Gold Ion Beam Milled Gold Zero-Mode Waveguides
Abstract
Zero-mode waveguides (ZMWs) are widely used in single molecule fluorescence microscopy for their enhancement of emitted light and the ability to study samples at physiological concentrations. ZMWs are typically produced using photo or electron beam lithography. We report a new method of ZMW production using focused ion beam (FIB) milling with gold ions. We demonstrate that ion-milled gold ZMWs with 200 nm apertures exhibit similar plasmon-enhanced fluorescence seen with ZMWs fabricated with traditional techniques such as electron beam lithography.
- Authors:
-
[1];
[2];
[2];
[2];
- Berea College, KY (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Univ. of Kentucky, Lexington, KY (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); Appalachian College Association Faculty Fellowship; National Institutes of Health (NIH)
- OSTI Identifier:
- 1870211
- Grant/Contract Number:
- AC05-00OR22725; R01GM138837
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nanomaterials
- Additional Journal Information:
- Journal Volume: 12; Journal Issue: 10; Journal ID: ISSN 2079-4991
- Publisher:
- MDPI
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 36 MATERIALS SCIENCE; single molecule spectroscopy; nanostructures; single molecule; sub-wavelength apertures; zero-mode waveguides
Citation Formats
Messina, Troy C., Srijanto, Bernadeta R., Collier, Charles Patrick, Kravchenko, Ivan I., and Richards, Christopher I. Gold Ion Beam Milled Gold Zero-Mode Waveguides. United States: N. p., 2022.
Web. doi:10.3390/nano12101755.
Messina, Troy C., Srijanto, Bernadeta R., Collier, Charles Patrick, Kravchenko, Ivan I., & Richards, Christopher I. Gold Ion Beam Milled Gold Zero-Mode Waveguides. United States. https://doi.org/10.3390/nano12101755
Messina, Troy C., Srijanto, Bernadeta R., Collier, Charles Patrick, Kravchenko, Ivan I., and Richards, Christopher I. Sat .
"Gold Ion Beam Milled Gold Zero-Mode Waveguides". United States. https://doi.org/10.3390/nano12101755. https://www.osti.gov/servlets/purl/1870211.
@article{osti_1870211,
title = {Gold Ion Beam Milled Gold Zero-Mode Waveguides},
author = {Messina, Troy C. and Srijanto, Bernadeta R. and Collier, Charles Patrick and Kravchenko, Ivan I. and Richards, Christopher I.},
abstractNote = {Zero-mode waveguides (ZMWs) are widely used in single molecule fluorescence microscopy for their enhancement of emitted light and the ability to study samples at physiological concentrations. ZMWs are typically produced using photo or electron beam lithography. We report a new method of ZMW production using focused ion beam (FIB) milling with gold ions. We demonstrate that ion-milled gold ZMWs with 200 nm apertures exhibit similar plasmon-enhanced fluorescence seen with ZMWs fabricated with traditional techniques such as electron beam lithography.},
doi = {10.3390/nano12101755},
journal = {Nanomaterials},
number = 10,
volume = 12,
place = {United States},
year = {Sat May 21 00:00:00 EDT 2022},
month = {Sat May 21 00:00:00 EDT 2022}
}
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Works referenced in this record:
Single-molecule approaches to characterizing kinetics of biomolecular interactions
journal, February 2011
- van Oijen, Antoine M.
- Current Opinion in Biotechnology, Vol. 22, Issue 1
Extending Single-Molecule Förster Resonance Energy Transfer (FRET) Range beyond 10 Nanometers in Zero-Mode Waveguides
journal, July 2019
- Baibakov, Mikhail; Patra, Satyajit; Claude, Jean-Benoît
- ACS Nano, Vol. 13, Issue 7
Nanoaperture Fluorescence Enhancement in the Ultraviolet
journal, March 2010
- Mahdavi, Farhad; Blair, Steve
- Plasmonics, Vol. 5, Issue 2
Markov processes in single molecule fluorescence
journal, December 2007
- Talaga, D.
- Current Opinion in Colloid & Interface Science, Vol. 12, Issue 6
Zero Mode Waveguides for Single-Molecule Spectroscopy on Lipid Membranes
journal, May 2006
- Samiee, K. T.; Moran-Mirabal, J. M.; Cheung, Y. K.
