Electronic structure of genomic DNA: a photoemission and X-ray absorption study

Superlow Power Consumption Memristor Based on Borphyrin-Deoxyribonucleic Acid Composite Films as Artificial Synapse for Neuromorphic Computing

Memristor synapses based on green and pollution-free organic materials are expected to facilitate biorealistic neuromorphic computing and to be an important step toward the next generation of green electronics. Metalloporphyrin is an organic compound that widely exists in nature with good biocompatibility and stable chemical properties, and has already been used to fabricate memristors. However, the application of metalloporphyrin-based memristors as synaptic devices still faces challenges, such as realizing a high switching ratio, low power consumption, and bidirectional conductance modulation. We developed a memristor that improves the resistive switching (RS) characteristics of Zn(II)meso-tetra(4-carboxyphenyl) porphine (ZnTCPP) by combining it with deoxyribonucleic acid (DNA) in a composite film. The as-fabricated ZnTCPP-DNA-based device showed excellent RS memory characteristics with a sufficiently high switching ratio of up to ∼104, super low power consumption of ∼39.56 nW, good cycling stability, and data retention capability. Moreover, bidirectional conductance modulation of the ZnTCPP-DNA-based device can be controlled by modulating the amplitudes, durations, and intervals of positive and negative pulses. The ZnTCPP-DNA-based device was used to successfully simulate a series of synaptic functions including long-term potentiation, long-term depression, spike time-dependent plasticity, paired-pulse facilitation, excitatory postsynaptic current, and human learning behavior, which demonstrates its potential applicability to neuromorphic devices. A two-layer artificial neural network was used to demonstrate the digit recognition ability of the ZnTCPP-DNA-based device, which reached 97.22% after 100 training iterations. These results create a new avenue for the research and development of green electronics and have major implications for green low-power neuromorphic computing in the future.

DNA-Assisted Creation of a Library of Ultrasmall Multimetal/Metal Oxide Nanoparticles Confined in Silica

Supported ultrasmall metal/metal oxide nanoparticles (UMNPs) with sizes in the range of 1-5 nm exhibit unique properties in sensing, catalysis, biomedicine, etc. However, the metal-support and metal-metal precursor interactions were not as well controlled to stabilize the metal nanoparticles on/in the supports. Herein, DNA is chosen as a template and a ligand for the silica-supported UMNPs, taking full use of its binding ability to metal ions via either electrostatic or coordination interactions. UMNPs thus are highly dispersed in silica via self-assembly of DNA and DNA-metal ion interactions with the assistance of a co-structural directing agent (CSDA). A large number of metal ions are easily retained in the mesostructured DNA-silica materials, and their growth is controlled by the channels after calcination. Based on this directing concept, a material library, consisting of 50 mono- and 54 bicomponent UMNPs confined within silica and with narrow size distribution, is created. Theoretical calculation proves the indispensability of DNA with combination of several organics in the synthesis of ultrasmall metal nanoparticles. The Pt-silica and Pt/Ni-silica chosen from the library exhibit good catalytic performance for toluene combustion. This generalizable and straightforward synthesis strategy is expected to widen the corresponding applications of supported UMNPs.

Study of porphyrin-modified liquid exfoliated graphene field-effect transistors for evaluating DNA methylation degree

