Glacial–interglacial changes in ocean surface conditions in the Southern Hemisphere

Water stable isotopes in snow along a traverse of the West Antarctic Ice Sheet: insights into moisture origins, air-masses distillation history, and climatic value

This study investigated the water isotopic content (δ18O, δD, d-excess) of the surface snow along a 995 km traverse over the West Antarctic Ice Sheet from the Möller Ice Stream - Institute Ice Stream to the upper reaches of the Pine Island Glacier drainage basin. The purpose of this study was to evaluate the climatic record preserved in the snow. We analyzed 92 surface samples (~0.15-0.20 m deep), retrieved during 2014/2015 austral summer from every ~10 km along the traverse route, using the laser spectroscopy technique. We computed the isotopic-geographical characteristics and spatial co-isotopic empirical relationships and compared the isotopic results with the tropospheric mean annual temperature and air mass trajectories. Our isotopic results were sensitive to capturing the well-known climatic asymmetry between the Amundsen-Bellingshausen Sea (ABS; which receives more influence from warmer (oceanic) air masses) and Weddell Sea (WS; more influenced by colder (continental) air masses) sectors. Further, the spatial distribution of δs and d-excess and the co-isotopic relationships reflect two preferential fractionation paths: one from the coast of the ABS sector to the WS sector, and another from the coast of the WS sector to the inland. The Pacific Ocean is confirmed as the primary source of moisture.

Spectroscopic investigation of hydrogen and triple-oxygen isotopes in atmospheric water vapor and precipitation during Indian monsoon season

Water vapor, the most important greenhouse gas in the atmosphere, has four natural stable isotopologues (H₂¹⁶O, H₂¹⁷O, H₂¹⁸O and HD¹⁶O), and their isotopic compositions can be used as hydrological tracers. But the underlying processes and pattern-dynamics of the isotopic compositions of atmospheric water vapor and precipitation in response to various meteorological conditions during monsoon season in a tropical hot and humid region is poorly understood. Here, we present results of H and triple-O-isotopes of water in precipitation and atmospheric water vapor during monsoon season exploiting high-resolution integrated cavity output spectroscopy technique. We observed a distinct temporal variation of the isotopic compositions of water at different phases of the monsoon. The diurnal patterns of the isotopic variations were influenced by the local meteorological factors such as temperature, relative humidity and amount of precipitation. We also investigated the monsoonal dynamics of the second-order isotopic parameters, so-called d-excess and ¹⁷O-excess along with the influence of local meteorological factors on isotopic variations to improve our understanding of the underlying isotopic fractionation processes. Consequently, our results provide a unique isotopic-fingerprint dataset of rainwater and atmospheric water vapor for a tropical region and thus shed a new light on hydrological and meteorological processes in the atmosphere.

Shut down of the South American summer monsoon during the penultimate glacial

We analysed changes in mean annual air temperature (MAAT), vegetation and biomass burning on a long and continuous lake-peat sediment record from the Colônia basin, southeastern Brazil, examining the responses of a wet tropical rainforest over the last 180 ka. Stronger southern atmospheric circulation up to the latitude of Colônia was found for the penultimate glacial with lower temperatures than during the last glacial, while strengthening of the South American summer monsoon (SASM) circulation started during the last interglacial and progressively enhanced a longer wet summer season from 95 ka until the present. Past MAAT variations and fire history were possibly modulated by eccentricity, although with signatures which differ in average and in amplitude between the last 180 ka. Vegetation responses were driven by the interplay between the SASM and southern circulation linked to Antarctic ice volume, inferred by the presence of a cool mixed evergreen forest from 180 to 45 ka progressively replaced by a rainforest. We report cooler temperatures during the marine isotope stage 3 (MIS 3: 57-29 ka) than during the Last Glacial Maximum (LGM: 23-19 ka). Our findings show that tropical forest dynamics display different patterns than mid-latitude during the last 180 ka.

