Standalone interferometry-based calibration of convex lens-induced confinement microscopy with nanoscale accuracy

Morrin, Gregory T.; Kienle, Daniel F.; Schwartz, Daniel K.

doi:10.1039/c8an02300j

Standalone interferometry-based calibration of convex lens-induced confinement microscopy with nanoscale accuracy

Journal Article · Thu Feb 28 00:00:00 EST 2019 · Analyst

DOI:https://doi.org/10.1039/c8an02300j· OSTI ID:1773869

^[1]; ^[2]; Schwartz, Daniel K. ^[2]

Univ. of Colorado, Boulder, CO (United States); University of Colorado Boulder
Univ. of Colorado, Boulder, CO (United States)

Strongly confined environments (confined dimensions between 1–100 nm) represent unique challenges and opportunities for understanding and manipulating molecular behavior due to the significant effects of electric double layers, high surface-area to volume ratios, and other phenomena at the nanoscale. Convex Lens-induced Confinement (CLiC) can be used to analyze the dynamics of individual molecules or particles confined in a planar slit geometry with continuously varying gap thickness. Here, we describe an interferometry-based method for precise measurement of the slit pore geometry. Specifically, this approach permitted accurate characterization of separation distances as small as 5 nm, with 1 nm precision, without a priori knowledge or assumptions about the contact geometry, as well as a greatly simplified experimental setup that required only a lens, coverslip, and inverted microscope. The interferometry-based measurement of gap height offered a distinct advantage over conventional fluorescent dye-based methods; e.g., accurate interferometric height measurements were made at low gap heights regardless of solution conditions, while the concentration of fluorescent dye was significantly impacted by solution conditions such as ionic strength or pH. The accuracy of the interferometric measurements was demonstrated by comparing the experimentally measured concentration of a charged fluorescent dye as a function of gap thickness with dye concentration profiles calculated using Debye–Hückel theory. Accurate characterization of nanoscale gap thickness will enable researchers to study a variety of practical and biologically relevant systems within the CLiC geometry.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Colorado, Boulder, CO (United States)

Sponsoring Organization:: Defense Threat Reduction Agency (DTRA); National Institute of Standards and Technology (NIST); National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC0001854

OSTI ID:: 1773869

Alternate ID(s):: OSTI ID: 1610582
OSTI ID: 1498184

Journal Information:: Analyst, Journal Name: Analyst Journal Issue: 8 Vol. 144; ISSN 0003-2654

Publisher:: Royal Society of ChemistryCopyright Statement

Country of Publication:: United States

Language:: English

References (42)

