Dip-pen nanolithography: controlling surface architecture on the sub-100 nanometer length scale

Thermal Effect on Positive Patterned Self-Assembled Monolayer Grown from a Droplet of Alkanethiol

Atomic force microscope technique is widely used for the spatial narrow deposition of molecules inside the bare space of preexisting self-assembled monolayer (SAM) matrix. Using molecular dynamics simulation, we studied the formation of positively patterned SAM from a globule of 1-octadecanethiol (ODT) on predesigned SAM matrix of 1-dodecanethiol (DDT) and effect of temperature on it. The alkyl chains of ODT SAM were densely packed and ordered by means of chemisorption through sulfur atoms. The circular SAM of ODT contained defects due to the molecules those were standing upside down or trapped inside ODT SAM. We found that with the increase of temperature, these defects moved out by flipping of inverted ODT molecules or building spaces to be adsorbed on Au surface. The ODT molecules on the top of the pile of stable circular SAM or those are upside down and trapped disperse in a unique fashion namely serial pushing through which molecules firstly make a free space to enter inside the adsorbed thiol molecules and then push neighboring molecules to get enough space to be adsorbed on the gold surface. The stability of ODT SAM was confirmed by analyzing different structural properties such as tilt angle, tilt orientation. and backbone orientation. We also calculated the diffusion coefficient of the ODT molecules which were on the top of SAM island. © 2019 Wiley Periodicals, Inc.

DNA-nanostructure-assembly by sequential spotting

BACKGROUND

The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions.

RESULTS

For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures.

CONCLUSIONS

The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element.

Strategies for patterning biomolecules with dip-pen nanolithography

Dip-pen nanolithography (DPN) is an atomic force microscopy (AFM)-based lithography technique, which has the ability to fabricate patterns with a feature size down to approximately 15 nm using both top-down and bottom-up approaches. DPN utilizes the water meniscus formed between an AFM tip and a substrate to transfer ink molecules onto surfaces. A major application of this technique is the fabrication of micro- and nano-arrays of patterned biomolecules. To achieve this goal, a variety of chemical approaches has been used. This review concisely describes the development of DPN in the past decade and presents the related chemical strategies that have been reported to fabricate biomolecular patterns with DPN at micrometer and nanometer scale, classified into direct- and indirect DPN methodologies, discussing tip-functionalization strategies as well.

Engineering Micrometer and Nanometer Scale Features in Polydimethylsiloxane Elastomers for Controlled Cell Function

Cell movement, differentiation and metabolic function must be controlled in precise ways to produce both regenerated tissues such as bone and functional tissue equivalents such as immuno-isolated islet cells. Close examination of extracellular matrix (ECM) reveals structures on the micron and nanometer scale that are shown to influence these factors and therefore we hypothesize that cells will move based on topographical cues in the scaffold. We have engineered siloxane elastomer surfaces that mimic the ECM by combining micron and nanometer scale topographic features. Micron scale pillars and ridges ranging in height from 1.5 to 5 microns and separated by 5, 10 and 20 microns were fabricated in a silicon wafer using micro- processing techniques and replicated in polydimethylsiloxane (PDMS) elastomer. Nanometer scale pillars, ridges and more complex shapes ranging in height from 12 to 300 nanometers were superimposed on the micron scale features using nanolithography. This was achieved by using a tapping mode tip in the atomic force microscope (AFM) to plastically deform the substrate surface. The AFM enabled nano-features to be placed on sloped surfaces and added directly to the PDMS elastomer surface. Surface topography was examined using scanning electron microscopy, atomic force microscopy and white light interference profilometry to verify surface modifications and fidelity of the replication process. Results indicate that it is possible to create spatially engineered surface textures from 10-5 m to 10-8 m in size, in specified patterns, by using a combination of microprocessing and nanolithography techniques. As better understanding of ECM function and design is gained, the processing methods outlined here will assist in fabricating tissue engineering scaffolds optimized at the nanometer and micron scale.

