Deoxyribose Nucleic Acid Molecules Research Articles

Provoking electrocatalytic activity with bio-molecules at inactive gas diffusion layers

Developments of earth abundant and highly active metal-free electrocatalysts pave a new way for nurturing economically viable water splitting for hydrogen production. Recent findings showed that deoxyribose nucleic acid (DNA) can be employed to reduce the loading of expensive catalysts like Pt and to increase the catalytic activity of catalysts in the streams of hydrogen evolution reaction (HER) and oxygen reduction reaction (ORR) respectively. Herein, for the very first time, we found an interesting property of DNA in electrocatalysis by a simple and fast physical modification over the gas diffusion layers (GDL). The DNA molecule while embedded over the GDL surface, it has modified the surface phenomenon in addition to the active functional groups to give the electrocatalytic activity. The DNA modified GDL (DGDL) has showed better kinetic trend and activity in both oxygen evolution reaction (OER) and HER in alkaline and acidic media respectively. To further ensure the nature of these surface modified GDL, we have utilized other important bio-molecules also and studied their activity in comparison with DNA. For that, we have chosen carboxymethyl cellulose (CMC) and bovine serum albumin (BSA) bio-molecules for the same. In OER in 1 M KOH, to reach 10 mA cm−2 current density, DGDL required an overpotential of 384 mV compared to CGDL and BGDL which required 402 and 414 mV respectively. Similarly, for HER too, for attaining 10 mA cm−2, DGDL, CGDL and BGDL required overpotentials 298, 369 and 393 mV respectively. The increase in activity was owing to the presence of surface functionalities that facilitated improved charge transfer kinetics and electrode-electrolyte interaction in an efficient manner. With these fruitful findings in activities, in futuristic, our proposed route can be extended to design various other smart, cost effective and self-standing metal free catalysts in a facile way.

Recent Developments in the Interactions of Classic Intercalated Ruthenium Compounds: [Ru(bpy)₂dppz]2+ and [Ru(phen)₂dppz]2+ with a DNA Molecule.

[Ru(bpy)2dppz]2+ and [Ru(phen)2dppz]2+ as the light switches of the deoxyribose nucleic acid (DNA) molecule have attracted much attention and have become a powerful tool for exploring the structure of the DNA helix. Their interactions have been intensively studied because of the excellent photophysical and photochemical properties of ruthenium compounds. In this perspective, this review describes the recent developments in the interactions of these two classic intercalated compounds with a DNA helix. The mechanism of the molecular light switch effect and the selectivity of these two compounds to different forms of a DNA helix has been discussed. In addition, the specific binding modes between them have been discussed in detail, for a better understanding the mechanism of the light switch and the luminescence difference. Finally, recent studies of single molecule force spectroscopy have also been included so as to precisely interpret the kinetics, equilibrium constants, and the energy landscape during the process of the dynamic assembly of ligands into a single DNA helix.

Re-evaluation of biotin-streptavidin conjugation in Förster resonance energy transfer applications.

Bioaffinity conjugation between streptavidin (SA) and biotin has been widely used to link donors and acceptors for investigating the distance-dependent Förster resonance energy transfer (FRET). When studying a commonly used FRET system of (QD-SA)-(biotin-DNA-dye) [donor: quantum dot (QD); acceptor: small organic fluorescent dye; and linker: deoxyribose nucleic acid (DNA) molecule via SA-biotin conjugation], however, a contradictory finding was recently reported in the literature. It was found that the FRET lost its dependence on the number of DNA base pairs when using a phosphate-buffered saline (PBS) solution. We found that the conflicted results were caused by the ionic strength of the adopted buffer solutions. Our results suggest that the dependent FRET on the number of DNA bases is favorable in a low-ionic-strength buffer, whereas in relatively high-ionic-strength buffers, the FRET loses the DNA length dependence. We propose that the independence is mainly caused by the conformational change of DNA molecules from a stretched to a coiled mode when the cations in the high-ionic-strength buffer neutralize the negatively charged backbone of DNA molecules, thereby bringing the acceptors close to the donors.

Conductivity of single-stranded and double-stranded deoxyribose nucleic acid under ambient conditions: The dominance of water

We investigate the conductivity of single-stranded and double-stranded herring deoxyribose nucleic acid (DNA) in buffer solution spotted and dried on Au nanocontacts. We find an exponential increase of the conductivity with increasing humidity that is identical for single- and double-stranded DNA within the measurement accuracy. While the small conductivity of dry DNA is comparable to that of a large band-gap semiconductor, we attribute the increase at high humidity levels to water molecules accumulated at the phosphate backbone. For high humidities we observe s-shaped current-voltage characteristics that can be well explained by the dissociation of water attached to the DNA molecules.

