A smart polymer for sequence-selective binding, pulldown, and release of DNA targets

被引：0
作者：
Elisha Krieg
Krishna Gupta
Andreas Dahl
Mathias Lesche
Susanne Boye
Albena Lederer
William M. Shih
机构：
[1] Harvard Medical School,Department of Biological Chemistry and Molecular Pharmacology
[2] Wyss Institute for Biologically Inspired Engineering at Harvard University,Department of Cancer Biology
[3] Dana-Farber Cancer Institute,School of Science
[4] Leibniz-Institut für Polymerforschung Dresden e.V.,Biotechnology Center (BIOTEC)
[5] Technische Universität Dresden,DRESDEN
[6] Technische Universität Dresden,concept Genome Center, Center for Molecular and Cellular Bioengineering
[7] Technische Universität Dresden,undefined
来源：
Communications Biology | / 3卷
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摘要：
Selective isolation of DNA is crucial for applications in biology, bionanotechnology, clinical diagnostics and forensics. We herein report a smart methanol-responsive polymer (MeRPy) that can be programmed to bind and separate single- as well as double-stranded DNA targets. Captured targets are quickly isolated and released back into solution by denaturation (sequence-agnostic) or toehold-mediated strand displacement (sequence-selective). The latter mode allows 99.8% efficient removal of unwanted sequences and 79% recovery of highly pure target sequences. We applied MeRPy for the depletion of insulin, glucagon, and transthyretin cDNA from clinical next-generation sequencing (NGS) libraries. This step improved the data quality for low-abundance transcripts in expression profiles of pancreatic tissues. Its low cost, scalability, high stability and ease of use make MeRPy suitable for diverse applications in research and clinical laboratories, including enhancement of NGS libraries, extraction of DNA from biological samples, preparative-scale DNA isolations, and sorting of DNA-labeled non-nucleic acid targets.
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共 63 条
[1]  
Praetorius F(2017)Biotechnological mass production of DNA origami Nature 552 84-87
[2]  
Krieg E(2018)Selective nascent polymer catch-and-release enables scalable isolation of multi-kilobase single-stranded DNA Angew. Chem. Int. Ed. 57 714-718
[3]  
Shih WM(2018)Simultaneous and stoichiometric purification of hundreds of oligonucleotides Nat. Commun. 9 835-842
[4]  
Pinto A(2012)Comparison of different methods for generation of single-stranded DNA for SELEX processes Anal. Bioanal. Chem. 404 1943-1947
[5]  
Chen SX(1991)Construction of a uniform-abundance (normalized) cDNA library Proc. Natl Acad. Sci. USA 88 2701-2721
[6]  
Zhang DY(2018)Capturing the “ome”: the expanding molecular toolbox for RNA and DNA library construction Nucleic Acids Res 46 623-629
[7]  
Svobodová M(2013)Comparative analysis of RNA sequencing methods for degraded or low-input samples Nat. Methods 10 e42882-e140
[8]  
Pinto A(2012)Selective depletion of rRNA enables whole transcriptome profiling of archival fixed tissue PLoS ONE 7 e140-503
[9]  
Nadal P(2011)Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq Nucleic Acids Res. 39 495-1464
[10]  
Sullivan CKO(1990)Rapid and simple method for purification of nucleic acids J. Clin. Microbiol. 28 1458-7138
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