Resolving the controls of water vapour isotopes in the Atlantic sector

Stable water isotopes are employed as hydrological tracers to quantify the diverse implications of atmospheric moisture for climate. They are widely used as proxies for studying past climate changes, e.g., in isotope records from ice cores and speleothems. Here, we present a new isotopic dataset of both near-surface vapour and ocean surface water from the North Pole to Antarctica, continuously measured from a research vessel throughout the Atlantic and Arctic Oceans during a period of two years. Our observations contribute to a better understanding and modelling of water isotopic composition. The observations reveal that the vapour deuterium excess within the atmospheric boundary layer is not modulated by wind speed, contrary to the commonly used theory, but controlled by relative humidity and sea surface temperature only. In sea ice covered regions, the sublimation of deposited snow on sea ice is a key process controlling the local water vapour isotopic composition.

Water isotope modelling is an important tool in climate reconstructions, but there remain gaps in our understanding of the effects upon oxygen and hydrogen isotope fractionation, and thus the source of the deposited signal. Here, the authors present a dataset assembled over two years that shows deuterium excess is controlled by humidity and sea surface temperature, and oxygen and hydrogen isotopes as well as deuterium excess are controlled by sublimation of snow in sea-ice regions.

Evidence of Isotopic Fractionation During Vapor Exchange Between the Atmosphere and the Snow Surface in Greenland

Several recent studies from both Greenland and Antarctica have reported significant changes in the water isotopic composition of near-surface snow between precipitation events. These changes have been linked to isotopic exchange with atmospheric water vapor and sublimation-induced fractionation, but the processes are poorly constrained by observations. Understanding and quantifying these processes are crucial to both the interpretation of ice core climate proxies and the formulation of isotope-enabled general circulation models. Here, we present continuous measurements of the water isotopic composition in surface snow and atmospheric vapor together with near-surface atmospheric turbulence and snow-air latent and sensible heat fluxes, obtained at the East Greenland Ice-Core Project drilling site in summer 2016. For two 4-day-long time periods, significant diurnal variations in atmospheric water isotopologues are observed. A model is developed to explore the impact of this variability on the surface snow isotopic composition. Our model suggests that the snow isotopic composition in the upper subcentimeter of the snow exhibits a diurnal variation with amplitudes in δ18O and δD of ~2.5‰ and ~13‰, respectively. As comparison, such changes correspond to 10-20% of the magnitude of seasonal changes in interior Greenland snow pack isotopes and of the change across a glacial-interglacial transition. Importantly, our observation and model results suggest, that sublimation-induced fractionation needs to be included in simulations of exchanges between the vapor and the snow surface on diurnal timescales during summer cloud-free conditions in northeast Greenland.

Reconciling glacial Antarctic water stable isotopes with ice sheet topography and the isotopic paleothermometer

Stable water isotope records from Antarctica are key for our understanding of Quaternary climate variations. However, the exact quantitative interpretation of these important climate proxy records in terms of surface temperature, ice sheet height and other climatic changes is still a matter of debate. Here we report results obtained with an atmospheric general circulation model equipped with water isotopes, run at a high-spatial horizontal resolution of one-by-one degree. Comparing different glacial maximum ice sheet reconstructions, a best model data match is achieved for the PMIP3 reconstruction. Reduced West Antarctic elevation changes between 400 and 800 m lead to further improved agreement with ice core data. Our modern and glacial climate simulations support the validity of the isotopic paleothermometer approach based on the use of present-day observations and reveal that a glacial ocean state as displayed in the GLAMAP reconstruction is suitable for capturing the observed glacial isotope changes in Antarctic ice cores.

Despite their importance, the accuracy of the quantitative interpretation of Antarctic ice core stable water isotope records remains a matter of debate. Here, the authors use an isotope-enabled atmospheric general circulation model to test and validate the isotopic paleothermometer approach.

