Publications
David L. V. Bauer, Rodolphe Marie, Kristian H. Rasmussen, Anders Kristensen, and Kalim U. Mir, DNA catenation maintains structure of human metaphase chromosomes, Nucleic Acids Research, 2012, 1-7, (September 2012).
Abstract: Nanochannel technology, coupled with a suitable DNA labeling chemistry, is a powerful approach for performing high-throughput single-molecule mapping of genomes. Yet so far nanochannel technology has remained inaccessible to the broader research community due to high fabrication cost and/or requirement of specialized facilities/skill-sets. In this article we show that nanochannel-based mapping can be performed in all polymer chips fabricated via injection molding: a fabrication process so inexpensive that the devices can be considered disposable. Fluorescent intensity variations can be obtained from molecules extended in the polymer nanochannels via chemical counterstaining against YOYO-1. In particular, we demonstrate that the counterstaining induced fluorescent intensity variations to a large degree appear to be proportional to the theoretically computed sequence-maps of both local AT and GC variation along DNA sequences.
Simon T. Larsen, Richard F. Vreeland, Michael L. Heien, and Rafael Taboryski, Characterization of Poly(3,4-ethylenedioxythiophene):tosylate conductive polymer microelectrodes for transmitter detection, Analyst. 137 (2012) 1831-1836, (January 2012).
Abstract: In this paper we investigate the physical and electrochemical properties of micropatterned Poly(3,4-ethylenedioxythiophene):tosylate (Pedot:tosylate) microelectrodes for neurochemical detection. Pedot:tosylate is a promising conductive polymer electrode material for chip-based bioanalytical applications such as capillary electrophoresis, high-performance liquid chromatography, and constant potential amperometry at living cells. Band electrodes with widths down to 3 µm where fabricated on polymer substrates using UV lithographic methods. The electrodes are electrochemically stable in a range between -200 mV and 700 mV vs. Ag/AgCl and show a relatively low resistance. A wide range of transmitters are shown to oxidize readily on the electrodes. Kinetic rate constants and half wave potentials are reported. The capacitance pr area was found to be high 1670 ± 130 µF/cm2 compared to other thin film microelectrode materials. Finally, we use constant potential amperometry to measure the release of transmitters from a group of PC 12 cells. The results show how the current response decreases for a series of stimulations with high K+ buffer.
Simone Tanzi, Peter Friis Østergaard, Marco Matteucci, Thomas Lehrmann Christiansen, Jiri Cech, Rodolphe Marie, and Rafael Taboryski, Fabrication of combined-scale nano- and microfluidic polymer systems using a multilevel dry etching, electroplating and molding process, Journal of Micromechanics and Microengineering, 22 (11) 115008, (2012).
Abstract: Microfabricated single-cell capture and DNA stretching devices have been produced by injection molding. The fabrication scheme employed deep reactive ion etching in a silicon substrate, electroplating in nickel and molding in cyclic olefin polymer. This work proposes technical solutions to fabrication challenges associated with chip sealing and demolding of polymer high-volume replication methods. UV-assisted thermal bonding was found to ensure a strong seal of the microstructures in the molded part without altering the geometry of the channels. In the DNA stretching device, a low aspect ratio nanoslit (1/200) connecting two larger micro-channels was used to stretch a 168.5 kbp DNA molecule, while in the other device single-HeLa cells were captured against a micro-aperture connecting two larger microfluidic channels. Different dry etching processes have been investigated for the master origination of the cell-capture device. The combination of a modified Bosch process and an isotropic polysilicon etch was found to ensure the ease of demolding by resulting in slightly positively tapered sidewalls with negligible undercut at the mask interface.
Simon T. Larsen, and Rafael Taboryski, All polymer chip for amperometric studies of transmitter release from large groups of neuronal cells, Analyst, 137, 5057, (2012).
Abstract: We present an all polymer electrochemical chip for simple detection of transmitter release from large groups of cultured PC 12 cells. Conductive polymer PEDOT:tosylate microelectrodes were used together with constant potential amperometry to obtain easy-to-analyze oxidation signals from potassium-induced release of transmitter molecules. The nature of the resulting current peaks is discussed, and the time for restoring transmitter reservoirs is studied. The relationship between released transmitters and potassium concentration was found to fit to a sigmoidal dose–response curve. Finally, we demonstrate how the presented device can be used for simple drug screening purposes, by measuring the increase of transmitter release due to short-term treatment with L-DOPA.