The applications of graphene field-effect transistors (FETs) for monitoring DNA hybridization have been widely accepted; however, for evaluating DNA methylation degree, an emerging requirement of epigenetic research, no work has been found due to the difficulties in detecting 5-methylcytosine (5mC) sites along the genomic sequence as well as counting their amount (NmC). Herein, to achieve this, a strategy for exploiting a liquid exfoliated graphene (LEG)-based FET (LEG-FET) as a sensing platform was proposed. First, LEG-FETs were prepared and activated by tetra-4-aminophenyl-porphyrin (TAPP) for anchoring single-strand DNAs (ssDNAs). Second, the 5mC sites in ssDNA were recognized by the specifically absorbed 5mC antibody (5mCab) and transduced to the changed currents (ΔIDS) by LEG-FET according to the integration of the methylation-immuno sensing principle and FET's working mechanism. Briefly, more 5mCab molecules could be captured by more 5mC sites, resulting in larger ΔIDS. The TAPP effects on LEG-FET were analyzed by SEM, Raman, AFM, and XPS characterizations as well as electronic measurements. The validity of this LEG-FET sensing platform for evaluating DNA methylation degree was proven step by step; this included the examinations of the synthesized ssDNAs with the known NmC and real ssDNA samples, whose methylation degrees were pre-determined by the gold-standard method, which is based on tedious bisulphite sequence operations and expensive mass spectrometry technology. Moreover, theoretical explanations were also provided for the sensing mechanism in the proposed DNA methylation analytical components. In conclusion, the positive and linear relations of IDS changing ratio vs. NmC as well as the detection limit of one 5mC site indicate that TAPP-modified LEG-FET can provide an alternative analytical tool to realize fast and economical DNA methylation evaluation.

Meso-tetra(4-carboxyphenyl)porphine-Enhanced DNA Methylation Sensing Interface on a Light-Addressable Potentiometric Sensor

DNA methylation (DNAm) sensors are an emerging branch in the discipline of sensors. It is believed to be able to promote the next generation of epigenetics-based diagnostic technology. Differing from the traditional biochemical sensors that aimed at individual molecules, the challenge in DNAm sensors is how to determine the amount of 5-methylcytosine (5mC) in a continuous nucleotide sequence. Here, we report a comparative study about meso-tetra(4-carboxyphenyl)porphine (TCPP)-based DNAm sensing interfaces on a light-addressable potentiometric sensor (LAPS), depending on TCPP's postures that are flat in the π-conjugated TCPP layer on reduced-graphene-oxide-decorated LAPS (#1) and stand-up in the covalently anchored TCPP on glutaraldehyde (GA)-treated LAPS (#2), along with the blank one (only GA-treated LAPS, #3). These DNAm sensing interfaces are also distinct from the traditional biosensing interface on LAPS, that is: it is not functionalized by the sensing indicator (5mC antibody, in this case) but by the target nucleotide sequence. The surface characterization techniques such as Raman spectra, scanning electron microscopy, and X-ray photoelectron spectroscopy are conducted to prove the decorations, as well as the anchored nucleotides. It is found that, though all of them can detect as low as one 5mC in the target sequence, the enhanced DNAm sensitivity is obtained by #2, which is evidenced by the higher output-voltage changing ratio for the 5mC site of #2 than those of #1 and #3. Furthermore, the underlying causes for the improved sensitivity in #2 are proposed, according to the conformational and electronic properties of TCPP molecules. Conclusively, TCPP's synergetic function, including the molecular configuration and the activate (carboxyl) groups on its peripheral substituents, to improve the DNAm sensing interface on LAPS is investigated and demonstrated. This can shed light on a new approach for DNA methylation detection, with the merits of low cost, independence on bisulfite conversion, and polymerase chain reaction.

Reduced Carboxylate Graphene Oxide based Field Effect Transistor as Pb2+ Aptamer Sensor

Aptamer functionalized graphene field effect transistor (apta-GFET) is a versatile bio-sensing platform. However, the chemical inertness of graphene is still an obstacle for its large-scale applications and commercialization. In this work, reduced carboxyl-graphene oxide (rGO-COOH) is studied as a self-activated channel material in the screen-printed apta-GFETs for the first time. Examinations are carefully executed using lead-specific-aptamer as a proof-of-concept to demonstrate its functions in accommodating aptamer bio-probes and promoting the sensing reaction. The graphene-state, few-layer nano-structure, plenty of oxygen-containing groups and enhanced LSA immobilization of the rGO-COOH channel film are evidenced by X-ray photoelectron spectroscopy, Raman spectrum, UV-visible absorbance, atomic force microscopy and scanning electron microscope. Based on these characterizations, as well as a site-binding model based on solution-gated field effect transistor (SgFET) working principle, theoretical deductions for rGO-COOH enhanced apta-GFETs’ response are provided. Furthermore, detections for disturbing ions and real samples demonstrate the rGO-COOH channeled apta-GFET has a good specificity, a limit-of-detection of 0.001 ppb, and is in agreement with the conventional inductively coupled plasma mass spectrometry method. In conclusion, the careful examinations demonstrate rGO-COOH is a promising candidate as a self-activated channel material because of its merits of being independent of linking reagents, free from polymer residue and compatible with rapidly developed print-electronic technology.

