DC electric-field-induced DNA stretching for AFM and SNOM studies

Electro-optical Study of the Anomalous Rotational Diffusion in Polymer Solutions

Brownian diffusion of spherical nanoparticles is usually exploited to ascertain the rheological properties of complex media. However, the behavior of the tracer particles is affected by a number of phenomena linked to the interplay between the dynamics of the particles and polymer coils. For this reason, the characteristic lengths of the dispersed entities, depletion phenomena, and the presence of sticking conditions have been observed to affect the translational diffusion of the probes. On the other hand, the retardation effect of the host fluid on the rotational diffusion of nonspherical particles is less understood. We explore the possibility of studying this phenomenon by analyzing the electro-orientation of the particles in different scenarios in which we vary the ratio between the particle and polymer characteristic size, and the geometry of the particles, including both elongated and oblate shapes. We find that the Stokes-Einstein relation only applies if the radius of gyration of the polymer is much shorter than the particle size and when some repulsive interaction between both is present.

Polymer-induced orientation of nanowires under electric fields

The controlled orientation of metallic wires inside a polymeric medium can enhance desired properties of the composites, such as the electrical conductivity or the optical transmittance. In this work, we study silver nanowire orientation in semidilute suspensions of DNA and find an intriguing effect: under the application of low-frequency AC electric fields with moderate amplitude, the DNA coils can provoke the orientation of the wires in solution. The phenomenon is entirely induced by the polymer, when it is deformed by the application of an electric field. This effect is explained using computer simulations based on excluded-volume interactions. Moreover, we experimentally show that such a behaviour is not exclusive of silver nanowire-DNA suspensions, but rather occurs for other particle-polymer systems. This phenomenon can be taken advantage of to achieve strong orientation of particles otherwise insensitive to electric fields.

Improved DNA straightening and attachment via optimal Mg2+ ionic bonding under electric field for AFM imaging in liquid phase

In this research, a novel method is proposed to improve DNA straightening under an applied electric field to facilitate imaging in a liquid phase by modifying the substrate with varying Mg²⁺ ion concentrations. A two-dimensional network of DNA structures was successfully stretched on Mg²⁺-modified mica substrates under a DC electric field (1 V, 1 A) and imaged in gaseous and aqueous phases by atomic force microscopy. The results revealed that an optimum concentration of Mg²⁺ ion (4.17 μmol/ml) allowed DNA straightening under an electric field, thus facilitating its imaging in the liquid phase. Furthermore, DNA adhesion under different concentrations of Mg²⁺ was measured and a maximum adhesion force of 76.19 pN was achieved. This vital work has great potential in gene knockout and targeted gene editing.

Microarrays and single molecules: an exciting combination

Biomolecules positioned at interfaces have spawned many applications in bioanalysis, biophysics, and cell biology. This Highlight describes recent developments in the research areas of protein and DNA arrays, and single-molecule sensing. We cover the ultrasensitive scanning of conventional microarrays as well as the generation of arrays composed of individual molecules. The combination of these tools has improved the detection limits and the dynamic range of microarray analysis, helped develop powerful single-molecule sequencing approaches, and offered biophysical examination with high throughput and molecular detail. The topic of this Highlight integrates several disciplines and is written for interested chemists, biophysicists and nanotechnologists.

Review: recent advances and current challenges in scanning probe microscopy of biomolecular surfaces and interfaces

The introduction of scanning probe microscopy (SPM) techniques revolutionized the field of condensed matter science by allowing researchers to probe the structure and composition of materials on an atomic scale. Although these methods have been used to make molecular- and atomic-scale measurements on biological systems with some success, the biophysical sciences remain on the cusp of a breakthrough with SPM technologies similar in magnitude to that experienced by fields related to solid-state surfaces and interfaces. Numerous challenges arise when attempting to connect biological molecules that are often delicate, dynamic, and complex with the experimental requirements of SPM techniques. However, there are a growing number of studies in which SPM has been successfully used to achieve subnanometer resolution measurements in biological systems where carefully designed and prepared samples have been paired with appropriate SPM techniques. We review significant recent innovations in applying SPM techniques to biological molecules, and highlight challenges that face researchers attempting to gain atomic- and molecular-level information of complex biomolecular structures.

Increased graphitization in electrospun single suspended carbon nanowires integrated with carbon-MEMS and carbon-NEMS platforms

Single suspended carbon nanowires (CNWs) integrated on carbon-MEMS (CMEMS) structures are fabricated by electrospinning of SU-8 photoresist followed by pyrolysis. These monolithic CNW-CMEMS structures enable fabrication of very high aspect ratio CNWs of predefined length. The CNWs thus fabricated display core-shell structures having a graphitic shell with a glassy carbon core. The electrical conductivity of these CNWs is increased by about 100% compared to glassy carbon as a result of enhanced graphitization. We suggest some tunable fabrication and pyrolysis parameters that may improve graphitization in the resulting CNWs, making them a good replacement for several carbon nanostructure-based devices.