Influence of sea ice on Arctic precipitation

Global climate is influenced by the Arctic hydrologic cycle, which is, in part, regulated by sea ice through its control on evaporation and precipitation. However, the quantitative link between precipitation and sea ice extent is poorly constrained. Here we present observational evidence for the response of precipitation to sea ice reduction and assess the sensitivity of the response. Changes in the proportion of moisture sourced from the Arctic with sea ice change in the Canadian Arctic and Greenland Sea regions over the past two decades are inferred from annually averaged deuterium excess (d-excess) measurements from six sites. Other influences on the Arctic hydrologic cycle, such as the strength of meridional transport, are assessed using the North Atlantic Oscillation index. We find that the independent, direct effect of sea ice on the increase of the percentage of Arctic sourced moisture (or Arctic moisture proportion, AMP) is 18.2 ± 4.6% and 10.8 ± 3.6%/100,000 km(2) sea ice lost for each region, respectively, corresponding to increases of 10.9 ± 2.8% and 2.7 ± 1.1%/1 °C of warming in the vapor source regions. The moisture source changes likely result in increases of precipitation and changes in energy balance, creating significant uncertainty for climate predictions.

Measurement of δ18O, δ17O, and 17O-excess in water by off-axis integrated cavity output spectroscopy and isotope ratio mass spectrometry

Stable isotopes of water have long been used to improve understanding of the hydrological cycle, catchment hydrology, and polar climate. Recently, there has been increasing interest in measurement and use of the less-abundant (17)O isotope in addition to (2)H and (18)O. Off-axis integrated cavity output spectroscopy (OA-ICOS) is demonstrated for accurate and precise measurements δ(18)O, δ(17)O, and (17)O-excess in liquid water. OA-ICOS involves no sample conversion and has a small footprint, allowing measurements to be made by researchers collecting the samples. Repeated (514) high-throughput measurements of the international isotopic reference water standard Greenland Ice Sheet Precipitation (GISP) demonstrate the precision and accuracy of OA-ICOS: δ(18)OVSMOW-SLAP = -24.74 ± 0.07‰ (1σ) and δ(17)OVSMOW-SLAP = -13.12 ± 0.05‰ (1σ). For comparison, the International Atomic Energy Agency (IAEA) value for δ(18)OVSMOW-SLAP is -24.76 ± 0.09‰ (1σ) and an average of previously reported values for δ(17)OVSMOW-SLAP is -13.12 ± 0.06‰ (1σ). Multiple (26) high-precision measurements of GISP provide a (17)O-excessVSMOW-SLAP of 23 ± 10 per meg (1σ); an average of previously reported values for (17)O-excessVSMOW-SLAP is 22 ± 11 per meg (1σ). For all these OA-ICOS measurements, precision can be further enhanced by additional averaging. OA-ICOS measurements were compared with two independent isotope ratio mass spectrometry (IRMS) laboratories and shown to have comparable accuracy and precision as the current fluorination-IRMS techniques in δ(18)O, δ(17)O, and (17)O-excess. The ability to measure accurately δ(18)O, δ(17)O, and (17)O-excess in liquid water inexpensively and without sample conversion is expected to increase vastly the application of δ(17)O and (17)O-excess measurements for scientific understanding of the water cycle, atmospheric convection, and climate modeling among others.

Interannual variation of water isotopologues at Vostok indicates a contribution from stratospheric water vapor

Combined measurements of water isotopologues of a snow pit at Vostok over the past 60 y reveal a unique signature that cannot be explained only by climatic features as usually done. Comparisons of the data using a general circulation model and a simpler isotopic distillation model reveal a stratospheric signature in the (17)O-excess record at Vostok. Our data and theoretical considerations indicate that mass-independent fractionation imprints the isotopic signature of stratospheric water vapor, which may allow for a distinction between stratospheric and tropospheric influences at remote East Antarctic sites.