- Biophysical Journal, Vol. 90, Issue 9
Fluorescence correlation spectroscopy at high concentrations using gold bowtie nanoantennas
journal, October 2012
- Kinkhabwala, Anika A.; Yu, Zongfu; Fan, Shanhui
- Chemical Physics, Vol. 406
Analyzing conformational dynamics of single P-glycoprotein transporters by Förster resonance energy transfer using hidden Markov models
journal, March 2014
- Zarrabi, Nawid; Ernst, Stefan; Verhalen, Brandy
- Methods, Vol. 66, Issue 2
Monitoring the Waiting Time Sequence of Single Ras GTPase Activation Events Using Liposome Functionalized Zero-Mode Waveguides
journal, March 2016
- Christensen, Sune M.; Triplet, Meredith G.; Rhodes, Christopher
- Nano Letters, Vol. 16, Issue 4
Real-Time Sensing of Single-Ligand Delivery with Nanoaperture-Integrated Microfluidic Devices
journal, July 2017
- Martin, W. Elliott; Ge, Ning; Srijanto, Bernadeta R.
- ACS Omega, Vol. 2, Issue 7
Improved fabrication of zero-mode waveguides for single-molecule detection
journal, February 2008
- Foquet, Mathieu; Samiee, Kevan T.; Kong, Xiangxu
- Journal of Applied Physics, Vol. 103, Issue 3
A Comparison of Single-Molecule Emission in Aluminum and Gold Zero-Mode Waveguides
journal, August 2016
- Martin, W. Elliott; Srijanto, Bernadeta R.; Collier, C. Patrick
- The Journal of Physical Chemistry A, Vol. 120, Issue 34
Real-Time DNA Sequencing from Single Polymerase Molecules
journal, January 2009
- Eid, John; Fehr, Adrian; Gray, Jeremy
- Science, Vol. 323, Issue 5910, p. 133-138
Cell investigation of nanostructures: zero-mode waveguides for plasma membrane studies with single molecule resolution
journal, April 2007
- Moran-Mirabal, Jose M.; Torres, Alexis J.; Samiee, Kevan T.
- Nanotechnology, Vol. 18, Issue 19
UV fluorescence enhancement by Al and Mg nanoapertures
journal, April 2015
- Jiao, Xiaojin; Wang, Yunshan; Blair, Steve
- Journal of Physics D: Applied Physics, Vol. 48, Issue 18
Real-Time Imaging of Single-Molecule Fluorescence with a Zero-Mode Waveguide for the Analysis of Protein−Protein Interaction
journal, June 2008
- Miyake, Takeo; Tanii, Takashi; Sonobe, Hironori
- Analytical Chemistry, Vol. 80, Issue 15
Live-Cell Imaging of Single Receptor Composition Using Zero-Mode Waveguide Nanostructures
journal, June 2012
- Richards, Christopher I.; Luong, Khai; Srinivasan, Rahul
- Nano Letters, Vol. 12, Issue 7
Single Molecules Observed by Near-Field Scanning Optical Microscopy
journal, November 1993
- Betzig, E.; Chichester, R. J.
- Science, Vol. 262, Issue 5138
DNA Origami Nanoantennas for Fluorescence Enhancement
journal, August 2021
- Glembockyte, Viktorija; Grabenhorst, Lennart; Trofymchuk, Kateryna
- Accounts of Chemical Research, Vol. 54, Issue 17
Single-Molecule Positioning in Zeromode Waveguides by DNA Origami Nanoadapters
journal, May 2014
- Pibiri, Enrico; Holzmeister, Phil; Lalkens, Birka
- Nano Letters, Vol. 14, Issue 6
Plasmonic antennas and zero-mode waveguides to enhance single molecule fluorescence detection and fluorescence correlation spectroscopy toward physiological concentrations: Plasmonic antennas and zero mode waveguides
journal, February 2014
- Punj, Deep; Ghenuche, Petru; Moparthi, Satish Babu
- Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, Vol. 6, Issue 3
Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations
journal, January 2003
- Levene, M. J.
- Science, Vol. 299, Issue 5607
Hidden Markov Analysis of Short Single Molecule Intensity Trajectories
journal, September 2009
- Jung, Soonkyo; Dickson, Robert M.