Low energy secondary electron induced damage of condensed nucleotides

Radiation damage and stimulated desorption of nucleotides 2'-deoxyadenosine 5'-monophosphate (dAMP), adenosine 5'-monophosphate (rAMP), 2'-deoxycytidine 5'-monophosphate (dCMP), and cytidine 5'-monophosphate (rCMP) deposited on Au have been measured using x-rays as both the probe and source of low energy secondary electrons. The fluence dependent behavior of the O-1s, C-1s, and N-1s photoelectron transitions was analyzed to obtain phosphate, sugar, and nucleobase damage cross sections. Although x-ray induced reactions in nucleotides involve both direct ionization and excitation, the observed bonding changes were likely dominated by the inelastic energy-loss channels associated with secondary electron capture and transient negative ion decay. Growth of the integrated peak area for the O-1s component at 531.3 eV, corresponding to cleavage of the C-O-P phosphodiester bond, yielded effective damage cross sections of about 23 Mb and 32 Mb (1 Mb = 10^-18 cm²) for AMP and CMP molecules, respectively. The cross sections for sugar damage, as determined from the decay of the C-1s component at 286.4 eV and the glycosidic carbon at 289.0 eV, were slightly lower (about 20 Mb) and statistically similar for the r- and d- forms of the nucleotides. The C-1s component at 287.6 eV, corresponding to carbons in the nucleobase ring, showed a small initial increase and then decayed slowly, yielding a low damage cross section (∼5 Mb). Although there is no statistical difference between the sugar forms, changing the nucleobase from adenine to cytidine has a slight effect on the damage cross section, possibly due to differing electron capture and transfer probabilities.

DNA nanostructures doped with lanthanide ions for highly sensitive UV photodetectors

Deoxyribonucleic acid (DNA) and lanthanide ions (Ln³⁺) exhibit exceptional optical properties that are applicable to the development of nanoscale devices and sensors. Although DNA nanostructures and Ln³⁺ ions have been investigated for use in the current state of technology for more than a few decades, researchers have yet to develop DNA and Ln³⁺ based ultra-violet (UV) photodetectors. Here, we fabricate Ln³⁺ (such as holmium (Ho³⁺), praseodymium (Pr³⁺), and ytterbium (Yb³⁺))‒doped double crossover (DX)‒DNA lattices through substrate-assisted growth and salmon DNA (SDNA) thin films via a simple drop-casting method on oxygen (O₂) plasma-treated substrates for high performance UV photodetectors. Topological (AFM), optical (UV-vis absorption and FTIR), spectroscopic (XPS), and electrical (I‒V and photovoltage) measurements of the DX‒DNA and SDNA thin films doped with various concentrations of Ln³⁺ ([Ln³⁺]) are explored. From the AFM analysis, the optimum concentrations of various Ln³⁺ ([Ln³⁺]_O) are estimated (where the phase transition of Ln³⁺‒doped DX‒DNA lattices takes place from crystalline to amorphous) as 1.2 mM for Ho³⁺, 1.5 mM for Pr³⁺, and 1.5 mM for Yb³⁺. The binding modes and chemical states are evaluated through optical and spectroscopic analysis. From UV-vis absorption studies, we found that as the [Ln³⁺] was increased, the absorption intensity decreased up to [Ln³⁺]_O, and increased above [Ln³⁺]_O. The variation in FTIR peak intensities in the nucleobase and phosphate regions, and the changes in XPS peak intensities and peak positions detected in the N 1 s and P 2p core spectra of Ln³⁺‒doped SDNA thin films clearly indicate that the Ln³⁺ ions are properly bound between the bases (through chemical intercalation) and to the phosphate backbone (through electrostatic interactions) of the DNA molecules. Finally, the I‒V characteristics and time-dependent photovoltage of Ln³⁺‒doped SDNA thin films are measured both in the dark and under UV LED illuminations (λ_LED = 382 nm) at various illumination powers. The photocurrent and photovoltage of Ln³⁺‒doped SDNA thin films are enhanced up to the [Ln³⁺]_O compared to pristine SDNA due to the charge carriers generated from both SDNA and Ln³⁺ ions upon the absorption of light. From our observations, the photovoltages as function of illumination power suggest higher responsivities, and the photovoltages as function of time are almost constant which indicates the stability and retention characteristics of the Ln³⁺‒doped SDNA thin films. Hence, our method which provides an efficient doping of Ln³⁺ into the SDNA with a simple fabrication process might be useful in the development of high-performance optoelectronic devices and sensors.