Abrupt change of Antarctic moisture origin at the end of Termination II

The deuterium excess of polar ice cores documents past changes in evaporation conditions and moisture origin. New data obtained from the European Project for Ice Coring in Antarctica Dome C East Antarctic ice core provide new insights on the sequence of events involved in Termination II, the transition between the penultimate glacial and interglacial periods. This termination is marked by a north-south seesaw behavior, with first a slow methane concentration rise associated with a strong Antarctic temperature warming and a slow deuterium excess rise. This first step is followed by an abrupt north Atlantic warming, an abrupt resumption of the East Asian summer monsoon, a sharp methane rise, and a CO(2) overshoot, which coincide within dating uncertainties with the end of Antarctic optimum. Here, we show that this second phase is marked by a very sharp Dome C centennial deuterium excess rise, revealing abrupt reorganization of atmospheric circulation in the southern Indian Ocean sector.

Direct electrical measurements on single-molecule genomic DNA using single-walled carbon nanotubes

A unique nanoelectronic platform, based on single-walled carbon nanotubes (SWNTs), has been fabricated for measuring electrical transport in single-molecule DNA. We have tested 80 base pairs of single- and double-stranded DNA (ssDNA and dsDNA, respectively) of complex base sequences. About a 25-40 pA current (at 1 V) was measured for the dsDNA molecule covalently attached to the SWNT electrode at its termini. In the absence of base pair stacking, a ssDNA carries a feeble current of approximately 1 pA or less. Gate-voltage-dependent I-V characteristics revealed that the bridging dsDNA molecule acts as a p-type channel between SWNT source and drain electrodes.

Structure of Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations

Chromophore-DNA complexes are useful for understanding charge transport along pi-stacks once their structural properties have been clarified. We studied two rhodamine 6G semicapping complexes with 15-mer B-DNA duplexes to determine the preferred orientation of the dye with respect to the neighboring base pair. For each of these systems, two distinct chromophore alignments were identified and quantified in terms of base-step parameters. The obtained geometries agree well with those derived from an NMR structure refinement of similar complexes. Cross-correlation analysis of the base-step parameters shows that slide and twist are highly interdependent during the structural transition from one conformation to the other.

Comparison of ribonucleic acid homopolymer ionization energies and charge injection barriers

Thin films of guanosine and uridine ribonucleic acid (RNA) homopolymers (poly rG, poly rU) were grown in high vacuum in several steps on highly oriented pyrolytic graphite (HOPG) using electrospray deposition. Between deposition steps, the sample surface was characterized with X-ray and ultraviolet photoemission spectroscopy (XPS, UPS). The resulting spectra series allowed the determination of the orbital alignment at the HOPG interface, as well as the ionization energies of the homopolymer thin films. Comparison with earlier results on cytidine and adenosine RNA homopolymers (poly rC, poly rA) indicates significant ionization energy and charge injection barrier differences between purines and pyrimidines.

Ionization energy and electronic structure of polycytidine

Ribonucleic acid (RNA) polycytidine (poly rC) homopolymer thin films were prepared on highly oriented pyrolytic graphite (HOPG) substrates. The films were grown from aqueous solution directly in a vacuum in multiple steps with use of an electrospray (ES) deposition system. Before poly rC deposition and after each deposition step the sample was characterized with X-ray and ultraviolet photoemission spectroscopy (XPS, UPS). Evaluation of the UP-spectra sequence allowed the determination of ionization energy and highest occupied molecular orbital (HOMO) electronic structure, as well as the charge injection barriers between HOPG and poly rC. Comparison with earlier results on polyadenosine (poly rA) indicates significant differences between ionization energies (poly rC: 8.1 eV; poly rA: 6.8 eV) and orbital alignment at the graphite interface. The larger ionization energy of poly rC results in a larger hole injection barrier and a smaller electron injection barrier relative to the HOPG Fermi level.

Molecular beam deposition of DNA nanometer films

The development of novel photonic devices which incorporate biological materials is strongly tied to the development of thin film forming processes. Solution-based ("wet") processes when used with biomaterials in device fabrication suffer from dissolution of underlying layers, incompatibility with clean environment, inconsistent film properties, etc. We have investigated ultra-high-vacuum molecular beam deposition of surfactant-modified deoxyribonucleic acid (DNA). We have obtained effective deposition rates of approximately 0.1-1 A/s, enabling reproducible and controllable deposition of nanometer-scale films.

