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Recording temporal data onto DNA with minutes resolution

View ORCID ProfileNamita J Bhan, Jonathan Strutz, Joshua Glaser, Reza Kalhor, Edward Boyden, George Church, Konrad Kording, Keith E.J. Tyo
doi: https://doi.org/10.1101/634790
Namita J Bhan
1Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
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  • ORCID record for Namita J Bhan
Jonathan Strutz
1Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
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Joshua Glaser
2Department of Neuroscience, University of Pennsylvania, Pennsylvania
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Reza Kalhor
3Department of Genetics, Harvard Medical School, Boston, MA, USA
4Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
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Edward Boyden
5Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
6McGovern Institute, MIT, Cambridge, MA, USA
7Department of Biological Engineering, Media Laboratory, Koch Institute, MIT, Cambridge, MA, USA
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George Church
3Department of Genetics, Harvard Medical School, Boston, MA, USA
4Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA
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Konrad Kording
2Department of Neuroscience, University of Pennsylvania, Pennsylvania
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Keith E.J. Tyo
1Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
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  • For correspondence: k-tyo@northwestern.edu
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Abstract

Recording biological signals can be difficult in three-dimensional matrices, such as tissue. We present a DNA polymerase-based strategy that records temporal biosignals locally onto DNA to be read out later, which could obviate the need to extract information from tissue on the fly. We use a template-independent DNA polymerase, terminal deoxynucleotidyl transferase (TdT) that probabilistically adds dNTPs to single-stranded DNA (ssDNA) substrates without a template. We show that in vitro, the dNTP-incorporation preference of TdT changes with the presence of Co2+, Ca2+, Zn2+ and temperature. Extracting the signal profile over time is possible by examining the dNTP incorporation preference along the length of synthesized ssDNA strands like a molecular ticker tape. We call this TdT-based untemplated recording of temporal local environmental signals (TURTLES). We show that we can determine the time of Co2+ addition to within two minutes over a 60-minute period. Further, TURTLES has the capability to record multiple fluctuations. We can estimate the rise and fall of an input Co2+ pulse to within three minutes. TURTLES has at least 200-fold better temporal resolution than all previous DNA-based recording techniques.

Footnotes

  • Figure 1 and 3 revised. Supplemental files updated.

  • https://www.ncbi.nlm.nih.gov/sra/PRJNA542184

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 05, 2019.
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Recording temporal data onto DNA with minutes resolution
Namita J Bhan, Jonathan Strutz, Joshua Glaser, Reza Kalhor, Edward Boyden, George Church, Konrad Kording, Keith E.J. Tyo
bioRxiv 634790; doi: https://doi.org/10.1101/634790
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Recording temporal data onto DNA with minutes resolution
Namita J Bhan, Jonathan Strutz, Joshua Glaser, Reza Kalhor, Edward Boyden, George Church, Konrad Kording, Keith E.J. Tyo
bioRxiv 634790; doi: https://doi.org/10.1101/634790

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