Mechanistic principles and applications of resonance energy transfer

Resonance energy transfer is the primary mechanism for the migration of electronic excitation in the condensed phase. Well-known in the particular context of molecular photochemistry, it is a phenomenon whose much wider prevalence in both natural and synthetic materials has only slowly been appreciated, and for which the fundamental theory and understanding have witnessed major advances in recent years. With the growing to maturity of a robust theoretical foundation, the latest developments have led to a more complete and thorough identification of key principles. The present review first describes the context and general features of energy transfer, then focusing on its electrodynamic, optical, and photophysical characteristics. The particular role the mechanism plays in photosynthetic materials and synthetic analogue polymers is then discussed, followed by a summary of its primarily biological structure determination applications. Lastly, several possible methods are described, by the means of which all-optical switching might be effected through the control and application of resonance energy transfer in suitably fabricated nanostructures.Key words: FRET, Förster energy transfer, photophysics, fluorescence, laser.

Scanning probe-based fabrication of 3D nanostructures via affinity templates, functional RNA, and meniscus-mediated surface remodeling

Developing generic platforms to organize discrete molecular elements and nanostructures into deterministic patterns on surfaces is one of the central challenges in the field of nanotechnology. Here we review three applications of the atomic force microscope (AFM) that address this challenge. In the first, we use two-step nanografting to create patterns of self-assembled monolayers (SAMs) to drive the organization of virus particles that have been either genetically or chemically modified to bind to the SAMs. Virus-SAM chemistries are described that provide irreversible and reversible binding, respectively. In the second, we use similar SAM patterns as affinity templates that have been designed to covalently bind oligonucleotides engineered to bind to the SAMs and selected for their ability to mediate the subsequent growth of metallic nanocrystals. In the final application, the liquid meniscus that condenses at the AFM tip-substrate contact is used as a physical tool to both modulate the surface topography of a water soluble substrate and guide the hierarchical assembly of Au nanoparticles into nanowires. All three approaches can be generalized to meet the requirements of a wide variety of materials systems and thereby provide a potential route toward development of a generic platform for molecular and materials organization.

Achieving precision and reproducibility for writing patterns of n-alkanethiol self-assembled monolayers with automated nanografting

Nanografting is a high-precision approach for scanning probe lithography, which provides unique advantages and capabilities for rapidly writing arrays of nanopatterns of thiol self-assembled monolayers (SAMs). Nanografting is accomplished by force- induced displacement of molecules of a matrix SAM, followed immediately by the self-assembly of n-alkanethiol ink molecules from solution. The feedback loop used to control the atomic force microscope tip position and displacement enables exquisite control of forces applied to the surface, ranging from pico to nanonewtons. To achieve high-resolution writing at the nanoscale, the writing speed, direction, and applied force need to be optimized. There are strategies for programing the tip translation, which will improve the uniformity, alignment, and geometries of nanopatterns written using open-loop feedback control. This article addresses the mechanics of automated nanografting and demonstrates results for various writing strategies when nanografting patterns of n-alkanethiol SAMs.

Morphology control of structured polymer brushes

The surface-initiated photopolymerization (SIPP) of vinyl monomers on structured self-assembled monolayers, as defined by two-dimensional (2D) initiator templates for polymer growth, is investigated. The 2D templates are prepared by electron-beam chemical lithography (EBCL) of 4'-nitro-4-mercaptobiphenyl (NBT) and chemical conversion to an asymmetric azo initiator (4'-azomethylmalonodinitrile-1,1'-biphenyl-4-thiol). Ex situ kinetic studies of the SIPP process reveal a linear increase in the thickness of the polymer layer with the irradiation/polymerization time. The effect of the applied electron dosage during the EBCL process upon the final thickness of the polymer layer is also studied. The correlation between the electron-induced conversion of the 4'-nitro to the 4'-amino group and the layer thickness of the resulting polymer brush indicates that the polymer-brush grafting density can be directly controlled by the EBCL process. NBT-based template arrays are used for the combinatorial study of the influence of the lateral structure size and the irradiation dosage on the morphology of the resulting polymer-brush layer. Analysis of the array topography reveals the dependence of the thickness of the dry polymer layer on both electron dosage and structure size. This unique combination of EBCL as a lithographic technique to locally manipulate the surface chemistry and SIPP to amplify the created differences allows the preparation of defined polymer-brush layers of controlled morphologies.

