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Charge migration along DNA molecules has attracted scientific interest for over half a century. Reports on possible high rates of charge transfer between donor and acceptor through the DNA, obtained in the last decade from solution chemistry experiments on large numbers of molecules, triggered a series of direct electrical transport measurements through DNA single molecules, bundles and networks. These measurements are reviewed and presented here. From these experiments we conclude that electrical transport is feasible in short DNA molecules, in bundles and networks, but blocked in long single molecules that are attached to surfaces. The experimental background is complemented by an account of the theoretical/computational schemes that are applied to study the electronic and transport properties of DNA-based nanowires. Examples of selected applications are given, to show the capabilities and limits of current theoretical approaches to accurately describe the wires, interpret the transport measurements, and predict suitable strategies to enhance the conductivity of DNA nanostructures.
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Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Using density functional theory and the Landauer-Buttiker method, we study the electronic properties and charge transport through an eight base-pair methylated DNA strand and its native counterpart. We first analyze the effect of cytosine methylation on the tight-binding parameters of two DNA strands and then model the transmission of the electrons and conductance through the strands both with and without decoherence. We find that the main difference of the tight-binding parameters between the native DNA and the methylated DNA lies in the on-site energies of (methylated) cytosine bases. The intra- and inter- strand hopping integrals between two nearest neighboring guanine base and (methylated) cytosine base also change with the addition of the methyl groups. Our calculations show that in the phase-coherent limit, the transmission of the methylated strand is close to the native strand when the energy is nearby the highest occupied molecular orbital level and larger than the native strand by 5 times in the bandgap. The trend in transmission also holds in the presence of the decoherence with the same rate. The lower conductance for the methylated strand in the experiment is suggested to be caused by the more stable structure due to the introduction of the methyl groups. We also study the role of the exchangecorrelation functional and the effect of contact coupling by choosing coupling strengths ranging from weak to strong coupling limit.
The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike. The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and theoretical investigations. Here, we review recent theoretical progress by concentrating on quantum-chemical, molecular dynamics-based approaches to short DNA strands and physics-motivated tight-binding transport studies of long or even complete DNA sequences. In both cases, we observe small, but significant differences between specific DNA sequences such as periodic repetitions and aperiodic sequences of AT bases, lambda-DNA, centromeric DNA, promoter sequences as well as random-ATGC DNA.
Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in protein devices. By studying two different model protein machines, with different biological functions, we show that genuinely non--linear phenomena are responsible for energy transport between the different machine sites involved in the biological functions. The energy transfer turns out to be extremely efficient from an energetic point of view: by changing the energy initially provided to the model device, we identify a well defined range of energies where the time for the energy transport to occur is minimal and the amount of transferred energy is maximum. Furthermore, by introducing an implicit solvent, we show that the energy is localized on the internal residues of the protein structure, thus minimizing the dissipation.
Semiflexible polymers characterized by the contour length $L$ and persistent length $ell_p$ confined in a spatial region $D$ have been described as a series of ``{em spherical blobs} and ``{em deflecting lines} by de Gennes and Odjik for $ell_p < D$ and $ell_p gg D$ respectively. Recently new intermediate regimes ({em extended de Gennes} and {em Gauss-de Gennes}) have been investigated by Tree {em et al.} [Phys. Rev. Lett. {bf 110}, 208103 (2013)]. In this letter we derive scaling relations to characterize these transitions in terms of universal scaled fluctuations in $d$-dimension as a function of $L,ell_p$, and $D$, and show that the Gauss-de Gennes regime is absent and extended de Gennes regime is vanishingly small for polymers confined in a 2D strip. We validate our claim by extensive Brownian dynamics (BD) simulation which also reveals that the prefactor $A$ used to describe the chain extension in the Odjik limit is independent of physical dimension $d$ and is the same as previously found by Yang {em et al.}[Y. Yang, T. W. Burkhardt, G. Gompper, Phys. Rev. E {bf 76}, 011804 (2007)]. Our studies are relevant for optical maps of DNA stretched inside a nano-strip.
DNA origami is a novel self-assembly technique allowing one to form various 2D shapes and position matter with nanometer accuracy. It has been used to coordinate placement of nanoscale objects, both organic and inorganic; to make molecular motors and walkers; and to create optically active nanostructures. Here we use DNA origami templates to engineer Surfaced Enhanced Raman Scattering (SERS) substrates. Specifically, gold nanoparticles were selectively attached to the corners of rectangular origami and subsequently enlarged via solution-based metal deposition. The resulting assemblies were designed to form hot spots of enhanced electromagnetic field between the nanoparticles. We observed a significant enhancement of the Raman signal from molecules covalently attached to the assemblies, as compared to control nanoparticle samples which lack inter-particle hot spots. Our method opens up the prospects of using DNA origami to rationally engineer and assemble plasmonic structures for molecular spectroscopy.
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