Detection of nucleobases on borophene nanosheet: A DFT investigation.

In this paper, we present a computational study investigating the electronic properties of DNA nucleobases (Adenine, Guanine, Cytosine and Thymine) on χ3 borophene using a combination of density functional theory (DFT) and non-equilibrium Green's function (NEGF) formalism.The adsorption energy, equilibrium distance, net charge of transfer, and density of states (DOSs) are obtained at different molecule orientations and selective positions.The most stable geometries of DNA molecules on χ3 borophene are also determined.By using (NEGF) formalism, the electronic transmission and electrical current are calculated separately as a function of applied bias voltage for each nucleobase. We find that attaching this molecule to borophene changes the electrical conductivity.Results indicate the strong potential of borophene in adsorption of the DNA molecules, meaning this two-dimensional material could be a suitable candidate for future DNA sequencing devices.

Chemical Probing of Thymine in the TGG/CGG Triad to Explore the Deamination of 5-Methylcytosine in the CGG Repeat.

The methylation of cytosine in the full mutation of the expanded CGG repeat and subsequent deamination to thymine could be a measure of repeat instability. We report the synthesis of NCD-Bpy, which binds to the TGG/CGG site in the repeat hairpin. NCD-Bpy forces the thymine in the TGG/CGG site to flip out from the π-stack, recruits osmium tetroxide in the vicinity of the flipped-out T, and oxidizes the T. The piperidine-induced cleavage band successfully determined the position of the T in the expanded CGG repeat.

Two-dimensional C3N based sub-10 nanometer biosensor.

Detection and sequencing of various nucleobases are of immense usefulness that can revolutionise future medical diagnostics procedures. In this regard, the newly discovered 2D material, C3N, has demonstrated supreme potential for future nanoelectronic and spintronic developments due to its unique sets of electronic properties and structural similarity to graphene. Herein, we have investigated the effect of various nucleobases in the close vicinity of a C3N nanoribbon. Our extensive calculations revealed significant changes in the transport behaviour in the presence of DNA/RNA molecules. The transport response can be further modified through the (i) incorporation of doping, (ii) presence of defects, (iii) concentration of the adsorbed molecule, etc. Furthermore, in the presence of a gate voltage in a field-effect transistor (FET) geometry, the conductivity response can be improved significantly with an ∼100% change in the presence of an adsorbed molecule. The observation of a negative differential resistance (NDR) in the C3N system has also been reported here for the first time. Our current observation demonstrates the usefulness of the C3N system as a next generation bio-sensor for the sequencing of various nucleobases, offering new leads for future developments in bioelectronics, superior sensing architectures and sustainable designs.

Detection of trifluridine in tumors of patients with metastatic colorectal cancer treated with trifluridine/tipiracil.

PURPOSE: Trifluridine (FTD) is the active component of the nucleoside chemotherapeutic drug trifluridine/tipiracil (FTD/TPI), which is approved worldwide for the treatment of patients with metastatic gastrointestinal cancer. FTD exerts cytotoxic effects via its incorporation into DNA, but FTD has not been detected in the tumor specimens of patients. The purpose of this study was to detect FTD in tumors resected from metastatic colorectal cancer (mCRC) patients who were administered FTD/TPI. Another purpose was to investigate the turnover rate of FTD in tumors and bone marrow in a mouse model. METHODS: Tumors and normal tissue specimens were obtained from mCRC patients who were administered FTD/TPI or placebo at Kyushu University Hospital. Tumors and bone marrow were resected from mice with peritoneal dissemination treated with FTD/TPI. To detect and quantitate FTD incorporated into DNA, immunohistochemical staining of paraffin-embedded specimens (IHC-p staining) and slot-blot analysis of DNA purified from these tissues were performed using an anti-BrdU antibody. IHC-p staining of proliferation and apoptosis markers was also performed. RESULTS: FTD was detected in metastatic tumors obtained from mCRC patients who were administered FTD/TPI, but who had discontinued the treatment several weeks before surgery. In a peritoneal dissemination mouse model, FTD was still detected in tumors 13 days after the cessation of FTD/TPI treatment, but had disappeared from bone marrow within 6 days. CONCLUSION: These results indicate that FTD persists longer in tumors than in bone marrow, which may cause a sustained antitumor effect with tolerable hematotoxicity.

