The effect of the number of parallel DNA molecules on electric charge transport through 'standing DNA'

DNA-Based Conductors: From Materials Design to Ultra-Scaled Electronics

Photolithography has been the foundational fabrication paradigm in current high-performance electronics. However, due to the limitation in fabrication resolution, scaling beyond a 20-nm critical dimension for metal conductors presents a significant challenge for photolithography. Structural DNA nanotechnology emerges as a promising alternative to photolithography, allowing for the site-specific assembly of nano-materials at single-molecule resolution. Substantial progresses have been achieved in the ultra-scaled DNA-based conductors, exhibiting novel transport characteristics and small critical dimensions. This review highlights the structure-transport property relationship for various DNA-based conductors and their potential applications in quantum /semiconductor electronics, going beyond the conventional scope focusing mainly on the shape diversity of DNA-templated metals. Different material synthesis methods and their morphological impacts on the conductivities are discussed in detail, with particular emphasis on the conducting mechanisms, such as insulating, metallic conducting, quantum tunneling, and superconducting. Furthermore, the ionic gating effect of self-assembled DNA structures in electrolyte solutions is examined. This review also suggests potential solutions to address current challenges in DNA-based conductors, encouraging multi-disciplinary collaborations for the future development of this exciting area.

Advances in Synthesis and Measurement of Charge Transport in DNA-Based Derivatives

Charge transport through molecular structures is interesting both scientifically and technologically. To date, DNA is the only type of polymer that transports significant currents over distances of more than a few nanometers in individual molecules. For molecular electronics, DNA derivatives are by far more promising than native DNA due to their improved charge-transport properties. Here, the synthesis of several unique DNA derivatives along with electrical characterization and theoretical models is surveyed. The derivatives include double stranded poly(G)-poly(C) DNA molecules, four stranded G4-DNA, metal-DNA hybrid molecular wires, and other DNA molecules that are modified either at the bases or at the backbone. The electrical characteristics of these nanostructures, studied experimentally by electrostatic force microscopy, conductive atomic force microscopy, and scanning tunneling microscopy and spectroscopy, are reviewed.

Probe Microscopic Studies of DNA Molecules on Carbon Nanotubes

Hybrids of DNA and carbon nanotubes (CNTs) are promising nanobioconjugates for nanobiosensors, carriers for drug delivery, and other biological applications. In this review, nanoscopic characterization of DNA-CNT hybrids, in particular, characterization by scanning probe microscopy (SPM), is summarized. In many studies, topographical imaging by atomic force microscopy has been performed. However, some researchers have demonstrated advanced SPM operations in order to maximize its unique and valuable functions. Such sophisticated approaches are attractive and will have a significant impact on future studies of DNA-CNT hybrids.

Dynamic light scattering on bioconjugated laser generated gold nanoparticles

Gold nanoparticles (AuNPs) conjugated to DNA are widely used for biomedical targeting and sensing applications. DNA functionalization is easily reached on laser generated gold nanoparticles because of their unique surface chemistry, not reproducible by other methods. In this context, we present an extensive investigation concerning the attachment of DNA to the surface of laser generated nanoparticles using Dynamic Light Scattering and UV-Vis spectroscopy. The DNA conjugation is highlighted by the increase of the hydrodynamic radius and by the UV-Vis spectra behavior. Our investigation indicates that Dynamic Light Scattering is a suitable analytical tool to evidence, directly and qualitatively, the binding between a DNA molecule and a gold nanoparticle, therefore it is ideal to monitor changes in the conjugation process when experimental conditions are varied.

Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structures

Verification by imaging of the structure of 3D DNA constructs, both bare and conjugated to metal nanoparticles, is challenging. We demonstrate here two transmission electron microscopy (TEM) based methods to distinguish between fully formed tetrahedra, synthesized from DNA conjugated with gold nanoparticles (GNPs) at their vertices, and structures which are only partially formed. When deposited on a surface, fully formed tetrahedra are expected to retain their 3D pyramidal structure, while partially formed structures are expected to form a 2D structure. The first method by which 3D and 2D structures were distinguished was imaging them at different defocusing values. While for 2D structures all the four GNPs acquire Fresnel fringes at the same defocusing value, for 3D structures at least one particle is at a different plane with respect to the others, and so it acquires Fresnel fringes at a different defocusing value. The second method we show is imaging of the structures at different angles. While a single TEM image gives only a 2D projection of the structure, by combining information achieved from imaging at several tilting angles one may verify the structural construct.

