Transfer-printing of highly aligned DNA nanowires

Intrinsic Flexibility beyond the Highly Ordered DNA Tetrahedron: An Integrative Spectroscopic and Molecular Dynamics Approach

Since the introduction of DNA-based architectures, in the past decade, DNA tetrahedrons have aroused great interest. Applications of such nanostructures require structural control, especially in the perspective of their possible functionalities. In this work, an integrated approach for structural characterization of a tetrahedron structure is proposed with a focus on the fundamental biophysical aspects driving the assembly process. To address such an issue, spin-labeled DNA sequences are chemically synthesized, self-assembled, and then analyzed by Continuous-Wave (CW) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopy. Interspin distance measurements based on PELDOR/DEER techniques combined with molecular dynamics (MD) thus revealed unexpected dynamic heterogeneity and flexibility of the assembled structures. The observation of flexibility in these ordered 3D structures demonstrates the sensitivity of this approach and its effectiveness in accessing the main dynamic and structural features with unprecedented resolution.

Tuning the fast generation of luminescent silver nanodots on a surface

Silver nanodots, predominantly a near-IR emitter, can be instantly generated on a surface by silver cluster transfer. Kinetic trapping of ssDNA molecules on the surface limits the reorganization of the resulting silver nanodots for other silver nanodot emitters. Adjusting the freedom of the adsorbed ssDNA can tune the generation of various silver nanodots on the surface.

DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications

DNA molecular combing is a technique that stretches thousands of long individual DNA molecules (up to 10 Mbp) into a parallel configuration on surface. It has previously been proposed to sequence these molecules by synthesis. However, this approach poses two critical challenges: 1-Combed DNA molecules are overstretched and therefore a nonoptimal substrate for polymerase extension. 2-The combing surface sterically impedes full enzymatic access to the DNA backbone. Here, we introduce a novel approach that attaches thousands of molecules to a removable surface, with a tunable stretching factor. Next, we dissolve portions of the surface, leaving the DNA molecules suspended as 'bridges'. We demonstrate that the suspended molecules are enzymatically accessible, and we have used an enzyme to incorporate labeled nucleotides, as predicted by the specific molecular sequence. Our results suggest that this novel platform is a promising candidate to achieve high-throughput sequencing of Mbp-long molecules, which could have additional genomic applications, such as the study of other protein-DNA interactions.

Putting DNA to Work as Generic Polymeric Materials

DNA is a true polymer that stores the genetic information of an organism. With its amazing biological and polymeric characteristics, DNA has been regarded as a universal building block for the construction of diverse materials for real-world applications. Through various approaches including ligation, polymerization, chemical crosslinking, and physical crosslinking, both pure and hybrid DNA gels have been developed as generic materials. This Review discusses recent advances in the construction of DNA-based networks without considering any of DNA's genetic properties. In addition, we highlight the biomedical and non-biomedical applications of DNA as generic materials. Owing to the superb molecular recognition, self-assembly, and responsiveness of DNA, a mushrooming number of DNA materials with various properties have been developed for general utilization.

Role of mechanical flow for actin network organization

The major cytoskeletal protein actin forms complex networks to provide structural support and perform vital functions in cells. In vitro studies have revealed that the structure of the higher-order actin network is determined primarily by the type of actin binding protein (ABP). By comparison, there are far fewer studies about the role of the mechanical environment for the organization of the actin network. In particular, the duration over which cells reorganize their shape in response to functional demands is relatively short compared to the in vitro protein polymerization time, suggesting that such changes can influence the actin network formation. We hypothesize that mechanical flows in the cytoplasm generated by exogenous and endogenous stimulation play a key role in the spatiotemporal regulation of the actin architecture. To mimic cytoplasmic streaming, we generated a circulating flow using surface acoustic wave in a microfluidic channel and investigated its effect on the formation of networks by actin and ABPs. We found that the mechanical flow affected the orientation and thickness of actin bundles, depending on the type and concentration of ABPs. Our computational model shows that the extent of alignment and thickness of actin bundle are determined by the balance between flow-induced drag forces and the tendency of ABPs to crosslink actin filaments at given angles. These results suggest that local intracellular flows can affect the assembly dynamics and morphology of the actin cytoskeleton. STATEMENT OF SIGNIFICANCE: Spatiotemporal regulation of actin cytoskeleton structure is essential in many cellular functions. It has been shown that mechanical cues including an applied force and geometric boundary can alter the structural characteristics of actin network. However, even though the cytoplasm accounts for a large portion of the cell volume, the effect of the cytoplasmic streaming flow produced during cell dynamics on actin network organization has not been reported. In this study, we demonstrated that the mechanical flow exerted during actin network organization play an important role in determining the orientation and dimension of actin bundle network. Our result will be beneficial in understanding the mechanism of the actin network reorganization occurred during physiological and pathological processes.