Fabrication of WO2/W@C core-shell nanospheres for voltammetric simultaneous determination of thymine and cytosine.

Pomegranate-like multicore WO2/W nanocrystals wrapped with layers of multiporous carbon were fabricated via carbonization of a copper(II)-organic framework host and a tungsten-based polyoxometalates guest, and subsequent etching off the metallic copper. The WO2/W@C core-shell nanospheres were employed to modify an electrode for the analysis of the DNA bases thymine (T) and cytosine (C) by differential pulse voltammetry. The WO2/W@C exhibited strongly increased oxidation signal of T and C. Under optimized conditions, the enhanced peak current represented excellent analytical performance for determination of T and C. This is attributed to the synergic effects of the porous multicore-shell microstructure and the use of tungsten-based materials with their excellent electrocatalytic activity for T and C, with typical peaks voltages near 1.26 V and 1.44 V. The calibration plots for T and C extend from 1 to 4000 µM and from 1 to 3000 µM, respectively, and both detection limits are 0.2 µM. The method was successfully applied to the determination of T and C in spiked blood and urine samples, and the recoveries are form 97.3 to 105.0%. Graphic abstractCore-shell nanospheres of type WO2/W-carbon were prepared for highly sensitive simultaneous voltammetric determination of thymine and cytosine.

SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping.

Surface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time that a DNA strand resides within the plasmonic hot spot. In fact, DNA molecules flow through the nanopores so rapidly that the SERS signals collected are not sufficient for single-molecule analysis. Here, we report an approach to control the residence time of molecules in the hot spot by an electro-plasmonic trapping effect. By directly adsorbing molecules onto a gold nanoparticle and then trapping the single nanoparticle in a plasmonic nanohole up to several minutes, we demonstrate single-molecule SERS detection of all four DNA bases as well as discrimination of single nucleobases in a single oligonucleotide. Our method can be extended easily to label-free sensing of single-molecule amino acids and proteins.

Charge Transfer Platform and Catalytic Amplification of Phenanthroimidazole Derivative: A New Strategy for DNA Bases Recognition.

Research about DNA composition has been concentrated on DNA damage in the past few decades. However, it still remains a great challenge to construct a rapid, facile, and accurate approach for simultaneously monitoring four DNA bases, guanine (G), adenine (A), thymine (T), and cytosine (C). Herein, a novel electrochemical sensor based on phenanthroimidazole derivative, 2-(4-bromophenyl)-1-phenyl-1H-phenanthro[9,10-d]-imidazole (PPI), is successfully fabricated by a simple electrochemical method. The bromophenyl group in PI could expand their aromatic plane, induce the π-conjugated extension, and enhance the charge transfer and π-π interaction. The phenyl group at N1 position could regulate the intermolecular interaction, which could promote the possibility of intermolecular connection. The PPI polymer (poly(PPI)) with π-electron enriched conjugation architecture has been applied in simultaneous determination of G, A, T, and C in neutral solution by square wave voltammetry (SWV) method with well-separated peak potentials at 0.714, 1.004, 1.177, and 1.353 V, respectively. The sensor functionalized with poly(PPI) exhibits wide linear response for G, A, T, and C in the concentration ranges of 3-300, 1-300, 30-800, and 20-750 µM, respectively. With favorable selectivity, stability, and reproducibility, the sensor is successfully utilized to monitor four DNA bases in real samples, displaying a promising prospect for electrochemical sensing devices.

Bacterial Nucleobases Synergistically Induce Larval Settlement and Metamorphosis in the Invasive Mussel Mytilopsis sallei.