Identifying diversity in nanoscale electrical break junctions

The realization of molecular-scale electronic devices will require the development of novel strategies for controlling electrical properties of metal/molecule/metal junctions, down to the single molecule level. Here, we show that it is possible to exert chemical control over the formation of metal/molecule...molecule/metal junctions in which the molecules interact by pi-stacking. The tip of an STM is used to form one contact, and the substrate the other; the molecules are conjugated oligophenyleneethynylenes (OPEs). Supramolecular pi-pi interactions allow current to flow through the junction, but not if bulky tert-butyl substituents on the phenyl rings prevent such interactions. For the first time, we find evidence that pi-stacked junctions can form even for OPEs with two thiol contacts. Furthermore, we find evidence for metal|molecule|metal junctions involving oligophenyleneethynylene monothiols, in which the second contact must be formed by the interaction of the pi-electrons of the terminal phenyl ring with the metal surface.

Rapid synthesis of DNA-functionalized gold nanoparticles in salt solution using mononucleotide-mediated conjugation

DNA functionalized gold-nanoparticles (Au-nps) have been broadly used as labeling reagents in the development of molecular diagnostics as well as building blocks in nanotechnology. Conventional methods for the synthesis of DNA functionalized Au-nps require long incubation, typically overnight, and delicate control of the ionic strength to compensate for the charge repulsion between the nanoparticles surface and the DNA strands, which generally affect the stability of the nanoparticles and the DNA loading density. In this study, we present a novel mononucleotide-mediated conjugation approach to synthesize DNA-functionalized Au-nps within 4 h in a high ionic strength environment. Au-nps covered with a thermally tunable stabilization layer through mononucleotide adsorption were shown to readily conjugate with thiol-DNAs in 0.1 M NaCl solution upon heating. Monitoring this mononucleotide-mediated conjugation reaction through dynamic light scattering and UV-vis spectroscopy demonstrated the formation of stable DNA/Au-nps conjugates. The resulting conjugates, as characterized by fluorescence spectroscopy, are loaded by approximately 80 strands per particle, comparable to the DNA loading density of current approaches. The general applicability of this approach was further verified in a nanoparticle-bound DNA hybridization test. Our results show that mononucleotide-mediated thermal conjugation is an attractive alternative that allows temperature-controlled and salt-enhanced functionalization of gold nanoparticles with DNAs in just a few hours.

A reliable confirmation of the chemical structure of synthetic oligonucleotides: detection of active protons in DNA oligomers by low-temperature FT infrared spectroscopy

Cooling the samples allowed us to characterize solid oligonucleotides such as dimers, trimers and pentamers of cytidine, for the first time, in the IR range of the out-of-plane bending molecular modes (1000-400 cm(-1)) at 20K. Especially interesting are the narrow IR bands of the out-of-plane bending nu(4) NH(2) proton mode, which are apparently invisible at room temperature. This unequivocally defined and well-resolved NH(2) bending band should provide important information on the exact chemical form and hydrogen bonding interactions of cytidine amine groups. As such, this unique IR spectroscopy is suggested as a practical analytical tool to validate and characterize synthetic DNA bases and oligonucleotides. Using an approach of this type it was found that desalted oligonucleotide samples of the same nominal composition, but which had been produced by three different manufacturers, differ significantly in their IR spectra. These data suggest that the presumably identical oligonucleotides are in fact different, at least with respect to the content and nature of their NH protons.

Modelling the effect of structure and base sequence on DNA molecular electronics

DNA is a material that has the potential to be used in nanoelectronic devices as an active component. However, the electronic properties of DNA responsible for its conducting behaviour remain controversial. Here we use a self-consistent quantum molecular dynamics method to study the effect of DNA structure and base sequence on the energy involved when electrons are added or removed from isolated molecules and the transfer of the injected charge along the molecular axis when an electric field is applied. Our results show that the addition or removal of an electron from DNA molecules is most exothermic for poly(dC)-poly(dG) in its B-form and poly(dA)-poly(dT) in its A-form, and least exothermic in its Z-form. Additionally, when an electric field is applied to a charged DNA molecule along its axis, there is electron transfer through the molecule, regardless of the number and sign of the injected charge, the molecular structure and the base sequence. Results from these simulations provide useful information that is hard to obtain from experiments and needs to be considered for further modelling aiming to improve charge transport efficiency in nanoelectronic devices based on DNA.

Conductivity of natural and modified DNA measured by scanning tunneling microscopy. The effect of sequence, charge and stacking

The conductivity of DNA covalently bonded to a gold surface was studied by means of the STM technique. Various single- and double-stranded 32-nucleotide-long DNA sequences were measured under ambient conditions so as to provide a better understanding of the complex process of charge-carrier transport in natural as well as chemically modified DNA molecules. The investigations focused on the role of several features of DNA structure, namely the role of the negative charge at the backbone phosphate group and the related complex effects of counterions, and of the stacking interactions between the bases in Watson-Crick and other types of base pairs. The measurements have indicated that the best conductor is DNA in its biologically most relevant double-stranded form with Watson-Crick base pairs and charged phosphates equilibrated with counterions and water. All the studied modifications, including DNA with non-Watson-Crick base pairs, the abasic form, and especially the form with phosphate charges eliminated by chemical modifications, lower the conductivity of natural DNA.