Three-dimensional nanolithography using proton beam writing

Kan, J.A. van; Bettiol, A.A.; Watt, F.

doi:10.1063/1.1604468

Cited by 152 publications

(93 citation statements)

References 10 publications

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“…The nanofluidic device was made by replication in PDMS of a patterned master stamp (13). The stamp was fabricated in hydrogen silsesquioxane (HSQ) resist (Dow Corning) using a lithography processes with proton beam writing (17,18). The 300 nm height of the positive channel structures on the stamp was measured with atomic force microscopy (Dimension 3000, Veeco).…”

Section: Experimental Methodsmentioning

confidence: 99%

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Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel

Zhang

Shao

Kan

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

115

136

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The effect of dextran nanoparticles on the conformation and compaction of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. It was observed that the DNA molecules elongate and eventually condense into a compact form with increasing volume fraction of the crowding agent. Under crowded conditions, the channel diameter is effectively reduced, which is interpreted in terms of depletion in DNA segment density in the interfacial region next to the channel wall. Confinement in a nanochannel also facilitates compaction with a neutral crowding agent at low ionic strength. The threshold volume fraction for condensation is proportional to the size of the nanoparticle, due to depletion induced attraction between DNA segments. We found that the effect of crowding is not only related to the colligative properties of the agent and that confinement is also important. It is the interplay between anisotropic confinement and osmotic pressure which gives the elongated conformation and the possibility for condensation at low ionic strength.A substantial fraction of the total volume of biological media is occupied by macromolecules, which do not directly participate in biochemical reactions. Nevertheless, it is now well established that these background species have an important effect on molecular transport, reaction rates, and chemical equilibrium (1). The steric repulsion between impenetrable macromolecules in a crowded medium is a major factor in determining the thermodynamic activities of the reactants. Crowding by an inert osmotic agent can also affect macromolecular structure. A well known example is the transition of DNA to a compact form (condensation) in the presence of overthreshold concentrations of simple neutral polymers and simple salts (2, 3, 4). It has been proposed that macromolecular crowding is the basis for phase separation in the cytoplasm (5) and condensation of DNA into the nucleoid of bacterial cells (6). The latter hypothesis is supported by the observation that DNA can be condensed by cytoplasmic extracts from Escherichia coli at extract concentrations corresponding to about 1 ⁄2 the cellular concentration (7). Besides background species, the cytoplasm of most eukaryotic cells contains stationary elements such as fiber lattices and membranes. These structures affect macromolecular conformation through confinement in 1D or 2D. Accordingly, macromolecular crowding and confinement are intimately related and deserve an integrated approach to understand their modes of operation and how they couple.DNA condensation can be assisted and directed by a surface. In surface directed condensation, DNA is first adsorbed onto an interface, after which it is condensed with an agent. Examples that have been reported in the literature are the condensation of single molecules into rods and toroidal structures with protamine or ethanol (8, 9). Single DNA molecules can be confined and visualized with f luorescence microscopy in quasi 1D nanochannels. The extension in the longitudinal ...

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Section: Experimental Methodsmentioning

confidence: 99%

“…Our experiments are done using nanofluidic devices made of poly-(dimethyl siloxane) (PDMS). We have used a lithography process with proton beam writing to fabricate a nanopatterned stamp (17,18). The stamp was subsequently replicated in PDMS, followed by curing and sealing with a glass slide (19).…”

mentioning

confidence: 99%

Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel

Zhang

Shao

Kan

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

115

136

View full text Add to dashboard Cite

show abstract

“…The stamp was fabricated in HSQ resist (Dow Corning, Midland, MI) using a lithography process with proton beam writing. 15,16 A scanning electron microscopy image of the HSQ stamp bearing the positive nanostructures is displayed in Fig. 3a.…”

Section: Experimental Procedures a Fabrication Of The Nanofluidmentioning

confidence: 99%

“…We have used a lithography process with proton beam writing to fabricate a nanopatterned stamp. 15,16 The stamp was subsequently replicated in poly(dimethyl siloxane) (PDMS) polymer, followed by curing and sealing with a glass slide. 17,18 In order to visualize the DNA molecules with fluorescence microscopy it is necessary to stain them with a dye.…”

Section: Introductionmentioning

confidence: 99%

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Zhang

Kan

et al. 2008

The Journal of Chemical Physics

154

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Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter.Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.

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“…22 The grid of nanochannels was made in HSQ resist (Dow Corning, Midland, MI) using a lithography process with proton beam writing. 23,24 The two intersecting arrays of nanochannels are connected to a superposing set of microchannels made in SU-8 resin with UV lithography. To promote the release of the PDMS replica, the stamp was coated with a layer of teflon with a thickness of 5 nm and baked at 393 K for 12 h. 25 As measured with scanning electron microscopy, the perpendicular nanochannels have widths of 150 ± 10 nm and 250 ± 10 nm, respectively.…”

Section: Chip Fabricationmentioning

confidence: 99%

A nanofluidic device for single molecule studies with in situ control of environmental solution conditions

et al. 2013

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We report an approach to study the in-situ conformational response of single biomolecules such as DNA to a change in environmental solution conditions. These conditions are, for instance, the composition of the buffer or the presence of protein. For this purpose, we designed and fabricated a nanofluidic device featuring two arrays of parallel nanochannels in a perpendicular configuration. The cross-sections of the channels are rectangular with a diameter down to 175 nm. The lab-on-chip devices were made of polydimethylsiloxane (PDMS) cast on a high quality master stamp, obtained by proton beam writing and UV lithography. Biomolecules can be inserted into the device through the array of channels in one direction, whereas the buffer can be exchanged through the intersecting array of channels in the other direction. A buffer exchange time inside the grid of nanochannels of less than one second is measured by monitoring the conductivity of solutions of salt. The exchange time of protein is typically a few seconds, as determined by imaging of the influx of fluorescence labelled protamine. We demonstrate the functionality of the device by investigating the compaction of DNA by protamine and unpacking of pre-compacted DNA through an increase in concentration of salt.

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Three-dimensional nanolithography using proton beam writing

Cited by 152 publications

References 10 publications

Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel

Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

A nanofluidic device for single molecule studies with in situ control of environmental solution conditions

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