Experimental and Theoretical Investigation of the Electronic Structure of 5-Fluorouracil Compounds

We present a comparison between experimental and theoretical X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) of 5-fluorouracil compounds, with an emphasis on the effects of the inclusion of nickel in the structure. By focusing on the 1s thresholds of carbon, nitrogen, oxygen, and fluorine it was possible to provide a complete picture of the occupied and unoccupied partial density of states of the 5-fluorouracil systems. Spectra calculated using density functional theory are compared to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of the compounds. All spectral features are assigned. Our results reveal that the nickel in the compound is coordinated with the nitrogen sites of the 5-fluorouracil ligands.

Atomic layer deposition on biological macromolecules: metal oxide coating of tobacco mosaic virus and ferritin

Decoration of nanoparticles, in particular biomolecules, gathered high attention in recent years.(1-7) Of special interest is the potential use of biomolecules as templates for the fabrication of semiconducting or metallic nanostructures.(1-7,26) In this work we show the application of atomic layer deposition, a gas-phase thin film deposition process, to biological macromolecules, which are frequently used as templates in nanoscale science, and the possibility to fabricate metal oxide nanotubes and thin films with embedded biomolecules.(1-13).

Microsolvation Effect, Hydrogen-Bonding Pattern, and Electron Affinity of the Uracil−Water Complexes U−(H2O)n (n = 1, 2, 3)

To achieve a systematic understanding of the influence of microsolvation on the electron accepting behaviors of nucleobases, the reliable theoretical method (B3LYP/DZP++) has been applied to a comprehensive conformational investigation on the uracil-water complexes U-(H(2)O)(n) (n = 1, 2, 3) in both neutral and anionic forms. For the neutral complexes, the conformers of hydration on the O2 of uracil are energetically favored. However, hydration on the O4 atom of uracil is more stable for the radical anions. The electron structure analysis for the H-bonding patterns reveal that the CH...OH(2) type H-bond exists only for di- and trihydrated uracil complexes in which a water dimer or trimer is involved. The electron density structure analysis and the atoms-in-molecules (AIM) analysis for U-(H(2)O)(n) suggest a threshold value of the bond critical point (BCP) density to justify the CH...OH(2) type H-bond; that is, CH...OH(2) could be considered to be a H-bond only when its BCP density value is equal to or larger than 0.010 au. The positive adiabatic electron affinity (AEA) and vertical detachment energy (VDE) values for the uracil-water complexes suggest that these hydrated uracil anions are stable. Moreover, the average AEA and VDE of U-(H(2)O)(n) increase as the number of the hydration waters increases.

Sequence Dependence of Charge Transport through DNA Domains

Here we examine the photooxidation of two kinetically fast electron hole traps, N4-cyclopropylcytosine (CPC) and N2-cyclopropylamine-guanosine (CPG), incorporated in DNA duplexes of various sequence using different photooxidants. DNA oxidation studies are carried out either with noncovalently bound [Ru(phen)(dppz)(bpy')]3+ (dppz = dipyridophenazine) and [Rh(phi)2(bpy)]3+ (phi = phenanthrenequinone diimine) or with anthraquinone tethered to DNA. Because the cyclopropylamine-substituted bases decompose rapidly upon oxidation, their efficiency of decomposition provides a measure of relative hole localization. Consistent with a higher oxidation potential for CPC versus CPG in DNA, CPC decomposes with photooxidation by [Rh(phi)2(bpy)]3+, while CPG undergoes ring-opening both with photoexcited [Rh(phi)2(bpy)]3+ and with [Ru(phen)(dppz)(bpy')]3+. Anthraquinone-modified DNA assemblies of identical base composition but different base sequence are also probed. Single and double base substitutions within adenine tracts modulate CPC decomposition. In fact, the entire sequence within the DNA assembly is seen to govern CPC oxidation, not simply the bases intervening between CPC and the tethered photooxidant. These data are reconciled in the context of a mechanistic model of conformationally gated charge transport through delocalized DNA domains. Photooxidations of anthraquinone-modified DNA assemblies containing both CPC and CPG, but with varied distances separating the modified bases, point to a domain size of at least three bases. Our model for DNA charge transport is distinguished from polaron models. In our model, delocalized domains within the base pair stack form transiently based upon sequence-dependent DNA structure and dynamics. Given these results, DNA charge transport is indeed remarkably sensitive to DNA sequence and structure.