Simon T. Larsen, Michael L. Heien, and Rafael Taboryski, Amperometric noise at thin film band electrodes,
Anal. Chem. 84 (2012) 7744-7749. Publiceret 28. August 2012.
Abstract: Background current noise is often a significant limitation
when using constant-potential amperometry for biosensor application
such as amperometric recordings of transmitter release from single cells
through exocytosis. In this paper, we fabricated thin-film electrodes of
gold and conductive polymers and measured the current noise in
physiological buffer solution for a wide range of different electrode areas.
The noise measurements could be modeled by an analytical expression,
representing the electrochemical cell as a resistor and capacitor in series.
The studies revealed three domains; for electrodes with low capacitance,
the amplifier noise dominated, for electrodes with large capacitances, the noise from the resistance of the electrochemical cell was
dominant, while in the intermediate region, the current noise scaled with electrode capacitance. The experimental results and the
model presented here can be used for choosing an electrode material and dimensions and when designing chip-based devices for
low-noise current measurements.
Marie, Rodolphe and Kristensen, Anders, Nanofluidic devices towards single DNA molecule sequence Mapping, Journal of Biophotonics. 2012 Jul 20.
Abstract: Nanofluidics enables the imaging of stretched single molecules
with potential applications for single molecule sequence
mapping. Lab-on-a-chip devices for single cell
trapping and lyzing, genomic DNA extraction from single
cells, and optical mapping of genomic length DNA
has been demonstrated separately. Yet the pursuit for
applying DNA optical mapping to solve real genomics
challenges is still to come. We review lab-on-a-chip devices
from literature that could be part of a complete
system for the sequence mapping of single DNA molecules.
Nanofluidics is used to produce optical maps of single
DNA molecules. Combined with other existing lab-on-achip
components, it could lead to new instruments for
sequence analysis of single genomes.
Robert L. Welch,a Robert Sladek,b Ken Dewar,band Walter W. Reisner, Denaturation Mapping of Saccharomyces cerevisiae,
Lab Chip. 2012 Sep 21;12(18):3314-21.
Abstract: Optical mapping of DNA provides large-scale genomic information that can be used to assemble contigs from next-generation
sequencing, and to detect re-arrangements between single cells. A recent optical mapping technique called denaturation mapping
has the unique advantage of using physical principles rather than the action of enzymes to probe genomic structure. Denaturation
mapping uses fluorescence microscopy to image the pattern of partial melting along a DNA molecule extended in a channel of
cross-section 120nm at the heart of a nanofluidic device. We used denaturation mapping to locate single DNA molecules on the
yeast genome (12.1Mbp) by comparing images to a computationally predicted map for the entire genome sequence. By locating
84 molecules we assembled an optical map of the yeast genome with >50% coverage.
Conferences
Thor Christian Hobæk, Henrik Pranov, Inge Marie Svane, and Niels Bent Larsen, Micro- and Nanopatterning Polymers for On-Chip Cell Selection in Toulouse France (September 2012).
Anders Kristensen, Christopher James Lüscher, Anil Thilsted, Johan Eriksen, Lasse Højlund Thamdrup, Jonas Nyvold Pedersen, Henrik Flyvbjerg, and Rodolphe Marie, Optothermally Actuated Nanofluidics for DNA Analysis in Toulouse France (September 2012).
M. Calaon, H.N. Hansen, G. Tosello, Jørgen Garnæs, C. Ravn, and P.T. Tang, Characterization of large area nanostructured surfaces using AFM measurements (June 2012).
Abstract: A surface characterisation study has been developed to validate an innovative tool making solution for nano patterning large areas via anodizing of aluminium (Al) and subsequent nickel electroforming. A surface topography characterization through atomic force microscopy (AFM) indicated a decreased magnitude of the 3D surface amplitude parameters chosen for the analysis, when increasing the Al purity from 99,5% to 99,999%. AFM was then employed to evaluate the periodical arrangements of the nano structured cells. Image processing was used to estimate the average areas value, the height variation relative to an average plane and the coefficient of variation of the fitted features curvature radius.