- The Journal of Physical Chemistry B, Vol. 113, Issue 42
A novel method to accurately locate and count large numbers of steps by photobleaching
journal, November 2016
- Tsekouras, Konstantinos; Custer, Thomas C.; Jashnsaz, Hossein
- Molecular Biology of the Cell, Vol. 27, Issue 22
Length-independent DNA packing into nanopore zero-mode waveguides for low-input DNA sequencing
journal, September 2017
- Larkin, Joseph; Henley, Robert Y.; Jadhav, Vivek
- Nature Nanotechnology, Vol. 12, Issue 12
Distance and Plasmon Wavelength Dependent Fluorescence of Molecules Bound to Silica-Coated Gold Nanorods
journal, July 2014
- Abadeer, Nardine S.; Brennan, Marshall R.; Wilson, William L.
- ACS Nano, Vol. 8, Issue 8
Variational Bayes Analysis of a Photon-Based Hidden Markov Model for Single-Molecule FRET Trajectories
journal, September 2012
- Okamoto, Kenji; Sako, Yasushi
- Biophysical Journal, Vol. 103, Issue 6
FRET Enhancement in Aluminum Zero-Mode Waveguides
journal, January 2015
- de Torres, Juan; Ghenuche, Petru; Moparthi, Satish Babu
- ChemPhysChem, Vol. 16, Issue 4
Breaking the Concentration Barrier for Single-Molecule Fluorescence Measurements
journal, November 2017
- Peng, Sijia; Wang, Wenjuan; Chen, Chunlai
- Chemistry - A European Journal, Vol. 24, Issue 5
Surface Plasmon-Assisted Fluorescence Enhancing and Quenching: From Theory to Application
journal, May 2021
- Su, Qiang; Jiang, Cheng; Gou, Deming
- ACS Applied Bio Materials, Vol. 4, Issue 6
Reversible Positioning of Single Molecules inside Zero-Mode Waveguides
journal, September 2014
- Larkin, Joseph; Foquet, Mathieu; Turner, Stephen W.
- Nano Letters, Vol. 14, Issue 10
Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells
journal, December 2010
- Huang, Bo; Babcock, Hazen; Zhuang, Xiaowei
- Cell, Vol. 143, Issue 7
Methods of single-molecule fluorescence spectroscopy and microscopy
journal, August 2003
- Moerner, W. E.; Fromm, David P.
- Review of Scientific Instruments, Vol. 74, Issue 8
Dependence of Fluorescence Intensity on the Spectral Overlap between Fluorophores and Plasmon Resonant Single Silver Nanoparticles
journal, March 2007
- Chen, Yeechi; Munechika, Keiko; Ginger, David S.
- Nano Letters, Vol. 7, Issue 3
Resolving the complexity of the human genome using single-molecule sequencing
journal, November 2014
- Chaisson, Mark J. P.; Huddleston, John; Dennis, Megan Y.
- Nature, Vol. 517, Issue 7536
Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models
journal, September 2003
- Andrec, Michael; Levy, Ronald M.; Talaga, David S.
- The Journal of Physical Chemistry A, Vol. 107, Issue 38
Going beyond five bases in DNA sequencing
journal, June 2012
- Korlach, Jonas; Turner, Stephen W.
- Current Opinion in Structural Biology, Vol. 22, Issue 3
Fluorescence microscopy for visualizing single-molecule protein dynamics
journal, February 2020
- Yokota, Hiroaki
- Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1864, Issue 2
A Zeptoliter Volume Meter for Analysis of Single Protein Molecules
journal, December 2011
- Sandén, Tor; Wyss, Romain; Santschi, Christian
- Nano Letters, Vol. 12, Issue 1
Hybrid Mushroom Nanoantenna for Fluorescence Enhancement by Matching the Stokes Shift of the Emitter
journal, June 2018
- Sun, Song; Li, Ru; Li, Mo
- The Journal of Physical Chemistry C, Vol. 122, Issue 26
Analyzing the Dynamics of Single TBP-DNA-NC2 Complexes Using Hidden Markov Models
journal, December 2018
- Zarrabi, Nawid; Schluesche, Peter; Meisterernst, Michael
- Biophysical Journal, Vol. 115, Issue 12
Single-molecule spectroelectrochemical cross-correlation during redox cycling in recessed dual ring electrode zero-mode waveguides
journal, January 2017
- Han, Donghoon; Crouch, Garrison M.; Fu, Kaiyu
- Chemical Science, Vol. 8, Issue 8
Placing Individual Molecules in the Center of Nanoapertures
journal, June 2013
- Heucke, Stephan F.; Baumann, Fabian; Acuna, Guillermo P.