Chip-scale alignment of long DNA nanofibers on a patterned self-assembled monolayer

Controlled alignment of long DNA nanofibers is challenging. This communication reports a method to align human genomic DNA with nearly unlimited length using lithographically produced micro-patterns of self-assembled monolayers (SAMs) with positively charged terminal groups. The micro-patterns act as local DNA reservoirs to supply DNAs for nanofiber formation, and can also stretch and align DNA nanofibers to form an ordered array by controlling the dewetting profile. By reducing the size and inter-patch distance of a micro-patch, a nearly uniform array of long DNA nanofibers can be patterned over a large area. A controlled motion of a DNA containing droplet allows for free patterning of DNA nanofibers and production of complex structures without a transfer process. Bending of DNA nanofibers due to local distortion of the contact line bridges more adjacent micro-patches and increases the chance of producing continuous nanofibers. The interplay between surface tension and electrostatic attraction of positively charged micro-patterns allows the production of long DNA nanofibers in a simple yet powerful way.

Collapse of chain anadiplosis-structured DNA nanowires for highly sensitive colorimetric assay of nucleic acids

In this work, we have proposed a chain anadiplosis-structured DNA nanowire by using two well-defined assembly strands (AS1 and AS2).

Molecular threading: mechanical extraction, stretching and placement of DNA molecules from a liquid-air interface

We present “molecular threading”, a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules. DNA is stretched into air at a liquid-air interface, and can be subsequently deposited onto a dry substrate isolated from solution. The design of an apparatus used for molecular threading is presented, and fluorescence and electron microscopies are used to characterize the angular distribution, straightness, and reproducibility of stretched DNA deposited in arrays onto elastomeric surfaces and thin membranes. Molecular threading demonstrates high straightness and uniformity over length scales from nanometers to micrometers, and represents an alternative to existing DNA deposition and linearization methods. These results point towards scalable and high-throughput precision manipulation of single-molecule polymers.

Transfer printing techniques for materials assembly and micro/nanodevice fabrication

Transfer printing represents a set of techniques for deterministic assembly of micro-and nanomaterials into spatially organized, functional arrangements with two and three-dimensional layouts. Such processes provide versatile routes not only to test structures and vehicles for scientific studies but also to high-performance, heterogeneously integrated functional systems, including those in flexible electronics, three-dimensional and/or curvilinear optoelectronics, and bio-integrated sensing and therapeutic devices. This article summarizes recent advances in a variety of transfer printing techniques, ranging from the mechanics and materials aspects that govern their operation to engineering features of their use in systems with varying levels of complexity. A concluding section presents perspectives on opportunities for basic and applied research, and on emerging use of these methods in high throughput, industrial-scale manufacturing.

Ordered arrays of native chromatin molecules for high-resolution imaging and analysis

Individual chromatin molecules contain valuable genetic and epigenetic information. To date, there have not been reliable techniques available for the controlled stretching and manipulation of individual chromatin fragments for high-resolution imaging and analysis of these molecules. We report the controlled stretching of single chromatin fragments extracted from two different cancerous cell types (M091 and HeLa) characterized through fluorescence microscopy and atomic force microscopy (AFM). Our method combines soft lithography with molecular stretching to form ordered arrays of more than 250,000 individual chromatin fragments immobilized into a beads-on-a-string structure on a solid transparent support. Using fluorescence microscopy and AFM, we verified the presence of histone proteins after the stretching and transfer process.

Fabrication of ultra-fine nanostructures using edge transfer printing

The exploration of new methods and techniques for application in diverse fields, such as photonics, microfluidics, biotechnology and flexible electronics is of increasing scientific and technical interest for multiple uses over distance of 10-100 nm. This article discusses edge transfer printing--a series of unconventional methods derived from soft lithography for nanofabrication. It possesses the advantages of easy fabrication, low-cost and great serviceability. In this paper, we show how to produce exposed edges and use various materials for edge transfer printing, while nanoskiving, nanotransfer edge printing and tunable cracking for nanogaps are introduced. Besides this, different functional materials, such as metals, inorganic semiconductors and polymers, as well as localised heating and charge patterning, are described here as unconventional "inks" for printing. Edge transfer printing, which can effectively produce sub-100 nm scale ultra-fine structures, has broad applications, including metallic nanowires as nanoelectrodes, semiconductor nanowires for chemical sensors, heterostructures of organic semiconductors, plasmonic devices and so forth.