A silanized mica substrate suitable for high-resolution fiber FISH analysis by scanning near-field optical/atomic force microscopy

We applied a novel silanized mica substrate with an extremely flat surface constructed according to Sasou et al. (Langmuir 19, 9845-9849 (2003)) to high-resolution detection of a specific gene on a DNA fiber by scanning near-field optical/atomic force microscopy (SNOM/AFM). The interaction between the substrate and fluorescence-dye conjugated peptide nucleic acid (PNA) probes, which causes fluorescence noise signal, was minimal. By using the substrate, we successfully obtained a fluorescence in situ hybridization signal from the ea47 gene on a λphage DNA labeled with an Alexa 532-conjugated 15-base PNA probe. As the results, no fluorescence noises were observed, indicating that the surface adsorbed almost none of the PNA probe. The combination of the substrate and SNOM/AFM is an effective tool for visualizing DNA sequences at nanometer-scale resolution.

Visualization of cellular DNA crosslinks by atomic force microscopy

Cellular DNA crosslinks are a type of DNA damage induced by toxic chemicals or high-energy radiation. If damaged DNA is not rapidly repaired, cells will die or mutate. To evaluate the types of DNA damage and their influence on vital cell activities, it is necessary to be able to detect DNA crosslinks. To date, indirect methods such as alkaline elution, potassium chloride-sodium dodecyl sulfate assay and comet assay have been used to detect DNA damage. Direct morphological observation, on the other hand, may be a useful tool to differentiate the types of DNA damage. In this report, atomic force microscopy (AFM) has been employed to visualize the breakage and crosslinking of cellular DNA strands in cells treated with formaldehyde and hydrogen peroxide. Our results showed that toxic chemical-induced crosslinking of cellular DNA occurred in a dose-dependent manner. DNA conglomerates were observed with high concentrations of formaldehyde, and the AFM observations were consistent with those of a comet assay. Our experiments demonstrate that AFM is an efficient method to differentiate the types of DNA damage. SCANNING 31: 75-82, 2009. (c) 2009 Wiley Periodicals, Inc.

DNA deposition on carbon electrodes under controlled dc potentials

The native calf-thymus DNA molecule fully dispersed in solution was deposited onto highly oriented pyrolytic graphite, carbon fiber column and disk electrodes under controlled dc potentials. X-ray photoelectron spectroscopy, atomic force microscopy and electrochemical investigations indicated that network structures of DNA could be formed on various carbon electrode surfaces resulting in significant surface enlargement. The conformation, conductivity and stability of the deposited DNA layer largely depended on the concentration of the DNA deposition solution, the applied dc potential and the mode of electric field. The optimal condition for deposition of the DNA on carbon fiber disk electrode was determined as a deposition potential of 1.8 +/- 0.3 V versus 50 mM NaCl-Ag/AgCl and a deposition DNA solution of 0.1 mg ml(-1). Under this condition, the DNA was covalently bonded on the electrode surface forming a three-dimensional modified layer, generating a 500-fold enlarged effective electrode surface area and similarly enlarged current sensitivity for redox species, such as Co(phen)3(3+). A possible mechanism for the formation of DNA networks is proposed.

Dynamics of single polymers in a stagnation flow induced by electrokinetics

An electrokinetics-induced stagnation flow was created inside a microscale cross-channel. Compared to hydrodynamic-induced microfluidics, this flow system can be readily assembled and the operation is very simple due to a low pressure drop. Through image analysis, a fairly homogeneous, two-dimensional elongational flow was observed. The initial conformation of DNA molecules and residence time inside the flow field play important roles in determining the extent of DNA stretching. A coarse-grain molecular simulation agrees reasonably well with experimental observations.

Method for patterning stretched DNA molecules on mica surfaces by soft lithography

Lambda DNA was stretched and patterned on mica surface using soft lithography. A highly diluted solution of amino propyl trimethoxy silane in hexane was deposited on a line patterned polydimethylsiloxane (PDMS) stamp. The functionalized stamp was then used to pick up DNA by molecular combing while the line patterns are parallel to the liquid surface. The stamp was then microcontact printed on freshly cleaved mica. We successfully obtained stretched DNA pattern on mica surface. DNA was found to be stretched in patterns perpendicular to those carved on the stamp. The stretched DNA population was large enough to be used for molecular biology mapping studies. Furthermore, the possibility of locating stretched DNA molecules in the desired position by stamping makes this method a good candidate for assembling non-semiconductor molecular devices.