- Nano Letters, Vol. 14, Issue 2
Observing Single-Molecule Dynamics at Millimolar Concentrations
journal, January 2017
- Goldschen-Ohm, Marcel P.; White, David S.; Klenchin, Vadim A.
- Angewandte Chemie International Edition, Vol. 56, Issue 9
Miniaturized DNA Sequencers for Personal Use: Unreachable Dreams or Achievable Goals
journal, February 2021
- Huo, Wenxing; Ling, Wei; Wang, Zilun
- Frontiers in Nanotechnology, Vol. 3
λ-Repressor Oligomerization Kinetics at High Concentrations Using Fluorescence Correlation Spectroscopy in Zero-Mode Waveguides
journal, March 2005
- Samiee, K. T.; Foquet, M.; Guo, L.
- Biophysical Journal, Vol. 88, Issue 3
Recent advances in plasmonic nanocavities for single-molecule spectroscopy
journal, January 2021
- Maccaferri, Nicolò; Barbillon, Grégory; Koya, Alemayehu Nana
- Nanoscale Advances, Vol. 3, Issue 3
Top-down machine learning approach for high-throughput single-molecule analysis
journal, April 2020
- White, David S.; Goldschen-Ohm, Marcel P.; Goldsmith, Randall H.
- eLife, Vol. 9
Single Photon Source from a Nanoantenna-Trapped Single Quantum Dot
journal, August 2021
- Jiang, Quanbo; Roy, Prithu; Claude, Jean-Benoît
- Nano Letters, Vol. 21, Issue 16
Structure and dynamics underlying elementary ligand binding events in human pacemaking channels
journal, November 2016
- Goldschen-Ohm, Marcel P.; Klenchin, Vadim A.; White, David S.
- eLife, Vol. 5
Zero-Mode Waveguides for Single-Molecule Analysis
journal, June 2012
- Zhu, Paul; Craighead, Harold G.
- Annual Review of Biophysics, Vol. 41, Issue 1
Single-molecule methods leap ahead
journal, September 2014
- Ha, Taekjip
- Nature Methods, Vol. 11, Issue 10
Hidden Markov Model Analysis of Multichromophore Photobleaching
journal, July 2006
- Messina, Troy C.; Kim, Hiyun; Giurleo, Jason T.
- The Journal of Physical Chemistry B, Vol. 110, Issue 33
Single-molecule detection at high concentrations with optical aperture nanoantennas
journal, January 2016
- Alam, Md Shah; Karim, Farzia; Zhao, Chenglong
- Nanoscale, Vol. 8, Issue 18
A hybrid metal–dielectric zero mode waveguide for enhanced single molecule detection
journal, January 2019
- Zambrana-Puyalto, Xavier; Ponzellini, Paolo; Maccaferri, Nicolò
- Chemical Communications, Vol. 55, Issue 65
Photoluminescence Enhancement, Blinking Suppression, and Improved Biexciton Quantum Yield of Single Quantum Dots in Zero Mode Waveguides
journal, March 2021
- Masud, Abdullah Al; Arefin, S. M. Nayeem; Fairooz, Fatema
- The Journal of Physical Chemistry Letters, Vol. 12, Issue 13
Zero-mode waveguide nanophotonic structures for single molecule characterization
journal, April 2018
- Crouch, Garrison M.; Han, Donghoon; Bohn, Paul W.
