Ab-initio study of model guanine assemblies: The role of pi-pi coupling and band transport

Several assemblies of guanine molecules are investigated by means of first-principle calculations. Such structures include stacked and hydrogen-bonded dimers, as well as vertical columns and planar ribbons, respectively, obtained by periodically replicating the dimers. Our results are in good agreement with experimental data for isolated molecules, isolated dimers, and periodic ribbons. For stacked dimers and columns, the stability is affected by the relative charge distribution of the pi orbitals in adjacent guanine molecules. pi-pi coupling in some stacked columns induces dispersive energy bands, while no dispersion is identified in the planar ribbons along the connections of hydrogen bonds. The implications for different materials comprised of guanine aggregates are discussed. The bandstructure of dispersive configurations may justify a contribution of band transport (Bloch type) in the conduction mechanism of deoxyguanosine fibres, while in DNA-like configurations band transport should be negligible.Comment: 21 pages, 6 figures, 3 tables, to be published in Phys. Rev.

Dipping-Induced Azimuthal Helix Orientation in Langmuir-Blodgett Monolayers of α-Helical Amphiphilic Diblock Copolypeptides

The azimuthal helix orientation of the rigid-rod amphiphilic diblock copolypeptides (PLGA-b-PMLGSLGs) of poly(α-L-glutamic acid) (PLGA) and poly(γ-methyl-L-glutamate-ran-γ-stearyl-L-glutamate) with 30 mol % of stearyl substituents (PMLGSLG) in Langmuir-Blodgett (LB) monolayers was investigated using polarized transmission Fourier transform infrared spectroscopy. The relative position of dipping with respect to the previous transfer position can be used to manipulate the azimuthal orientation of the helices parallel to or tilted by an angle of 45° with respect to the dipping direction in the transferred films. The study of the azimuthal order for the LB monolayers of PLGA-b-PMLGSLGs of various block lengths revealed that the observed effect arises mainly from the deformation of the PMLGSLG top brush layer, induced by the flow orientation around the transfer region. In those cases where the PMLGSLG block is tilted by a sufficiently large angle with respect to the surface normal, high azimuthal order parameters of 0.5-0.75 were obtained.

Effect of probe characteristics on the subtractive hybridization efficiency of human genomic DNA

<p>Abstract</p> <p>Background</p> <p>The detection sensitivity of low abundance pathogenic species by polymerase chain reaction (PCR) can be significantly enhanced by removing host nucleic acids. This selective removal can be performed using a magnetic bead-based solid phase with covalently immobilized capture probes. One of the requirements to attain efficient host background nucleic acids subtraction is the capture probe characteristics.</p> <p>Findings</p> <p>In this study we investigate how various capture probe characteristics influence the subtraction efficiency. While the primary focus of this report is the impact of probe length, we also studied the impact of probe conformation as well as the amount of capture probe attached to the solid phase. The probes were immobilized on magnetic microbeads functionalized with a phosphorous dendrimer. The subtraction efficiency was assessed by quantitative real time PCR using a single-step capture protocol and genomic DNA as target. Our results indicate that short probes (100 to 200 bp) exhibit the best subtraction efficiency. Additionally, higher subtraction efficiencies with these probes were obtained as the amount of probe immobilized on the solid phase decreased. Under optimal probes condition, our protocol showed a 90 - 95% subtraction efficiency of human genomic DNA.</p> <p>Conclusions</p> <p>The characteristics of the capture probe are important for the design of efficient solid phases. The length, conformation and abundance of the probes determine the capture efficiency of the solid phase.</p

Investigating the dynamics of surface-immobilized DNA nanomachines

Surface-immobilization of molecules can have a profound influence on their structure, function and dynamics. Toehold-mediated strand displacement is often used in solution to drive synthetic nanomachines made from DNA, but the effects of surface-immobilization on the mechanism and kinetics of this reaction have not yet been fully elucidated. Here we show that the kinetics of strand displacement in surface-immobilized nanomachines are significantly different to those of the solution phase reaction, and we attribute this to the effects of intermolecular interactions within the DNA layer. We demonstrate that the dynamics of strand displacement can be manipulated by changing strand length, concentration and G/C content. By inserting mismatched bases it is also possible to tune the rates of the constituent displacement processes (toehold-binding and branch migration) independently, and information can be encoded in the time-dependence of the overall reaction. Our findings will facilitate the rational design of surface-immobilized dynamic DNA nanomachines, including computing devices and track-based motors

Charge Transport in DNA-Based Devices

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.Comment: A single pdf file of 52 pages, containing the text and 23 figures. Review about direct measurements of DNA conductivity and related theoretical studies. For higher-resolution figures contact the authors or retrieve the original publications cited in the caption

Enzymes immobilized in Langmuir-Blodgett films: Why determining the surface properties in Langmuir monolayer is important?

ABSTRACT In this review we discuss about the immobilization of enzymes in Langmuir-Blodgett films in order to determine the catalytic properties of these biomacromolecules when adsorbed on solid supports. Usually, the conformation of enzymes depends on the environmental conditions imposed to them, including the chemical composition of the matrix, and the morphology and thickness of the film. In this review, we show an outline of manuscripts that report the immobilization of enzymes as LB films since the 1980’s, and also some examples of how the surface properties of the floating monolayer prepared previously to the transfer to the solid support are important to determine the efficiency of the resulting device