Synthesis and characteristics of NH2-functionalized polymer films to align and immobilize DNA molecules

We developed a method to use NH2-functionalized polymer films to align and immobilize DNA molecules on a Si substrate. The plasma-polymerized cyclohexane film was deposited on the Si substrate according to the radio frequency plasma-enhanced chemical vapor deposition method using a single molecular precursor, and it was then treated by the dielectric barrier discharge method in a nitrogen environment under atmospheric pressure. Changes in the chemistry of the surface functional groups were studied using X-ray photoelectron spectroscopy and Fourier transformed infrared spectroscopy. The wettability of the surfaces was examined using dynamic contact angle measurements, and the surface morphology was evaluated using atomic force microscopy.We utilized a tilting method to align λ-DNA molecules that were immobilized by the electrostatic interaction between the amine groups in NH2-functionalized polymer films and the phosphate groups in the DNA. The DNA was treated with positively charged gold nanoparticles to make a conductive nanowire that uses the DNA as a template. We observed that the NH2-functionalized polymer film was useful for aligning and immobilizing the DNA, and thus the DNA-templated nanowires.

Synthesis and bioanalytical applications of specific-shaped metallic nanostructures: a review

Many successful synthesis routes for producing different shapes of metallic nanostructures, including sphere, rod, cube, and hollow shapes, have been developed in the past few decades. Many applications using these nanostructures have been studied because the outstanding properties of the nanostructures are not exhibited by their bulk-state counterparts. This review paper reports some recent developments in clinical and biosensor applications. The first part focused on the synthesis methods of metallic nanostructures having various shapes along with their optical properties. The second and third part is an introduction of the gold nanoparticle assemblies and arrays, explaining the conjugation methods of metallic nanostructures with biological entities. The final part reviews on the recent bioanalytical applications using various shapes of metallic nanostructures.

Selective formation of a latticed nanostructure with the precise alignment of DNA-templated gold nanowires

A very efficient method is introduced to selectively align and uniformly separate λ-DNA molecules and thus DNA-templated gold nanowires (AuNW's) using a combination of molecular combing and surface-patterning techniques. By the method presented in this work, it is possible to obtain parallel and latticed nanostructures consisting of DNA molecules and thus DNA-templated AuNW's aligned at 400 nm intervals. DNA-templated AuNW's are uniformly formed with an average height of 2.5 nm. This method is expected to hold potential for the integration of nanosized building blocks applicable to nanodevice construction.

Novel DNA materials and their applications

The last two decades have witnessed the exponential development of DNA as a generic material instead of just a genetic material. The biological function, nanoscale geometry, biocompatibility, biodegradability, and molecular recognition capacity of DNA make it a promising candidate for the construction of novel functional nanomaterials. As a result, DNA has been recognized as one of the most appealing and versatile nanomaterial building blocks. Scientists have used DNA in this way to construct various amazing nanostructures, such as ordered lattices, origami, supramolecular assemblies, and even three-dimensional objects. In addition, DNA has been utilized as a guide and template to direct the assembly of other nanomaterials including nanowires, free-standing membranes, and crystals. Furthermore, DNA can also be used as structural components to construct bulk materials such as DNA hydrogels, demonstrating its ability to behave as a unique polymer. Overall, these novel DNA materials have found applications in various areas in the biomedical field in general, and nanomedicine in particular. In this review, we summarize the development of DNA assemblies, describe the innovative progress of multifunctional and bulk DNA materials, and highlight some real-world nanomedical applications of these DNA materials. We also show our insights throughout this article for the future direction of DNA materials.

Micrometer-sized DNA-single-fluorophore-DNA supramolecule: synthesis and single-molecule characterization

The synthesis of single-fluorophore-bis(micrometer-sized DNA) triblock supramolecules and the optical and structural characterization of the construct at the single-molecule level is reported. A fluorophore-bis(oligodeoxynucleotide) triblock is synthesized via the amide-coupling reaction. Subsequent protocols of DNA hybridization/ligation are developed to form the supramolecular triblock structure with lambda-DNA fragments on the micrometer length scale. The successful synthesis of the micrometer-sized DNA-single-fluorophore-DNA supramolecule is confirmed by agarose gel electrophoresis with fluorescence imaging under UV excitation. Single triblock structures are directly imaged by combined scanning force microscopy and single-molecule fluorescence microscopy, and provide unambiguous confirmation of the existence of the single fluorophore inserted in the middle of the long DNA. This type of triblock structure is a step closer to providing a scaffold for single-molecule electronic devices after metallization of the DNAs.