Electromagnetic and optical characteristics of Nb5+-doped double-crossover and salmon DNA thin films

We report the fabrication and physical characteristics of niobium ion (Nb⁵⁺)-doped double-crossover DNA (DX-DNA) and salmon DNA (SDNA) thin films. Different concentrations of Nb⁵⁺ ([Nb⁵⁺]) are coordinated into the DNA molecules, and the thin films are fabricated via substrate-assisted growth (DX-DNA) and drop-casting (SDNA) on oxygen plasma treated substrates. We conducted atomic force microscopy to estimate the optimum concentration of Nb⁵⁺ ([Nb⁵⁺]_O = 0.08 mM) in Nb⁵⁺-doped DX-DNA thin films, up to which the DX-DNA lattices maintain their structures without deformation. X-ray photoelectron spectroscopy (XPS) was performed to probe the chemical nature of the intercalated Nb⁵⁺ in the SDNA thin films. The change in peak intensities and the shift in binding energy were witnessed in XPS spectra to explicate the binding and charge transfer mechanisms between Nb⁵⁺ and SDNA molecules. UV-visible, Raman, and photoluminescence (PL) spectra were measured to determine the optical properties and thus investigate the binding modes, Nb⁵⁺ coordination sites in Nb⁵⁺-doped SDNA thin films, and energy transfer mechanisms, respectively. As [Nb⁵⁺] increases, the absorbance peak intensities monotonically increase until ∼[Nb⁵⁺]_O and then decrease. However, from the Raman measurements, the peak intensities gradually decrease with an increase in [Nb⁵⁺] to reveal the binding mechanism and binding sites of metal ions in the SDNA molecules. From the PL, we observe the emission intensities to reduce them at up to ∼[Nb⁵⁺]_O and then increase after that, expecting the energy transfer between the Nb⁵⁺ and SDNA molecules. The current-voltage measurement shows a significant increase in the current observed as [Nb⁵⁺] increases in the SDNA thin films when compared to that of pristine SDNA thin films. Finally, we investigate the temperature dependent magnetization in which the Nb⁵⁺-doped SDNA thin films reveal weak ferromagnetism due to the existence of tiny magnetic dipoles in the Nb⁵⁺-doped SDNA complex.

Chiral Selective Chemistry Induced by Natural Selection of Spin-Polarized Electrons

The search to understand the origin of homochirality in nature has been ongoing since the time of Pasteur. Previous work has shown that DNA can act as a spin filter for low-energy electrons and that spin-polarized secondary electrons produced by X-ray irradiation of a magnetic substrate can induce chiral selective chemistry. In the present work it is demonstrated that secondary electrons from a substrate that are transmitted through a chiral overlayer cause enantiomeric selective chemistry in an adsorbed adlayer. We determine the quantum yields (QYs) for dissociation of (R)- or (S)-epichlorohydrin adsorbed on a chiral self-assembled layer of DNA on gold and on bare gold (for control). The results show that there is a significant difference in the QYs between the two enantiomers when adsorbed on DNA, but none when they are adsorbed on bare Au. We propose that the effect results from natural spin filtering effects cause by the chiral monolayer.