- Journal of Physics D: Applied Physics, Vol. 51, Issue 19
Optical Antenna-Based Fluorescence Correlation Spectroscopy to Probe the Nanoscale Dynamics of Biological Membranes
journal, December 2017
- Winkler, Pamina M.; Regmi, Raju; Flauraud, Valentin
- The Journal of Physical Chemistry Letters, Vol. 9, Issue 1
Saturated excitation of fluorescence to quantify excitation enhancement in aperture antennas
journal, January 2012
- Aouani, Heykel; Hostein, Richard; Mahboub, Oussama
- Optics Express, Vol. 20, Issue 16
Silver-copper alloy nanoparticles for metal enhanced luminescence
journal, September 2009
- Chowdhury, Sanchari; Bhethanabotla, Venkat R.; Sen, Rajan
- Applied Physics Letters, Vol. 95, Issue 13
Genetic variation and the de novo assembly of human genomes
journal, October 2015
- Chaisson, Mark J. P.; Wilson, Richard K.; Eichler, Evan E.
- Nature Reviews Genetics, Vol. 16, Issue 11
Dual-color fluorescence cross-correlation spectroscopy in a single nanoaperture : towards rapid multicomponent screening at high concentrations
journal, January 2006
- Wenger, Jérôme; Gérard, Davy; Lenne, Pierre-François
- Optics Express, Vol. 14, Issue 25
Nanoaperture fabrication via colloidal lithography for single molecule fluorescence analysis
journal, October 2019
- Jamiolkowski, Ryan M.; Chen, Kevin Y.; Fiorenza, Shane A.
- PLOS ONE, Vol. 14, Issue 10
Information Theoretical Approach to Single-Molecule Experimental Design and Interpretation
journal, July 2006
- Talaga, David S.
- The Journal of Physical Chemistry A, Vol. 110, Issue 31
Simultaneous Observation of Kinesin-Driven Microtubule Motility and Binding of Adenosine Triphosphate Using Linear Zero-Mode Waveguides
journal, November 2018
- Fujimoto, Kazuya; Morita, Yuki; Iino, Ryota
- ACS Nano, Vol. 12, Issue 12
UV Fluorescence Lifetime Modification by Aluminum Nanoapertures
journal, November 2014
- Jiao, Xiaojin; Peterson, Eric M.; Harris, Joel M.
- ACS Photonics, Vol. 1, Issue 12
Large single-molecule fluorescence enhancements produced by a bowtie nanoantenna
journal, October 2009
- Kinkhabwala, Anika; Yu, Zongfu; Fan, Shanhui
- Nature Photonics, Vol. 3, Issue 11, p. 654-657
Excitation enhancement of CdSe quantum dots by single metal nanoparticles
journal, August 2008
- Chen, Yeechi; Munechika, Keiko; Jen-La Plante, Ilan
- Applied Physics Letters, Vol. 93, Issue 5
Cell biology beyond the diffraction limit: near-field scanning optical microscopy
journal, December 2001
- de Lange, Frank; Cambi, Alessandra; Huijbens, Richard
- Journal of Cell Science, Vol. 114, Issue 23
Quantum yield and excitation rate of single molecules close to metallic nanostructures
journal, November 2014
- Holzmeister, Phil; Pibiri, Enrico; Schmied, Jürgen J.
- Nature Communications, Vol. 5, Issue 1
Mixed metal zero-mode guides (ZMWs) for tunable fluorescence enhancement
journal, January 2020
- Al Masud, Abdullah; Martin, W. Elliott; Moonschi, Faruk H.
- Nanoscale Advances, Vol. 2, Issue 5
Zero-mode waveguides can be made better: fluorescence enhancement with rectangular aluminum nanoapertures from the visible to the deep ultraviolet
journal, January 2020
- Baibakov, Mikhail; Barulin, Aleksandr; Roy, Prithu
- Nanoscale Advances, Vol. 2, Issue 9
DNA-Guided Delivery of Single Molecules into Zero-Mode Waveguides
journal, August 2017
- Plénat, Thomas; Yoshizawa, Satoko; Fourmy, Dominique
- ACS Applied Materials & Interfaces, Vol. 9, Issue 36
Surface passivation of zero-mode waveguide nanostructures: benchmarking protocols and fluorescent labels
journal, March 2020
- Patra, Satyajit; Baibakov, Mikhail; Claude, Jean-Benoît
- Scientific Reports, Vol. 10, Issue 1
Direct detection of DNA methylation during single-molecule, real-time sequencing
journal, May 2010
- Flusberg, Benjamin A.; Webster, Dale R.; Lee, Jessica H.
- Nature Methods, Vol. 7, Issue 6