Fabrication of Nanoporous Alumina Ultrafiltration Membrane with Tunable Pore Size Using Block Copolymer Templates Zhou, Chun; Segal-Peretz, Tamar; Oruc, Muhammed Enes Advanced Functional Materials, Vol. 27, Issue 34 https://doi.org/10.1002/adfm.201701756	journal	July 2017
Critical polyelectrolyte adsorption under confinement: Planar slit, cylindrical pore, and spherical cavity Cherstvy, A. G. Biopolymers, Vol. 97, Issue 5 https://doi.org/10.1002/bip.22023	journal	January 2012
Fabrication of Nanofluidic Biochips with Nanochannels for Applications in DNA Analysis Xia, Deying; Yan, Juchao; Hou, Shifeng Small, Vol. 8, Issue 18 https://doi.org/10.1002/smll.201200240	journal	July 2012
Biomimetic nanochannels based biosensor for ultrasensitive and label-free detection of nucleic acids Sun, Zhongyue; Liao, Tangbin; Zhang, Yulin Biosensors and Bioelectronics, Vol. 86 https://doi.org/10.1016/j.bios.2016.06.059	journal	December 2016
Convex Lens-Induced Confinement for Imaging Single Molecules Leslie, Sabrina R.; Fields, Alex; Cohen, Adam Biophysical Journal, Vol. 100, Issue 3 https://doi.org/10.1016/j.bpj.2010.12.2778	journal	February 2011
Electrokinetic Transport in Nanochannels. 2. Experiments Pennathur, Sumita; Santiago, Juan G. Analytical Chemistry, Vol. 77, Issue 21 https://doi.org/10.1021/ac0508346	journal	November 2005
Electrokinetic Transport in Nanochannels. 2. Experiments Pennathur, Sumita; Santiago, Juan G. Analytical Chemistry, Vol. 78, Issue 3 https://doi.org/10.1021/ac052141v	journal	December 2005
Convex Lens-Induced Confinement for Imaging Single Molecules Leslie, Sabrina R.; Fields, Alexander P.; Cohen, Adam E. Analytical Chemistry, Vol. 82, Issue 14 https://doi.org/10.1021/ac101041s	journal	July 2010
Nanofluidic Devices with Two Pores in Series for Resistive-Pulse Sensing of Single Virus Capsids Harms, Zachary D.; Mogensen, Klaus B.; Nunes, Pedro S. Analytical Chemistry, Vol. 83, Issue 24 https://doi.org/10.1021/ac202358t	journal	December 2011
Electrokinetically-Driven Transport of DNA through Focused Ion Beam Milled Nanofluidic Channels Menard, Laurent D.; Ramsey, J. Michael Analytical Chemistry, Vol. 85, Issue 2 https://doi.org/10.1021/ac303074f	journal	December 2012
Analyzing Refractive Index Profiles of Confined Fluids by Interferometry Kienle, Daniel F.; Kuhl, Tonya L. Analytical Chemistry, Vol. 86, Issue 23 https://doi.org/10.1021/ac503469x	journal	November 2014
Fundamental Studies of Nanofluidics: Nanopores, Nanochannels, and Nanopipets Haywood, Daniel G.; Saha-Shah, Anumita; Baker, Lane A. Analytical Chemistry, Vol. 87, Issue 1 https://doi.org/10.1021/ac504180h	journal	December 2014
Nanofluidic Devices and Their Applications Abgrall, Patrick; Nguyen, Nam Trung Analytical Chemistry, Vol. 80, Issue 7 https://doi.org/10.1021/ac702296u	journal	April 2008
Nanofluidics in Lab-on-a-Chip Devices Kovarik, Michelle L.; Jacobson, Stephen C. Analytical Chemistry, Vol. 81, Issue 17 https://doi.org/10.1021/ac900614k	journal	September 2009
Direct Observation of Transitions between Surface-Dominated and Bulk Diffusion Regimes in Nanochannels Durand, Nicolas F. Y.; Dellagiacoma, Claudio; Goetschmann, Raphaël Analytical Chemistry, Vol. 81, Issue 13 https://doi.org/10.1021/ac900617b	journal	July 2009
Nanometric Gap Structure with a Fluid Lipid Bilayer for the Selective Transport and Detection of Biological Molecules Ando, Koji; Tanabe, Masashi; Morigaki, Kenichi Langmuir, Vol. 32, Issue 31 https://doi.org/10.1021/acs.langmuir.6b01405	journal	July 2016
Continuous Confinement Fluidics: Getting Lots of Molecules into Small Spaces with High Fidelity Ahamed, Mohammed Jalal; Mahshid, Sara; Berard, Daniel J. Macromolecules, Vol. 49, Issue 7 https://doi.org/10.1021/acs.macromol.5b02617	journal	March 2016
Free Energy of a Polymer in Slit-like Confinement from the Odijk Regime to the Bulk Leith, Jason S.; Kamanzi, Albert; Sean, David Macromolecules, Vol. 49, Issue 23 https://doi.org/10.1021/acs.macromol.6b01805	journal	November 2016
Single Nanochannel-Aptamer-Based Biosensor for Ultrasensitive and Selective Cocaine Detection Wang, Jian; Hou, Jue; Zhang, Huacheng ACS Applied Materials & Interfaces, Vol. 10, Issue 2 https://doi.org/10.1021/acsami.7b16539	journal	January 2018
NMR Studies of Structure and Dynamics of Liquid Molecules Confined in Extended Nanospaces Tsukahara, Takehiko; Mizutani, Wataru; Mawatari, Kazuma The Journal of Physical Chemistry B, Vol. 113, Issue 31 https://doi.org/10.1021/jp903275t	journal	August 2009
