T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures

Schaffter, Samuel W.; Green, Leopold N.; Schneider, Joanna; Subramanian, Hari K. K.; Schulman, Rebecca; Franco, Elisa

doi:10.1093/nar/gky283

Title: T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures

Journal Article · Mon Apr 30 00:00:00 EDT 2018 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gky283· OSTI ID:1435363

Schaffter, Samuel W. ^[1]; Green, Leopold N. ^[2]; Schneider, Joanna ^[1]; Subramanian, Hari K. K. ^[2]; Schulman, Rebecca ^[3];

^[2]

Department of Chemical and Biomolecular Engineering – Johns Hopkins University
Department of Mechanical Engineering – University of California - Riverside
Department of Chemical and Biomolecular Engineering – Johns Hopkins University, Department of Computer Science – Johns Hopkins University

The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes. A better understanding of these undesired interactions will enable the construction of robust DNA nanostructure-enzyme hybrid systems. Here, we investigate the undesired disassembly of DNA nanotubes in the presence of viral RNA polymerases (RNAPs) under conditions used for in vitro transcription. We show that nanotubes and individual nanotube monomers (tiles) are non-specifically transcribed by T7 RNAP, and that RNA transcripts produced during non-specific transcription disassemble the nanotubes. Disassembly requires a single-stranded overhang on the nanotube tiles where transcripts can bind and initiate disassembly through strand displacement, suggesting that single-stranded domains on other DNA nanostructures could cause unexpected interactions in the presence of viral RNA polymerases.

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Research Organization:: Johns Hopkins Univ., Baltimore, MD (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0010426

OSTI ID:: 1435363

Alternate ID(s):: OSTI ID: 1502443

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 46 Journal Issue: 10; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 12 works

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