Replica mold for nanoimprint lithography from a novel hybrid resin

The use of durable replica molds with high feature resolution has been proposed as an inexpensive and convenient route for manufacturing nanostructured materials. A simple and fast duplication method, involving the use of a master mold to create durable polymer replicas as imprinting molds, has been demonstrated using both UV- and thermal nanoimprinting lithography (NIL). To obtain a high-durability replicating material, a dual UV/thermal-curable, organic-inorganic hybrid resin was synthesized using a sol-gel-based combinatorial method. The cross-linked hybrid resin exhibited high transparency to UV light and resistance to organic solvents. Molds made of this material showed good mechanical properties (Young's modulus=1.76 GPa) and gas permeability. The low viscosity of the hybrid resin (approximately 29 cP) allowed it to be easily transferred to relief nanostructures on transparent glass substrates using UV-NIL at room temperature and low pressure (0.2 MPa) over a relatively short time (80 s). A low surface energy release agent was successfully coated onto the hybrid mold surface without destroying the imprinted nanostructures, even after O2 plasma treatment. Nanostructures with feature sizes down to 80 nm were successfully reproduced using these molds in both UV- and thermal-NIL processes. After repeating 10 imprinting cycles at relatively high temperature and pressure, no detectable collapse or contamination of the replica surface was observed. These results indicate that the hybrid molds could tolerate repeated UV- and thermal-NIL processes.

Fabrication of DNA nanowires by orthogonal self-assembly and DNA intercalation on a Au patterned Si/SiO2 surface

A novel Ru complex bearing both an acridine group and anchoring phosphonate groups was immobilized on a surface in order to capture double-stranded DNAs (dsDNAs) from solution. At low surface coverage, the atomic force microscopy (AFM) image revealed the "molecular dot" morphology with the height of the Ru complex ( approximately 2.5 nm) on a mica surface, indicating that four phosphonate anchor groups keep the Ru complex in an upright orientation on the surface. Using a dynamic molecular combing method, the DNA capture efficiency of the Ru complex on a mica surface was examined in terms of the effects of the number of molecular dots and surface hydrophobicity. The immobilized surface could capture DNAs; however, the optimal number of molecular dots on the surface as well as the optimal pull-up speed exist to obtain the extended dsDNAs on the surface. Applying this optimal condition to a Au-patterned Si/SiO 2 (Au/SiO 2) surface, the Au electrode was selectively covered with the Ru complex by orthogonal self-assembly of 4-mercaptbutylphosphonic acid (MBPA), followed by the formation of a Zr (4+)-phosphonate layer and the Ru complex. At the same time, the remaining SiO 2 surface was covered with octylphosphonic acid (OPA) by self-assembly. The selective immobilization of the Ru complex only on the Au electrode was identified by time-of-flight secondary-ion mass spectrometry (TOF-SIMS) imaging on the chemically modified Au/SiO 2 surface. The construction of DNA nanowires on the Au/SiO 2 patterned surface was accomplished by the molecular combing method of the selective immobilized Ru complex on Au electrodes. These interconnected nanowires between Au electrodes were used as a scaffold for the modification of Pd nanoparticles on the DNA. Furthermore, Cu metallization was achieved by electroless plating of Cu metal on a priming of Pd nanoparticles on the Pd-covered DNA nanowires. The resulting Cu nanowires showed a metallic behavior with relatively high resistance.

One-dimensional SAMs of (12-pyrrol-1-yl-dodecyl)-phosphonic acid templated by polyelectrolyte molecules

We present a novel method for the fabrication of one-dimensional (1-D) self-assembled monolayers and multilayers (SAMs) of (12-pyrrol-1-yl-dodecyl)-phosphonic acid (Py-DPA) on various polar surfaces using polyelectrolyte nanostructures as positive templates. Particularly, we demonstrate that (i) patterns of aligned 1-D polycation structures on a poly(dimethylsiloxane) stamp can be prepared by moving a droplet of polycation solution along the surface; (ii) these patterns can be used as templates for the ordered assembly of Py-DPA in water where Py-DPA carries a charge opposite to the charge of the template; and (iii) Py-DPA SAMs can then be transferred onto mica or silicon wafers by a printing process. These nanostructures with a polymerizable pyrrole headgroup might be useful for the creation of electrically conductive patterns of conjugated polymers.