Bio-nanopatterning of Surfaces

Bio-nanopatterning of surfaces is a very active interdisciplinary field of research at the interface between biotechnology and nanotechnology. Precise patterning of biomolecules on surfaces with nanometre resolution has great potential in many medical and biological applications ranging from molecular diagnostics to advanced platforms for fundamental studies of molecular and cell biology. Bio-nanopatterning technology has advanced at a rapid pace in the last few years with a variety of patterning methodologies being developed for immobilising biomolecules such as DNA, peptides, proteins and viruses at the nanoscale on a broad range of substrates. In this review, the status of research and development are described, with particular focus on the recent advances on the use of nanolithographic techniques as tools for biomolecule immobilisation at the nanoscale. Present strengths and weaknesses, as well future challenges on the different nanolithographic bio-nanopatterning approaches are discussed.

Nanostructured polymer brushes

Nanopatterned polymer brushes with sub-50-nm resolution were prepared by a combination of electron-beam chemical lithography (EBCL) of self-assembled monolayers (SAMs) and surface-initiated photopolymerization (SIPP). As a further development of our previous work, selective EBCL was performed with a highly focused electron beam and not via a mask, to region-selectively convert a SAM of 4'-nitro-1,1'-biphenyl-4-thiol to defined areas of crosslinked 4'-amino-1,1'-biphenyl-4-thiol. These "written" structures were then used to prepare surface-bonded, asymmetric, azo initiator sites of 4'-azomethylmalonodinitrile-1,1'-biphenyl-4-thiol. In the presence of bulk styrene, SIPP amplified the primary structures of line widths from 500 to 10 nm to polystyrene structures of line widths 530 nm down to approximately 45 nm at a brush height of 10 or 7 nm, respectively, as measured by scanning electron microscopy and atomic force microscopy (AFM). The relative position of individual structures was within a tolerance of a few nanometers, as verified by AFM. At line-to-line spacings down to 50-70 nm, individual polymer brush structures are still observable. Below this threshold, neighboring structures merge due to chain overlap.

Supramolecular Microcontact Printing and Dip-Pen Nanolithography on Molecular Printboards

The transfer of functional molecules onto self-assembled monolayers (SAMs) by means of soft and scanning-probe lithographic techniques-microcontact printing (muCP) and dip-pen nanolithography (DPN), respectively-and the stability of the molecular patterns during competitive rinsing conditions were examined. A series of guests with different valencies were transferred onto beta-cyclodextrin- (beta-CD-) terminated SAMs and onto reference hydroxy-terminated SAMs. Although physical contact was sufficient to generate patterns on both types of SAMs, only molecular patterns of multivalent guests transferred onto the beta-CD SAMs were stable under the rinsing conditions that caused the removal of the same guests from the reference SAMs. The formation of kinetically stable molecular patterns by supramolecular DPN with a lateral resolution of 60 nm exemplifies the use of beta-CD-terminated SAMs as molecular printboards for the selective immobilization of printboard-compatible guests on the nanometer scale through the use of specific, multivalent supramolecular interactions. Electroless deposition of copper on the printboard was shown to occur selectively on the areas patterned with dendrimer-stabilized gold nanoparticles.

Biological nanostructures: platforms for analytical chemistry at the sub-zeptomolar level

The analysis and manipulation of molecules at the sub-zeptomolar level (i.e., from 1 to 600 molecules) remains the unconquered frontier of analytical chemistry. While some techniques offer sensitivity to single molecules, there are no established tools for the manipulation of such small quantities of material. Scanning probe lithography has begun to provide practicable means to manipulate biological organisation on length scales of 100 nm and less, and three promising approaches (dip-pen nanolithography, nanoshaving, and scanning near-field photolithography) are reviewed. Each offers extraordinary spatial resolution combined with the capability for use under ambient and, in some cases, fluid conditions. These techniques offer a multitude of strategies that may at last make the manipulation of handfuls of molecules--and perhaps single molecules--a practical possibility for the analytical chemist.

Effect of dissolution kinetics on feature size in dip-pen nanolithography

We have investigated the effects of humidity, tip speed, and dwell time on feature size during dip pen nanolithography. Our results indicate a transition between two distinct deposition regimes occurs at a dwell time independent of humidity. While feature size increases with humidity, the relative increase is independent of dwell time. The results are described by a model that accounts for detachment and reattachment at the tip. The model suggests that, at short dwell times (high speed), the most important parameter controlling the feature size is the activation energy for thiol detachment.