Insight into bio-metal interface formation in vacuo: interplay of S-layer protein with copper and iron

The mechanisms of interaction between inorganic matter and biomolecules, as well as properties of resulting hybrids, are receiving growing interest due to the rapidly developing field of bionanotechnology. The majority of potential applications for metal-biohybrid structures require stability of these systems under vacuum conditions, where their chemistry is elusive, and may differ dramatically from the interaction between biomolecules and metal ions in vivo. Here we report for the first time a photoemission and X-ray absorption study of the formation of a hybrid metal-protein system, tracing step-by-step the chemical interactions between the protein and metals (Cu and Fe) in vacuo. Our experiments reveal stabilization of the enol form of peptide bonds as the result of protein-metal interactions for both metals. The resulting complex with copper appears to be rather stable. In contrast, the system with iron decomposes to form inorganic species like oxide, carbide, nitride, and cyanide.

Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials

In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed.

Electronic structure, stacking energy, partial charge, and hydrogen bonding in four periodic B-DNA models

We present a theoretical study of the electronic structure of four periodic B-DNA models labeled (AT)(10), (GC)(10), (AT)(5)(GC)(5), and (AT-GC)(5) where A denotes adenine, T denotes thymine, G denotes guanine, and C denotes cytosine. Each model has ten base pairs with Na counterions to neutralize the negative phosphate group in the backbone. The (AT)(5)(GC)(5) and (AT-GC)(5) models contain two and five AT-GC bilayers, respectively. When compared against the average of the two pure models, we estimate the AT-GC bilayer interaction energy to be 19.015 Kcal/mol, which is comparable to the hydrogen bonding energy between base pairs obtained from the literature. Our investigation shows that the stacking of base pairs plays a vital role in the electronic structure, relative stability, bonding, and distribution of partial charges in the DNA models. All four models show a highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) gap ranging from 2.14 to 3.12 eV with HOMO states residing on the PO(4) + Na functional group and LUMO states originating from the bases. Our calculation implies that the electrical conductance of a DNA molecule should increase with increased base-pair mixing. Interatomic bonding effects in these models are investigated in detail by analyzing the distributions of the calculated bond order values for every pair of atoms in the four models including hydrogen bonding. The counterions significantly affect the gap width, the conductivity, and the distribution of partial charge on the DNA backbone. We also evaluate quantitatively the surface partial charge density on each functional group of the DNA models.

The relationship between interfacial bonding and radiation damage in adsorbed DNA

Illustration showing that secondary electrons have a higher damage probability for thiolated DNA as opposed to unthiolated DNA, due to the former's higher density of LUMO states, which leads to more efficient capture of the low energy electrons.

Observation of cleavage in DNA and nucleotides following oxygen K-shell ionization by measuring X-ray absorption near edge structure

PURPOSE

To investigate which type of bond is more likely to be cleaved in functional groups in DNA including the nucleobases by the K-shell ionization of oxygen of DNA, and to determine whether the production of propenal is specific to the oxygen resonant excitation. To investigate the degradation pattern which depends on the type of nucleobase in the DNA monomer.

MATERIALS AND METHODS

Calf thymus DNA film and four nucleotides (dAMP, TMP, dGMP, and dCMP) films were used as samples. Soft X-rays with energy of 560 eV were used to irradiate the samples, and the changes in the X-ray absorption near edge structure (XANES) spectra during the irradiation were measured. The XANES measurements were performed by using a 0.02 eV scanning photon energy step.

RESULTS

The difference spectra for DNA and nucleotides were similar to those for pyridine deprotonation. The oxygen K-edge regions in the difference spectra were all similar apart from the spectrum obtained at the resonant excitation energy of oxygen in DNA. The spectral change did not depend on the type of nucleotide.

CONCLUSION

(1) Deprotonation of the nucleobase -NH is usually induced by core ionization of carbon, nitrogen, and oxygen; (2) propenal production is specific to the oxygen K-shell resonant excitation; and (3) the pattern of XANES spectral changes does not significantly depend on the type of nucleobase.