Marine bacterial biofilms have long been recognized as potential inducers of larval settlement and metamorphosis in marine invertebrates, but few chemical cues from bacteria have been identified. Here, we show that larval settlement and metamorphosis of an invasive fouling mussel, Mytilopsis sallei, could be induced by biofilms of bacteria isolated from its adult shells and other substrates from the natural environment. One of the strains isolated, Vibrio owensii MS-9, showed strong inducing activity which was attributed to the release of a mixture of nucleobases including uracil, thymine, xanthine, hypoxanthine, and guanine into seawater. In particular, the synergistic effect of hypoxanthine and guanine was sufficient for the inducing activity of V. owensii MS-9. The presence of two or three other nucleobases could enhance, to some extent, the activity of the mixture of hypoxanthine and guanine. Furthermore, we determined that bacteria producing higher concentrations of nucleobases were more likely to induce larval settlement and metamorphosis of M. sallei than were bacteria producing lower concentrations of nucleobases. The present study demonstrates that bacterial nucleobases play an important role in larval settlement and metamorphosis of marine invertebrates. This provides new insights into our understanding of the role of environmental bacteria in the colonization and aggregation of invasive fouling organisms and of the metabolites used as chemical mediators in cross-kingdom communication within aquatic systems.IMPORTANCE Invasive species are an increasingly serious problem globally. In aquatic ecosystems, invasive dreissenid mussels are well-known ecological and economic pests because they appear to effortlessly invade new environments and foul submerged structures with high-density aggregations. To efficiently control exotic mussel recruitment and colonization, the need to investigate the mechanisms of substrate selection for larval settlement and metamorphosis is apparent. Our work is one of very few to experimentally demonstrate that compounds produced by environmental bacteria play an important role in larval settlement and metamorphosis in marine invertebrates. Additionally, this study demonstrates that bacterial nucleobases can be used as chemical mediators in cross-kingdom communication within aquatic systems, which will enhance our understanding of how microbes induce larval settlement and metamorphosis of dreissenid mussels, and it furthermore may allow the development of new methods for application in antifouling.

Artificial Sandwich Base for Monitoring Single-Nucleobase Changes and Charge-Transfer Rates in DNA.

Developing a convenient method to discriminate among different types of DNA nucleotides within a target sequence of the human genome is extremely challenging. We herein report an artificial ferrocene-base (Fe-base) that was synthesized and incorporated into different loci of a DNA strand. The Fe-base replacement on a nucleobase can interact with DNA bases and efficiently discriminate among A, T, G, and C DNA bases of the complementary locus on the basis of interacting electrochemical properties. Furthermore, cyclic-voltammetry (CV) studies demonstrated the electrochemical stability of DNA strands incorporated with Fe-bases and the reversibility of the incorporation. Square-wave voltammetry (SWV) was performed to measure current changes between Fe-bases and bases of interest in the DNA duplex. The changes in the charge-transfer rates appeared to be correlated with the position of the Fe-base in the DNA strand, allowing rapid and efficient sensing of single-nucleobase changes in DNA and showing promise for the design of Fe-oligomer chip technology as a tool for DNA sequencing.

A novel mass spectrometry method based on competitive non-covalent interaction for the detection of biomarkers.

We report a novel biosensor platform based on competitive non-covalent interaction between ssDNA and a mass tag towards AuNPs, which detects PSA biomarkers sensitively, observed using MALDI MS. A detection limit of 57 pg mL-1 has been achieved, showing an improvement of two orders of magnitude compared to the traditional spectroscopic method.

Profiles of a broad spectrum of epigenetic DNA modifications in normal and malignant human cell lines: Proliferation rate is not the major factor responsible for the 5-hydroxymethyl-2'-deoxycytidine level in cultured cancerous cell lines.

Active demethylation of 5-methylcytosine moiety in DNA occurs by its sequential oxidation to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, catalysed by enzymes of the Ten-Eleven Translocation family proteins (TETs 1, 2 and 3). Here we analyzed for the first time all the intermediate products of DNA demethylation pathway in the form of deoxynucleosides (5-methyl-2'-deoxycytidine, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine and 5-carboxy-2'-deoxycytidine as well as 5-(hydroxymethyl)-2'-deoxyuridine) using automated isotope-dilution online two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry. DNA was isolated from human malignant cell lines of colon adenocarcinoma (HCT 116), melanoma (Me45), myelogenous leukemia bone marrow blasts (K562), EBV-positive Burkitt's lymphoma lymphoblasts (Raji), EBV-negative Burkitt's lymphoma lymphoblasts (male-CA46 and female-ST486), as well as normal neonatal dermal fibroblasts (NHDF-Neo). The expression levels of TET1, TET2, TET3, SMUG1, and TDG genes were also assayed by RT-qPCR. Our results show a global erasure of 5-hydroxymethyl-2'-deoxycytidine and 5-carboxy-2'-deoxycytidine in DNA of cultured cells compared with DNA from primary malignant tissue. Moreover, malignant cells in culture have a quite different DNA epigenetic profile than cultured normal cells, and different types of malignant cells display different and characteristic profiles of DNA epigenetic marks. Similar analyses of a broader spectrum of epigenetic modifications, not restricted to 5-methyl-2'-deoxycytidine, could lead to better understanding of the mechanism(s) responsible for emergence of different types of cancer cells.