Ionic Transport Phenomena in Nanofluidics: Experimental and Theoretical Study of the Exclusion-Enrichment Effect on a Chip Plecis, Adrien; Schoch, Reto B.; Renaud, Philippe Nano Letters, Vol. 5, Issue 6 https://doi.org/10.1021/nl050265h	journal	June 2005
Nanogap Detector Inside Nanofluidic Channel for Fast Real-Time Label-Free DNA Analysis Liang, Xiaogan; Chou, Stephen Y. Nano Letters, Vol. 8, Issue 5 https://doi.org/10.1021/nl080473k	journal	May 2008
DNA Translocation through Graphene Nanopores Schneider, Grégory F.; Kowalczyk, Stefan W.; Calado, Victor E. Nano Letters, Vol. 10, Issue 8, p. 3163-3167 https://doi.org/10.1021/nl102069z	journal	August 2010
High spatial resolution nanoslit SERS for single-molecule nucleobase sensing Chen, Chang; Li, Yi; Kerman, Sarp Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04118-7	journal	April 2018
Nanofluidics in chemical analysis Piruska, Aigars; Gong, Maojun; Sweedler, Jonathan V. Chem. Soc. Rev., Vol. 39, Issue 3 https://doi.org/10.1039/B900409M	journal	January 2010
Protein diffusion through charged nanopores with different radii at low ionic strength Stroeve, Pieter; Rahman, Masoud; Naidu, Lekkala Dev Phys. Chem. Chem. Phys., Vol. 16, Issue 39 https://doi.org/10.1039/C4CP03198A	journal	January 2014
Physics and technological aspects of nanofluidics Bocquet, Lyderic; Tabeling, Patrick Lab Chip, Vol. 14, Issue 17 https://doi.org/10.1039/C4LC00325J	journal	January 2014
Development of a platform for single cell genomics using convex lens-induced confinement Mahshid, Sara; Ahamed, Mohammed Jalal; Berard, Daniel Lab on a Chip, Vol. 15, Issue 14 https://doi.org/10.1039/C5LC00492F	journal	January 2015
Inverted critical adsorption of polyelectrolytes in confinement de Carvalho, Sidney J.; Metzler, Ralf; Cherstvy, Andrey G. Soft Matter, Vol. 11, Issue 22 https://doi.org/10.1039/C5SM00635J	journal	January 2015
Continuous high throughput nanofluidic separation through tangential-flow vertical nanoslit arrays Bassu, Margherita; Holik, Peter; Schmitz, Sam Lab on a Chip, Vol. 16, Issue 23 https://doi.org/10.1039/C6LC01089J	journal	January 2016
Technologies for nanofluidic systems: top-down vs. bottom-up—a review Mijatovic, D.; Eijkel, J. C. T.; van den Berg, A. Lab on a Chip, Vol. 5, Issue 5 https://doi.org/10.1039/b416951d	journal	January 2005
Nanofluidic technology for biomolecule applications: a critical review Napoli, M.; Eijkel, J. C. T.; Pennathur, S. Lab on a Chip, Vol. 10, Issue 8 https://doi.org/10.1039/b917759k	journal	January 2010
Nonequilibrium separation of short DNA using nanoslit arrays Strychalski, Elizabeth A.; Lau, Henry W.; Archer, Lynden A. Journal of Applied Physics, Vol. 106, Issue 2 https://doi.org/10.1063/1.3183953	journal	July 2009
Review article: Fabrication of nanofluidic devices Duan, Chuanhua; Wang, Wei; Xie, Quan Biomicrofluidics, Vol. 7, Issue 2 https://doi.org/10.1063/1.4794973	journal	March 2013
Precision platform for convex lens-induced confinement microscopy Berard, Daniel; McFaul, Christopher M. J.; Leith, Jason S. Review of Scientific Instruments, Vol. 84, Issue 10 https://doi.org/10.1063/1.4822276	journal	October 2013
Open-frame system for single-molecule microscopy Arsenault, Adriel; Leith, Jason S.; Henkin, Gil Review of Scientific Instruments, Vol. 86, Issue 3 https://doi.org/10.1063/1.4913271	journal	March 2015
Convex lens-induced nanoscale templating Berard, Daniel J.; Michaud, François; Mahshid, Sara Proceedings of the National Academy of Sciences, Vol. 111, Issue 37 https://doi.org/10.1073/pnas.1321089111	journal	August 2014
Visualizing structure-mediated interactions in supercoiled DNA molecules Scott, Shane; Xu, Zhi Ming; Kouzine, Fedor Nucleic Acids Research, Vol. 46, Issue 9 https://doi.org/10.1093/nar/gky266	journal	April 2018
Nanoconfinement-Enhanced Conformational Response of Single DNA Molecules to Changes in Ionic Environment Reisner, Walter; Beech, Jason P.; Larsen, Niels B. Physical Review Letters, Vol. 99, Issue 5 https://doi.org/10.1103/PhysRevLett.99.058302	journal	August 2007
Transport phenomena in nanofluidics Schoch, Reto B.; Han, Jongyoon; Renaud, Philippe Reviews of Modern Physics, Vol. 80, Issue 3 https://doi.org/10.1103/RevModPhys.80.839	journal	July 2008
Electrokinetically-Driven Transport of DNA through Focused Ion Beam Milled Nanofluidic Channels Michael, Ramsey, J.; D., Menard, Laurent The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/ea9w-ra20	text	January 2013
Inverted critical adsorption of polyelectrolytes in confinement de Carvalho, Sidney J.; Metzler, Ralf; Cherstvy, Andrey G. arXiv https://doi.org/10.48550/arxiv.1503.02040	preprint	January 2015

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