A DNA trapping and extraction microchip using periodically crossed electrophoresis in a micropillar array

This paper presents an integrated deoxyribose nucleic acid (DNA) trapping and extraction microchip based on the electrophoresis using periodically crossed electric fields in the micropillar array. The extraction microchip, integrated with a micropillar array, microchannels, nano-gap entropic barriers, loading and unloading windows, has been fabricated by a 3-mask microfabrication process. Using the electric field crossed at 120°, the microchip is designed to trap the DNA molecules, whose reorientation time is longer than the period of the crossed field, within the micropillars distributed at 60° direction. In the fabricated extraction microchip, three different DNA molecules, including λ DNA (48.5 kbp), micrococcus DNA (115 kbp) and T4 DNA (168.9 kbp) show the reorientation times of 4.80 ± 0.44 s, 7.12 ± 0.75 s and 9.71 ± 0.30 s, respectively, at the crossed electric field of 6.25 V/cm. Among three DNA molecules, T4 DNA could not come out of the micropillar array for the electric field of 6.25 V/cm crossed at the period of 10 s. We have demonstrated that the present DNA extraction microchip separates DNA molecules larger than a critical value, which can be adjusted by the period of the electric field across the micropillar array.

DNA configurations and concentration in shearing flow near a glass surface in a microchannel

We characterize the configurations and concentration of λ-phage deoxyribose nucleic acid (DNA) molecules in shear flow near a glass surface in a microchannel through epifluorescence microscopy. We observe that in Poiseuille flow, over a region extending from a glass surface up to about one third of the contour length of the DNA molecule, the average stretch of a λ-phage DNA molecule is significantly lower than in the bulk, in agreement with results obtained in a steady torsional shear flow by Li et al. (2004). We also find that the concentration of DNA molecules in this same region is notably lower than in the bulk, to a degree that increases with increasing Weissenberg number. A simplified explanation is proposed for the behavior of DNA molecules near the glass surface based on wall influences on hydrodynamic interaction within the chain, motivated by the recent theoretical work of Jendrejack et al. (2003, 2004).

Adsorption of monovalent and multivalent cations and anions on DNA molecules.

Adsorption of monovalent and multivalent cations and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modeled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modeled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major-groove cationic charge is independent of the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salts. Simulations for larger ion radii, which mimic the effect of ion hydration, indicate an increased adsorbtion of cations in the major groove.

A partially incoherent rate theory of long-range charge transfer in deoxyribose nucleic acid

A quantum chemistry based Green’s function formulation of long-range charge transfer in deoxyribose nucleic acid (DNA) double helix is proposed. The theory takes into account the effects of DNA’s electronic structure and its incoherent interaction with aqueous surroundings. In the implementation, the electronic tight-binding parameters for unsolvated DNA molecules are determined at the HF/6-31G* level, while those for individual nucleobase–water couplings are at a semiempirical level by fitting with experimental redox potentials. Numerical results include that: (i) the oxidative charge initially at the donor guanine site does hop sequentially over all guanine sites; however, the revealed rates can be of a much weaker distance dependence than that described by the ordinary Ohm’s law; (ii) the aqueous surroundings-induced partial incoherences in thymine/adenine bridge bases lead them to deviate substantially from the superexchange regime; (iii) the time scale of the partially incoherent hole transport through the thymine/adenine π stack in DNA is about 5 ps.

Ordered stretching of single molecules of deoxyribose nucleic acid between microfabricated polystyrene lines

A technique for creating arrays of parallel, stretched single molecules of deoxyribose nucleic acid (DNA) on an arbitrary substrate for high-resolution scanning-probe imaging is discussed. The technique consists of lithographically patterning polystyrene lines on a substrate which then provide attachment sites for the ends of individual DNA molecules. Molecular combing is performed to stretch DNA from one polystyrene line to the other. Scanning-tunneling and atomic-force microscope images of single molecules of bacteriophage-lambda DNA are shown to demonstrate the advantages of this technique. Several applications, from high-resolution genomics to molecular electronics, are discussed.

Atomic force microscope observation of plasmid deoxyribose nucleic acid with restriction enzyme

We have observed plasmid deoxyribose nucleic acid (DNA), in real space images, before and after treating with restriction enzyme (Pvu II or Hinc II) using an atomic force microscope (AFM). The enzyme is recognized on DNA even in the absence of Mg2+ ions. In the presence of Mg2+, on the other hand, direct evidence was obtained that the enzyme could bind to circular plasmid DNA without cutting and cleaved it at the site corresponding to the specificity. Lengths of the DNA fragments observed by AFM were consistent with the values estimated by agarose gel electrophoresis. In addition, as substrates for the AFM observation, rutile TiO2(110) single crystal surface was found to be effective in expanding and fixing the DNA molecules as straight chains along the stepped surface.

Ultrasonic investigation of aqueous solutions of deoxyribose nucleic acid.

The ultrasonic absorption of aqueous solutions of salmon sperm deoxyribose nucleic acid (DNA), molecular weight of the order of 106, was determined as a function of pH in the neutral and acidic regions over the frequency range 5–50 MHz at 25°C. The viscous relaxation frequencies appear to be well below 1 MHz. At neutral pH values, viscosity and molecular conformation appear to contribute little in determining the ultrasonic absorption spectrum. The DNA solution absorption spectrum appears to be similar to that of globular protein aqueous solutions implying that the mechanisms may be the same. The ultrasonic absorption acid titration curves for DNA exhibit maxima around pH 2.6 and 12 [J. Chim. Phys. 66, 81 (1969)] which can be attributed to either or both hydrogen bond transfer and proton transfer as the double helix DNA molecule denatures.