huang, Guoliang Ke, Hua Kuang, Fan Li, Jiang Li, Min Li, Na Li, Zhenyu Lin, Dingbin Liu, Juewen Liu, Libing Liu, Xiaoguo Liu, Chunhua Lu, Fang Luo, Xiuhai Mao, Jiashu Sun, Bo Tang, Fei Wang, Jianbin Wang, Lihua Wang, Shu Wang, Lingling Wu, Zai-Sheng Wu, Fan Xia, Chuanlai Xu, Yang Yang, Bi-Feng Yuan, Quan Yuan, Chao Zhang, Zhi Zhu, Chaoyong Yang, Xiao-Bing Zhang, Huanghao Yang, Weihong Tan, Chunhai Fan. Nucleic Acids Analysis. Science China Chemistry 2021, 64 (2) , 171-203. https://doi.org/10.1007/s11426-020-9864-7
  6. Erika Schaudy, Mark M. Somoza, Jory Lietard. l ‐DNA Duplex Formation as a Bioorthogonal Information Channel in Nucleic Acid‐Based Surface Patterning. Chemistry – A European Journal 2020, 26 (63) , 14310-14314. https://doi.org/10.1002/chem.202001871
  7. Erin M. Euliano, Austin N. Hardcastle, Christia M. Victoriano, William E. Gabella, Frederick R. Haselton, Nicholas M. Adams. Multiplexed Adaptive RT-PCR Based on L-DNA Hybridization Monitoring for the Detection of Zika, Dengue, and Chikungunya RNA. Scientific Reports 2019, 9 (1) https://doi.org/10.1038/s41598-019-47862-6
  8. Mindy Leelawong, Nicholas M. Adams, William E. Gabella, David W. Wright, Frederick R. Haselton. Detection of Single-Nucleotide Polymorphism Markers of Antimalarial Drug Resistance Directly from Whole Blood. The Journal of Molecular Diagnostics 2019, 21 (4) , 623-631. https://doi.org/10.1016/j.jmoldx.2019.02.004
  9. Brian E. Young, Nandini Kundu, Jonathan T. Sczepanski. Mirror‐Image Oligonucleotides: History and Emerging Applications. Chemistry – A European Journal 2019, 25 (34) , 7981-7990. https://doi.org/10.1002/chem.201900149
  10. Zackary A. Zimmers, Nicholas M. Adams, William E. Gabella, Frederick R. Haselton. Fluorophore-quencher interactions effect on hybridization characteristics of complementary oligonucleotides. Analytical Methods 2019, 11 (22) , 2862-2867. https://doi.org/10.1039/C9AY00584F
  11. Marjorie A. Hoy. DNA Amplification by the Polymerase Chain Reaction: Providing a Revolutionary Method for All Biologists. 2019,,, 263-314. https://doi.org/10.1016/B978-0-12-815230-0.00007-8

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