Alignment of a conjugated polymer onto amyloid-like protein fibrils

The amyloid-like fibril is a biomolecular nanowire template of very high stability. Here we describe the coordination of a conjugated polyelectrolyte, poly(thiophene acetic acid) (PTAA), to bovine insulin fibrils with widths of <10 nm and lengths of up to more than 10 microm. Fibrils complexed with PTAA are aligned on surfaces through molecular combing and transfer printing. Single-molecule spectroscopy techniques are applied to chart spectral variation in the emission of these wires. When these results are combined with analysis of the polarization of the emitted light, we can conclude that the polymer chains are preferentially aligned along the fibrillar axis.

Methods of stretching DNA molecules using flow fields

Using fluorescence microscopy, we compare the degree of adsorption and stretching of DNA onto surfaces achieved by published stretching methods that use fluid flow: molecular combing, spin-stretching, and air-blowing. Molecular combing uses a receding meniscus to stretch out and deposit the DNA onto a hydrophobic surface. In spin-stretching, we find that the effect of radial hydrodynamic flow created by the centrifugal force of the rotating disk is minimal and that the DNA is stretched out on a hydrophobic substrate by the moving meniscus. In air-blowing, a jet of gas pushes liquid across a substrate, depositing stretched DNA molecules along the way. In our study, DNA molecules either combed or spin-stretched onto hydrophobic surfaces stretch to a greater degree than those that are air-blown; fewer are deposited at pH 8.0 than at lower pH, apparently because at pH 8.0 DNA adhesion occurs primarily only at the DNA extremities and so avoids trapped regions of incompletely stretched DNA, with the side effect that more molecules avoid adhesion altogether. We find by high-speed video microscopy that there is complex droplet deformation and motion during air-blowing, which complicates the deposition and stretching process, leading to radial alignment. Our results are a first step toward understanding and optimizing the various proposed methods of DNA stretching and anchoring onto surfaces, which is important in studying their interactions with proteins.

Soft lithographic printing of patterns of stretched DNA and DNA/electronic polymer wires by surface-energy modification and transfer

Aligned and stretched lambda DNA is directed to specific locations on solid substrates. Surface-energy modification of glass substrates by using patterned polydimethylsiloxane (PDMS) stamps is used to direct DNA onto the surface-energy-modified micrometer-scale pattern through molecular combing. As an alternative, patterned and nonpatterned PDMS stamps modified with polymethylmethacrylate (PMMA) are utilized to direct the stretched DNA to the desired location and the results are compared. The DNA is elongated through molecular combing on the stamp and transfer printed onto the surfaces. PMMA-modified stamps show a more defined length of the stretched DNA, as compared to bare PDMS stamps. A combination of these two methods is also demonstrated. As an application example, transfer printing of DNA decorated with a semiconducting conjugated polyelectrolyte is shown. The resulting patterned localization of stretched DNA can be utilized for functional nanodevice structures, as well as for biological applications.

Simple method for the stretching and alignment of single adsorbed synthetic polycations

Spin-coating of isolated positively charged macromolecules onto mica in the presence of octylamine was found to be a simple and general method of stretching and aligning the macromolecular chains. The contour length and molar mass for the stretched macromolecules can be directly measured by atomic force microscopy, which makes this method a very useful analytical tool. Moreover, the molecular height is increased by co-deposition with octylamine, which drastically improves the molecular resolution and allows even ultrathin polycations to be visualized. The reason for the key role of the octylamine is found in the formation of an ultrathin liquidlike alkylamine film, which reduces the surface energy of mica and weakens the interactions between the surface and the charged macromolecules.

Guided alignment and positioning of single DNA molecules by a structured contact line on a block copolymer surface

A nanostructured dynamical contact line is generated when the meniscus of a droplet of water solution is moving on the structured surface of a thin film of a block copolymer of poly(styrene-b-methyl methacrylate) (PS-b-PMMA) because of the difference in the water contact angles on PS and PMMA. Such a structured receding contact line extends DNA molecules as in the molecular combing process. More importantly, it aligns DNA molecules following the position and orientation of the PMMA domains on the surface. The driving force of this phenomenon is discussed as the lateral motion of the locally modified contact line.