Methods of Synthesis and Characterization of Conductive DNA Nanowires Based on Metal Ion-Mediated Base Pairing for Single-Molecule Electronics

Authors

  • Simon Vecchioni Department of Biomedical Engineering at Columbia University, New York, NY 10027, USA
  • Mark C. Capece Department of Chemistry, Stanford University, Stanford, CA 94305, USA
  • Emily Toomey Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
  • Lynn Rothschild NASA Ames Research Center, Space Science and Astrobiology Division, Moffett Field, CA 94035, USA
  • Shalom J. Wind Department of Applied Physics and Applied Mathematics at Columbia University, New York, NY 10027, USA

DOI:

https://doi.org/10.13052/jsame2245-4551.6.004

Keywords:

Molecular electronics, DNA nanowire, nanomaterials, cytosine mismatch, methods.

Abstract

Advances in the field of molecular electronics have made possible the direct
measurement of charge transport across single molecules. In particular, work
on DNA oligomers has demonstrated that this weakly-conducting biomolecule
can be functionalized through metal-mediated nucleobase pairing in order to
significantly increase electron mobility across the molecule. The introduction
of interacting stacks of single metal ions inside the DNA helix is an attractive
platform for assay and optimization; for this reason we present a protocol
for the production and processing of nanowires with a metal base pair for
single-molecule applications. In particular, we describe the construction of DNA duplex wires with a cytosine-Ag+-cytosine base pair (dC:Ag+:dC).
A thorough investigation of buffer components suggests the use of divalent
magnesium counterions to stabilize highly mismatched oligonucleotides in
solution. We further analyse cleaning and processing of thin gold films for
batch-fabrication of conductive imaging substrates for use in conductive
scanning probe assays of single-molecule conductivity. With a clear path to
electrical assays, we suggest that the C:Ag+:C orthogonal nucleotide pair and
other similar chemistries may provide a foundation for molecular electronic
components in integrated devices

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Author Biographies

Simon Vecchioni, Department of Biomedical Engineering at Columbia University, New York, NY 10027, USA

Simon Vecchioni received his B.S. in Biology from Brown University in 2013.
That same year he joined the laboratory of Lynn Rothschild at NASA Ames
Research Center to investigate the biosynthesis of electronic materials. After
moving to Columbia University in New York to pursue a Ph.D. in Biomedical
Engineering, he joined the group of Shalom Wind to focus on nanoscale self-
assembly and DNA nanotechnology. Since 2014, he has been supported by a
NASA Space Technology Research Fellowship and has continued to pursue
work on DNA nanoelectronics with the support of Wind and Rothschild.

Mark C. Capece, Department of Chemistry, Stanford University, Stanford, CA 94305, USA

Mark C. Capece earned a B.S. in Chemistry and Physics from the University
of Louisville in 2011, where his honors thesis demonstrated the practical
lumped-element design of a magic angle spinning triple-resonance solid-
state NMR probe. He then received a Ph.D. in Chemistry from Stanford
University in 2018. His graduate work used solution NMR and single-
molecule fluorescence to model functional mRNA structures that regulate
translation. Capece’s research interests continue to focus on NMR technology
development and biological applications.

Emily Toomey, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

Emily Toomey received her Sc.B. in Electrical Engineering from Brown
University in 2015, where she studied the electrical characterization of DNA
in the laboratory of Prof. Jimmy Xu. She had previously interned at the
NASA Ames Research Center under Dr. Lynn Rothschild in 2013, where
she explored the modification of DNA structures by metal ion intercalation
in collaboration with Simon Vecchioni. Emily has been pursuing a Ph.D.
in Electrical Engineering from the Massachusetts Institute of Technology
since 2015. Her current work under Prof. Karl K. Berggren focuses on
superconducting nanoelectronics and nanofabrication.

Lynn Rothschild, NASA Ames Research Center, Space Science and Astrobiology Division, Moffett Field, CA 94035, USA

Lynn Rothschild is passionate about the origin and evolution of life on Earth
or elsewhere, while at the same time pioneering the use of synthetic biology
to enable space exploration. She is a senior scientist NASA’s Ames Research
Center, as well as Adjunct Professor at Brown University. Since 2011 she
has been the faculty advisor of the award-winning Stanford-Brown iGEM
team, which has pioneered the use of synthetic biology to accomplish NASA’s
missions, focusing on the human settlement of Mars, astrobiology and such
innovative projects as BioWires, making a biodegradable UAS (drone) and
using fungal mycelia as a building material. She is a fellow of the Linnean
Society of London, The California Academy of Sciences and the Explorer’s
Club

Shalom J. Wind, Department of Applied Physics and Applied Mathematics at Columbia University, New York, NY 10027, USA

Shalom J. Wind received his Ph.D. in Physics from Yale University in
1987. Following his doctoral studies, he worked at IBM’s Thomas J. Watson
Research Center, focusing primarily on nanoelectronic devices. He moved to
the Department of Applied Physics and Applied Mathematics at Columbia
University in 2003. Wind’s present research focuses on molecular-scale
fabrication and the interface between biological and technological materials
and systems.

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Published

2023-03-18

How to Cite

Vecchioni, S., Capece, M. C., Toomey, E., Rothschild, L., & Wind, S. J. (2023). Methods of Synthesis and Characterization of Conductive DNA Nanowires Based on Metal Ion-Mediated Base Pairing for Single-Molecule Electronics. Journal of Self Assembly and Molecular Electronics, 6(1), 61–90. https://doi.org/10.13052/jsame2245-4551.6.004

Issue

2018: Vol 6 Iss1 2018

Section

Articles