On the Magnetic Alignment of Metal Ions in a DNA-Mimic Double Helix

We computed by spin-polarized DFT the structure and the electronic properties of an infinite periodic wire constituted of planar Cu-bridged hydroxypyridone chelator base pairs and of a similarly stacked finite dimer. The Cu centers undergo electronic hybridization with the bases. There is an unpaired spin per plane, and the majority-spins manifest ordering: The ferromagnetic and antiferromagnetic phases are energetically degenerate. The total magnetization of the ferromagnetic wire depends linearly on the number of planes in the stack. The combination of interplane spin coupling and intraplane metal-hydroxypyridone coupling makes this system very appealing for electronic and magnetic device exploitation.

Uncovering Transport Properties of 4,4‘-Bipyridine/Gold Molecular Nanobridges

Here, the fascinating connection between the chemical and the transport properties of recently fabricated 4,4'-bipyridine/gold nanobridges is addressed. By means of first-principles ab initio calculations, the remarkable reproducibility of the 4,4'-bipyridine conductance properties is explained as the combined result of (i) the bonding of the molecule to the metallic leads through hybridization between the 4,4'-bipyridine highest occupied molecular orbitals and lowest unoccupied molecular orbitals (LUMOs) with s and d orbitals at low-coordination gold atoms, (ii) the limited number of molecule-lead arrangements due to gold-hydrogen steric repulsions, and (iii) the electron transmission through a LUMO-derived resonance, whose positioning with respect to the Fermi level determines which of the above arrangements yields nonnegligible conductance. Structural and electronic interpretations to the stepped dependence reported for the electronic transport of 4,4'-bipyridine as a function of the distance between the gold tips are also given.

Synergistic stabilization of nucleic acid assembly by oligo-N3'-->P5' phosphoramidate modification and additions of comb-type cationic copolymers

Synergic stabilization of DNA triplexes by oligo-N3'-->P5' phosphoramidate (PN) modification and additions of comb-type cationic copolymers was demonstrated. The combination of the copolymer and the PN modification increased triplex K(a) about 4 orders of magnitude. Kinetic analysis revealed that observed stabilization resulted from kinetic complimentarity between increased association rates by the copolymer and decreased dissociation rates by the PN modification of triplex forming oligonucleotides. No countering interference between these stabilizing effects was observed. We propose that kinetic analyses of stabilizing effects permit selection of a rational combination of stabilizing methods for successful synergy in stabilizing complex formation.

Charge Injection Barriers at a Ribonucleic Acid/Inorganic Material Contact Determined by Photoemission Spectroscopy

Ribonucleic acid (RNA) homopolymer thin films on highly oriented pyrolytic graphite (HOPG) were prepared in ultrahigh vacuum (UHV) directly from aqueous solution by electrospray (ES) injection. The polyadenosine (poly rA) films were prepared in several steps of increasing thickness without breaking the vacuum. Before deposition and between deposition steps, the samples were characterized with photoemission spectroscopy (PES). Both X-ray and ultraviolet photoemission spectroscopy (XPS and UPS) were employed. XPS enabled the detailed measurement of core level peaks, giving insight into the chemical interaction at the interface and the layer morphology. The corresponding UP-spectra sequence allowed us to directly follow the transition from HOPG valence bands to the poly rA highest occupied molecular orbital (HOMO) structure. This enabled the determination of the poly rA ionization energy and work function as well as the charge injection barriers between the Fermi level of the HOPG substrate and the poly rA HOMO. The injection barrier between the lowest unoccupied molecular orbital (LUMO) and the HOPG Fermi level was determined using the HOMO-LUMO gap value determined by optical absorption. The results indicate that significant injection barriers exist between HOPG and the poly rA overlayer, limiting conductivity across this interface.