Copper-Nitrogen-Doped Graphene Hybrid as an Electrochemical Sensing Platform for Distinguishing DNA Bases.

An electrochemical sensor using ultralight and porous copper-nitrogen-doped graphene (CuNRGO) nanocomposite as the electrocatalyst has been constructed to simultaneously determine DNA bases such as guanine (G) and cytosine (C), adenine (A), and thymine (T). The nanocomposite is synthesized by thermally annealing an ice-templated structure of graphene oxide (GO) and Cu(phen)2. Because of the unique structure and the presence of Cu2+-N active sites, the CuNRGO exhibits outstanding electrocatalytic activity toward the oxidation of free DNA bases. After optimizing the experimental conditions, the CuNRGO-based electrochemical sensor shows good linear responses for the G, A, T, and C bases in the concentration ranges of 0.132-6.62 µM, 0.37-5.18 µM, 198.2-5551 µM, and 270.0-1575 µM, respectively. The results demonstrate that CuNRGO is a promising electrocatalyst for electrochemical sensing devices.

Graphite-Based Nanocomposite Electrochemical Sensor for Multiplex Detection of Adenine, Guanine, Thymine, and Cytosine: A Biomedical Prospect for Studying DNA Damage.

Guanine (G), adenine (A), thymine (T), and cytosine (C) are the four basic constituents of DNA. Studies on DNA composition have focused especially on DNA damage and genotoxicity. However, the development of a rapid, simple, and multiplex method for the simultaneous measurement of the four DNA bases remains a challenge. In this study, we describe a graphite-based nanocomposite electrode (Au-rGO/MWCNT/graphite) that uses a simple electro-co-deposition approach. We successfully applied the developed sensor for multiplex detection of G, A, T, and C, using square-wave voltammetry. The sensor was tested using real animal and plant DNA samples in which the hydrolysis of T and C could be achieved with 8 mol L-1 of acid. The electrochemical sensor exhibited excellent sensitivity (G = 178.8 nA/µg mL-1, A = 92.9 nA/µg mL-1, T = 1.4 nA/µg mL-1, and C = 15.1 9 nA/µg mL-1), low limit of detection (G, A = 0.5 µg mL-1; T, C = 1.0 µg mL-1), and high selectivity in the presence of common interfering factors from biological matrixes. The reliability of the established method was assessed by method validation and comparison with the ultraperformance liquid chromatography technique, and a correlation of 103.7% was achieved.

Zn(2+)-cyclen-based complex enable a selective detection of single-stranded thymine-rich DNA in aqueous buffer.

It is a big challenge to develop fluorescent probes for selective detection of DNA with specific sequences in aqueous buffers. We report a new tetraphenylethene-based Zn(2+)-cyclen complex (TPECyZn), and a chemo-sensing ensemble of the Zn complex with phenol red. TPECyZn showed significant fluorescence enhancement upon binding to thymine-rich DNA in HEPES buffers. But its selectivity was not high enough to eliminate the interference from some random DNA. By constructing the chemo-sensing ensemble of TPECyZn with phenol red, the background fluorescence was eliminated due to the energy transfer from TPECyZn to phenol red. Moreover, this chemo-sensing ensemble revealed high selectivity in detecting thymine-rich single-stranded DNA over other DNA in aqueous buffer. It can detect poly deoxythymidylic acid sequence as short as 2 nt. This detection in aqueous media makes this probe feasible in real application.

Synthesis and photophysical properties of pyrene-labeled 3-deaza-2'-deoxyadenosines comprising a non-π-conjugated linker: fluorescence quenching-based oligodeoxynucleotide probes for thymine identification.