M. Calaon, G. Tosello, H. N. Hansen, C. Ravn, and A. Islam, Packing parameters effect on injection molding of polypropylene nanostructured surfaces in Florida, USA. (April 2012).
Abstract: In today´s industry, applications involving surface patterning of sub-μm to nanometer scale structures have shown a high growth potential. To investigate the injection molding capability of replicating sub-μm surface texture on a large scale area, a 30x80 mm2 tool insert with surface structures having a diameter of 500 nm was employed. The tool insert surface was produced using chemical-based-batch techniques such aluminum anodization and nickel electroplating. During the injection molding process, polypropylene (PP) was employed as material and packing phase parameters (packing time, packing pressure) were investigated. The replicated surface topographies were quantitatively characterized by atomic force microscopy using specific three-dimensional surface parameters and qualitatively inspected by scanning electron microscopy. Results showed that the degree of replication from the toll to the polymer part was mainly influenced by packing pressure level and distance from the gate.
Peter Østergaard, Marco Mateucci, Rodolphe Marie, Anders Kristensen, and Rafael Taboryski, All polymer, injection molded nanoslits, fabricated through two-level UV-LIGA processes in California, USA, (2012).
Simon Tylsgaard Larsen, Marco Matteucci, and Rafael Taboryski, Conductive Polymer Microelectrodes for on-chip measurement of transmitter release from living cells in California, USA, (2012).
Matteo Calaon, Hans N. Hansen, Guido Tosello, Jørgen Garnaes, Jesper Nørregaard, Markus Guttmann, Production quality control of microfluidic chip designs, Submitted version of draft paper for the upcoming microfluidic conference in Heidelberg, Germany. December 3-5, 2012.
Abstract: The challenge of fabricating geometries with critical dimensions ranging from few microns down to 10 nanometers with high production rate is delaying the development of nanotechnology based products. Diverse research works have shown the capability of technologies such as UV lithography, nano imprint lithography and e-beam lithography to produce micro and nano features. However, their application for tooling purposes is relatively new and the potential to produce nanometer features with high volume low cost production is enormous. Considering possible implementation in a mass production environment the precision of measuring results and the accuracy of measurement relocation are very relevant. In this paper, the possibility of producing with high volume Lab-on-chip devices through injection molding are presented. Preparation of master geometries was made by etching a Si wafer by e-beam lithography. Subsequent nickel electroplating was employed to replicate the obtained geometries on the tool, which was used to mold on transparent polymer substrates the functional structures. To assess the critical factors affecting the replication quality throughout the different steps of the proposed process chain, test geometries were designed and produced on the side of the functional features. The so called “Finger Print” of the lithography and molding processes was qualitatively and quantitatively evaluated through scanning electron microscopy and atomic force microscopy respectively. The entire process chain is therefore characterized and the degree of replication among the different replication steps quantified with precise measurements using a high accuracy relocation technique on the produced key test geometries.
Karen S. Sørensen, Peter F. Østergaard, Rafael J. Taboryski, and Mikkel F. Hansen, On-chip liquid control using striped surface topography fabricated by polymer injection molding,
Poster, 16th Int. Conf. on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2012), Okinawa, Japan, Oct. 28 - Nov 1, 2012.
Lasse Højlund Thamdrup, Jonas Nyvold Pedersen, Henrik Flyvbjerg, Rodolphe Marie, Nanofluidic devices for DNA analysis,
NanoLitho2012, San Sebastian, 13-15 November 2012.
A. Kristensen, M. B. Christiansen, C. Vannahme, C. J. Lüscher, K. H. Rasmussen, A. H. Thilsted, J. Eriksen, T. Mappes, L. H. Thamdrup, R. Marie, Nanoimprint lithography for optofluidics,
Invited Paper at SPIE Photonics Europe, Brussels, Belgium, 16 - 19 April 2012.
A. Kristensen, T. Buss, M. B. Christiansen, C. Smith, and N. A. Mortensen, Optofluidic tuning of photonic crystal lasers,
Invited Paper at SPIE Photononics West 2012, San Francisco, CA USA, 21-26 January 2012.