A Chiral Molecular Conductor: Synthesis, Structure, and Physical Properties of [ET]3[Sb2(l-tart)2]·CH3CN (ET = Bis(ethylendithio)tetrathiafulvalene; l-tart = (2R,3R)-(+)-Tartrate)

The salt [ET](3)[Sb(2)(L-tart)(2)].CH(3)CN (1) has been obtained by electrocrystallization of the organic donor bis(ethylendithio)tetrathiafulvalene (ET or BEDT-TTF) in the presence of the chiral anionic complex [Sb(2)(L-tart)(2)](2-) (L-tart = (2R,3R)-(+)-tartrate). This salt crystallizes in the chiral space group P2(1)2(1)2(1) (a = 11.145(2) angstroms, b = 12.848(2) angstroms, c = 40.159(14) angstroms, V = 5750.4(14) angstroms(3), Z = 4) and is formed by alternating layers of the anions and of the organic radicals in a noncentrosymmetric alpha-type packing. This compound shows a room temperature electrical conductivity of approximately 1 S.cm(-1) and semiconducting behavior with an activation energy of approximately 85 meV. Analysis of the magnetic susceptibility and band structure, however, suggests that this compound should be a narrow band gap semiconductor.

Optical properties of an immobilized DNA monolayer from 255 to 700 nm

The real (n) and imaginary (k) refractive indices of an immobilized monolayer of 27 nucleotide (nt) single stranded DNA (ssDNA) and the corresponding double stranded DNA (dsDNA) are measured in the 255-700 nm range. Multiple techniques are used to obtain consistent estimation. The coverage is approximately 6.5% with an average interchain distance of tethered ssDNA molecules of approximately 11.8 nm, which is significantly larger than the "footprint" of the chain on the surface. The measured increase in n by approximately 5% between the ssDNA and the dsDNA is 20% smaller than the expected change due to doubling of the molecular weight. The change in k is not significant, indicating that the electron delocalization effect expected in dsDNA due to base pair stacking is not important at optical frequencies.

Mechanism for radical cation transport in duplex DNA oligonucleotides

We investigated the photoinduced one-electron oxidation of a series of DNA oligomers having a covalently linked anthraquinone group (AQ) and containing [(A)(n)GG](m) or [(T)(n)GG](m) segments. These oligomers have m GG steps, where m = 4 or 6, separated by (A)(n) or (T)(n) segments, where n = 1-7 for the (A)(n) set and 1-5 for the (T)(n) set. Irradiation with UV light that is absorbed by the AQ causes injection of a radical cation into the DNA. The radical cation migrates through the DNA, causing chemical reaction, primarily at GG steps, that leads to strand cleavage after piperidine treatment. The uniform, systematic structure of the DNA oligonucleotides investigated permits the numerical solution of a kinetic scheme that models these reactions. This analysis yields two rate constants, k(hop), for hopping of the radical cation from one site to adjacent sites, and k(trap), for irreversible reaction of the radical cation with H(2)O or O(2). Analysis of these findings indicates that radical cation hopping in these duplex DNA oligomers is a process that occurs on a microsecond time scale. The value of k(hop) depends on the number of base pairs in the (A)(n) and (T)(n) segments in a systematic way. We interpret these results in terms of a thermally activated adiabatic mechanism for radical cation hopping that we identify as phonon-assisted polaron hopping.

Polyaniline Nanowires on Si Surfaces Fabricated with DNA Templates

It is essential to put individual, free-standing nanowires onto insulating substrates and integrate them to useful devices. Here we report a strategy for fabrication of conducting polymer nanowires on thermally oxidized Si surfaces by use of DNA as templates. The direct use of stretched and immobilized DNA strands as templates avoids the agglomeration of DNA caused by shielding of charges on DNA when polyaniline/DNA complexes formed in solution. Most importantly, the oriented DNA strands immobilized on the Si surface predetermine the position and the orientation of the nanowires. The approach described here is the first step toward uniting the programmable-assembly ability of DNA with the unique electronic properties of conducting polymers for high-density functional nanodevices. The conductivity of the nanowires is very sensitive to the proton doping-undoping process, suggesting that the nanowires hold great promise for sensitive chemical sensor applications.