Pyrene-labeled 3-deaza-2'-deoxyadenosine comprising a non-π-conjugated linker (py3z)A (1) was synthesized and its photophysical properties were investigated. Oligodeoxynucleotide (ODN) probes containing (py3z)A (1) exhibited remarkable fluorescence quenching only when the opposite base of the complementary strand was the perfectly matched thymine. Such fluorescence quenching-based ODN probes exhibited excellent on-off switching properties, making them useful tools for single nucleotide polymorphism (SNP) genotyping and for the identification of target genes and structural studies of nucleic acids.

Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine.

The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.

CuFe2O4 magnetic nanocrystal clusters as a matrix for the analysis of small molecules by negative-ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

CuFe2O4 magnetic nanocrystal clusters (CuFe2O4 MNCs) were proposed as a new matrix for small molecule analysis by negative ion matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the first time. We demonstrated its advantages over conventional organic matrices in the detection of small molecules such as amino acids, peptides, nucleobases, fatty acids, and steroid hormones. A systematic comparison of CuFe2O4 MNCs with different ionization modes revealed that MS spectra obtained for the CuFe2O4 MNC matrix in the negative ion mode was only featured by deprotonated ion peaks with a free matrix background, which was different from the complicated alkali metal adducts produced in the positive ion mode. The developed method was found relatively tolerant to salt contamination and exhibited good reproducibility. A detection limit down to the subpicomolar level was achieved when testosterone was analyzed. In addition, by comparison of the MS spectra obtained from bare Fe3O4 and MFe2O4 MNC (M = Co, Ni, Cu, Zn) matrices, two main factors of MFe2O4 MNC matrices were revealed to play a vital role in assisting the negative ion desorption/ionization (D/I) process: doping transition metals into ferrite nanocrystals favoring laser absorption and energy transfer and a good match between the UV absorption of MFe2O4 MNCs and the excitation of nitrogen laser source facilitating LDI efficiency. This work creates a new branch of application for MFe2O4 MNCs and provides an alternative solution for small molecule analysis.

Identification of charge separated states in thymine single strands.

UV excitation of the DNA single strand (dT)18 leads to electronically excited states that are potential gateways to DNA photolesions. Using time-resolved infrared spectroscopy we characterized a species with a lifetime of ∼100 ps and identified it as a charge separated excited state between two thymine bases.

Real-time analysis of self-assembled nucleobases by Venturi easy ambient sonic-spray ionization mass spectrometry.

In this study, the real-time analysis of self-assembled nucleobases was employed by Venturi easy ambient sonic-spray ionization mass spectrometry (V-EASI-MS). With the analysis of three nucleobases including 6-methyluracil (6MU), uracil (U) and thymine (T) as examples, different orders of clusters centered with different metal ions were recorded in both positive and negative modes. Compared with the results obtained by traditional electrospray ionization mass spectrometry (ESI-MS) under the same condition, more clusters with high orders, such as [6MU7+Na](+), [6MU15+2NH4](2+), [6MU10+Na](+), [T7+Na](+), and [T15+2NH4](2+) were detected by V-EASI-MS, which demonstrated the soft ionization ability of V-EASI for studying the non-covalent interaction in a self-assembly process. Furthermore, with the injection of K(+) to the system by a syringe pumping, the real-time monitoring of the formation of nucleobases clusters was achieved by the direct extraction of samples from the system under the Venturi effect. Therefore, the effect of cations on the formation of clusters during self-assembly of nucleobases was demonstrated, which was in accordance with the reports. Free of high voltage, heating or radiation during the ionization, this technique is much soft and suitable for obtaining the real-time information of the self-assembly system, which also makes it quite convenient for extraction samples from the reaction system. This "easy and soft" ionization technique has provided a potential pathway for monitoring and controlling the self-assembly processes.

Molecular design of an environmentally sensitive fluorescent nucleoside, 3-deaza-2'-deoxyadenosine derivative: distinguishing thymine by probing the DNA minor groove.

An environmentally sensitive fluorescent nucleoside containing a 3-deazaadenine skeleton has been developed, and its photophysical properties were investigated. Newly developed C3-naphthylethynylated 3-deaza-2'-deoxyadenosine ((3nz) A, 1) exhibited dual fluorescence emission from an intramolecular charge-transfer state and a locally excited state, depending upon molecular coplanarity. DNA probes containing 1 clearly discriminated a perfectly matched thymine base on the complementary strand by a distinct change in emission wavelength.