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Edwards RL, Takach JE, McAndrew MJ, Menteer J, Lestz RM, Whitman D, Baxter-Lowe LA. Next generation multiplexing for digital PCR using a novel melt-based hairpin probe design. Front Genet 2023; 14:1272964. [PMID: 38028620 PMCID: PMC10667681 DOI: 10.3389/fgene.2023.1272964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Digital PCR (dPCR) is a powerful tool for research and diagnostic applications that require absolute quantification of target molecules or detection of rare events, but the number of nucleic acid targets that can be distinguished within an assay has limited its usefulness. For most dPCR systems, one target is detected per optical channel and the total number of targets is limited by the number of optical channels on the platform. Higher-order multiplexing has the potential to dramatically increase the usefulness of dPCR, especially in scenarios with limited sample. Other potential benefits of multiplexing include lower cost, additional information generated by more probes, and higher throughput. To address this unmet need, we developed a novel melt-based hairpin probe design to provide a robust option for multiplexing digital PCR. A prototype multiplex digital PCR (mdPCR) assay using three melt-based hairpin probes per optical channel in a 16-well microfluidic digital PCR platform accurately distinguished and quantified 12 nucleic acid targets per well. For samples with 10,000 human genome equivalents, the probe-specific ranges for limit of blank were 0.00%-0.13%, and those for analytical limit of detection were 0.00%-0.20%. Inter-laboratory reproducibility was excellent (r 2 = 0.997). Importantly, this novel melt-based hairpin probe design has potential to achieve multiplexing beyond the 12 targets/well of this prototype assay. This easy-to-use mdPCR technology with excellent performance characteristics has the potential to revolutionize the use of digital PCR in research and diagnostic settings.
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Affiliation(s)
- Rebecca L. Edwards
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | | | | | - Jondavid Menteer
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Division of Cardiology, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Rachel M. Lestz
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Division of Nephrology, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Douglas Whitman
- Luminex Corporation, A Diasorin Company, Austin, TX, United States
| | - Lee Ann Baxter-Lowe
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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Gräwe C, Hernandez-Quiles M, Jansen PWTC, Brimmers A, Vermeulen M. Determining DNA-Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy. J Proteome Res 2023; 22:2683-2693. [PMID: 37466164 PMCID: PMC10407929 DOI: 10.1021/acs.jproteome.3c00248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 07/20/2023]
Abstract
In recent years, quantitative mass spectrometry-based interaction proteomics technology has proven very useful in identifying specific DNA-protein interactions using single pull-downs from crude lysates. Here, we applied a SILAC/TMT-based higher-order multiplexing approach to develop an interaction proteomics workflow called Protein-nucleic acid Affinity and Specificity quantification by MAss spectrometry in Nuclear extracts or PASMAN. In PASMAN, DNA pull-downs using a concentration range of specific and control DNA baits are performed in SILAC-labeled nuclear extracts. MS1-based quantification to determine specific DNA-protein interactions is then combined with sequential TMT-based quantification of fragmented SILAC peptides, allowing the generation of Hill-like curves and determination of apparent binding affinities. We benchmarked PASMAN using the SP/KLF motif and further applied it to gain insights into two CGCG-containing consensus DNA motifs. These motifs are recognized by two BEN domain-containing proteins, BANP and BEND3, which we find to interact with these motifs with distinct affinities. Finally, we profiled the BEND3 proximal proteome, revealing the NuRD complex as the major BEND3 proximal protein complex in vivo. In summary, PASMAN represents, to our knowledge, the first higher-order multiplexing-based interaction proteomics method that can be used to decipher specific DNA-protein interactions and their apparent affinities in various biological and pathological contexts.
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Affiliation(s)
- Cathrin Gräwe
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Miguel Hernandez-Quiles
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
- Division
of Molecular Genetics, The Netherlands Cancer
Institute, 1066CX Amsterdam, the Netherlands
| | - Pascal W. T. C. Jansen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Annika Brimmers
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
- Division
of Molecular Genetics, The Netherlands Cancer
Institute, 1066CX Amsterdam, the Netherlands
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