Synthesis, Structure, and Photophysical and Electrochemical Properties of a π-Stacked Polymer

Dibenzofulvene (DBF) was polymerized using anionic initiators to afford a vinyl polymer. Oligo(DBF)s having from two to eight side-chain fluorene moieties bearing different chain-terminal groups were isolated by preparative size-exclusion chromatography. The structures of the isolated oligomers were revealed by single-crystal X-ray and (1)H NMR analyses. Both in solution and in crystal, the in-chain fluorene moieties stacked on top of each other, while the terminal conformation varied depending on the terminal group. These conformational characteristics were supported by molecular mechanics and dynamics calculations. The oligomers and polymers indicated hypochromism and red shift in UV absorption spectra and exclusive excimer emission in fluorescence spectra. In addition, reduced oxidation potentials were observed for the oligomers in electrochemical analyses, which suggests charge delocalization over the pi-stacked electron systems. The photophysical and electrochemical effects increased with the chain length of the oligomers and leveled off around the chain length of an oligomer consisting of five fluorene units.

In Situ Scanning Tunneling Microscopy of DNA-Modified Gold Surfaces: Bias and Mismatch Dependence

In situ scanning tunneling microscopy has been performed on DNA-modified gold surfaces under physiological conditions. The STM images of DNA-modified gold surfaces are strongly dependent on the applied potential and percentage of DNA duplexes containing a single base mismatch. At negative surface potentials we observe reproducible features that are attributed to DNA agglomerates where the DNA duplexes are in the upright orientation; at positive potentials, when DNA molecules lie down on the surface, the film is transparent, and only the gold surface is distinguishable. These observations indicate that DNA possesses a non-negligible local density of states which can be probed when the DNA duplex is in the upright orientation. By varying the percentage of DNA duplexes containing a single base mismatch, we have observed a dramatic change in the image contrast as a result of the perturbation induced by the mismatch on the electronic pathway inside the DNA. These results emphasize the central role of the integrity of the pi-stack for DNA charge transport. Duplex DNA is a promising candidate in molecular electronics, but only in arrangements where the orbitals can efficiently overlap with the electronic states of the electrodes and the environment does not constrain the DNA in non-native, poorly stacked conformations.

Excess electron transfer from an internally conjugated aromatic amine to 5-bromo-2'-deoxyuridine in DNA

DNA duplexes containing an N,N,N',N'-tetramethyl-1,5-diaminonaphthalene analogue and 5-bromo-2'-deoxyuridine (BrdU) provide a readily accessible system for investigating excess electron transfer in DNA. Photoexcitation of the aromatic amine (lambda > 335 nm) induces reductive electron transfer as observed by strand cleavage adjacent to the BrdU residue. The weak exponential distance dependence (0.3 A-1) of electron transfer determined for this system of mixed dA-T and dG-dC base pairs suggests that thermally activated electron hopping is competitive with proton transfer within the dG.dC radical anion. The UV-dependent transfer of excess electrons and subsequent strand cleavage proceeds equivalently under anaerobic and aerobic conditions and is not sensitive to e-(aq) or hydroxyl radical trapping agents.

Rational design of a DNA wire possessing an extremely high hole transport ability

DNA is a promising conductive biopolymer. However, there are problems that need to be solved to realize real DNA wires. These include the low efficiency of hole transport and the serious oxidative damage that can occur during hole transport. We have demonstrated a protocol for the design of a DNA wire that can effectively mediate hole transport that is not adversely affected by oxidation during hole transport through the DNA duplex. We have synthesized a stable and effective DNA wire by incorporating a designer nucleobase, benzodeazaadenine derivatives, which have lower oxidation potentials and wider stacking areas but are not decomposed during hole transport.