Interaction of Self-Assembled Monolayers of DNA with Electrons: HREELS and XPS Studies

Metal Ion-Condensed DNA Nanoparticle Library: Phase Separation and Transition and Antisense Therapy Applications

DNA condensation has long been investigated as a fundamental cellular activity and is known to be driven by the mediation of diverse condensing agents. The phase behaviors of DNA during condensation are particularly interesting because the complicated molecular structure of natural nucleotides fundamentally allows electrostatic, coordinate covalent, and various other secondary interactions with the condensing agents. Recently, metal ion (Mn+)-induced DNA condensation has emerged as a powerful approach to synthesizing nanoparticulate DNA structures suitable for therapeutic gene delivery. However, how the DNA phase changes during Mn+-induced DNA condensation has rarely been observed and is not understood yet. In this study, a library of Mn+-condensed DNA nanoparticles (Mn+-CDNPs) was established using 30 different types of Mn+s, and their phase behaviors during condensation were elucidated using spherical nucleic acids (SNAs) as electron microscopic labels. Importantly, the phase transition and separation of DNA were demonstrated to be driven by the Mn+s into either the growth of individual DNA particles or the fission of bulky DNA aggregates. Pt2+ and Eu3+ were chosen as model systems for the demonstration. The hard and soft acid nature of Mn+ is presumably the underlying driving force of these phase transitions. In addition, the Mn+-controlled anticancer therapeutic efficiency of the Mn+-CDNP library as a state-of-the-art gene delivery platform was demonstrated even for unmodified antisense oligonucleotides in association with the potential toxicity of the Mn+s released from the Mn+-CDNPs. This comprehensive study of the Mn+-dependent condensation of nucleic acids provides profound insights into the chemistry of the nucleic acid-Mn+ interactions and the reliable theragnostic applications of Mn+-CDNPs as functional nucleic acid nanostructures.

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.

Exploiting epoxy-rich poly(ethylene glycol) films for highly selective ssDNA sensing via electrochemical impedance spectroscopy

This study introduces an alternative approach to immobilize thiolated single-stranded DNA (ssDNA) for the DNA sensing. In contrast to the standard, monomolecular assembly of such moieties on gold substrate, over the thiolate-gold anchors, we propose to use bioinert, porous polyethylene glycol (PEG) films as a 3D template for ssDNA immobilization. The latter process relies on the reaction between the thiol group of the respectively decorated ssDNA and the epoxy groups in the epoxy-rich PEG matrix. The immobilization process and subsequent hybridization ability of the resulting sensing assembly were monitored using cyclic voltammetry and electrochemical impedance spectroscopy, with the latter tool proving itself as the most suitable transduction technique. Electrochemical data confirmed the successful immobilization of thiol-decorated ssDNA probes into the PEG matrix over the thiol-epoxy linkage as well as high hybridization efficiency, selectivity, and sensitivity of the resulting DNA sensor. Whereas this sensor was equivalent to the direct ssDNA assembly in terms of the efficiency, it exhibited a better selectivity and bioinert properties in view of the bioinert character of the PEG matrix. The above findings place PEG films as a promising platform for highly selective ssDNA sensing, leveraging their flexible chemistry, 3D character, and bioinert properties.

Elution-free DNA detection using CRISPR/Cas9-mediated light-up aptamer transcription: Toward all-in-one DNA purification and detection tube

Accurate and efficient detection of DNA is crucial for disease diagnosis and health monitoring. The traditional methods for DNA analysis involve multiple steps, including sample preparation, lysis, extraction, amplification, and detection. In this study, we present a one-step elution-free DNA analysis method based on the combination of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated light-up aptamer transcription (CLAT) assay and a DNA-capturing poly(2-dimethylaminomethyl styrene) (pDMAMS)-coated tube. The sample solution and lysis buffer are added to the pDMAMS-coated tube, and the DNA is efficiently captured on the surface via electrostatic interaction and directly detected by CLAT assay. The ability of the CRISPR/Cas9 system to specifically recognize DNA enables direct detection of DNA captured on the pDMAMS-coated tube. The combination of CLAT assay and pDMAMS-coated tube simplifies DNA detection in a single tube without the need for complicated extraction steps, improving sensitivity. Our platform demonstrated attomolar sensitivity in the detection of target DNA in cell lysate (0.92 aM), urine (7.7 aM), and plasma (94.6 aM) samples within 1 h. The practical applicability of this method was further demonstrated in experiments with tumor-bearing mice. We believe that this approach brings us closer to an all-in-one DNA purification and detection tube system and has potential applications in tissue and liquid biopsies, as well as various other DNA sensing applications.

Novel thermo and ion-responsive copolymers based on metallo-base pair directed host-guest complexation for highly selective recognition of Hg2+ in aqueous solution

The development of materials with highly selective recognition towards Hg²⁺ is of great significance in environmental monitoring. Herein, a novel thermo-responsive copolymer with Hg²⁺ recognition property is prepared via thermally-initiated copolymerization of 5'-O-Acryloyl 5-methyl-uridine (APU) and N-isopropylacrylamide (NIPAM). The chemical structure and stimuli-sensitive properties of poly(N-isopropylacrylamide-co-5-methyl-uridine) (P(NIPAM-co-APU)) linear polymers and hydrogel are thoroughly investigated. At the supramolecular level, P(NIPAM-co-APU) linear polymers could respond to both temperature and Hg²⁺ stimuli with highly selective recognition towards Hg²⁺ over other 18 metal ion species (at least 5 fold difference) and common anions. Upon capturing Hg²⁺ by APU units as host metal receptors, the lower critical solution temperature (LCST) of P(NIPAM-co-APU, PNU-7 and PNU-11) linear polymers are significantly shifted more than 10 °C due to the formation of stable APU-Hg²⁺-APU directed host-guest complexes. Accordingly, at the macroscopic level, P(NIPAM-co-APU) hydrogel display selective and robust recognition of Hg²⁺ under optimum conditions, and its maximum Hg²⁺ uptake capacity was 33.1 mg g^-1. This work provides a new option for Hg²⁺ recognition with high selectivity, which could be facilely integrated with other smart systems to achieve satisfactory detection of environmental Hg²⁺.

Light-Amplified CISS-Based Hybrid QD-DNA Impedimetric Device for DNA Hybridization Detection

We design and build a novel light-amplified electrochemical impedimetric device based on the CISS effect to detect DNA hybridization using a hybrid quantum dot (QD)-DNA monolayer on a ferromagnetic (FM) Ni/Au thin film for the first time. Using spin as a detection tool, the current research considers the chiral-induced spin selectivity (CISS) phenomenon. After injecting a spin current into the QD-DNA system with opposite polarities (up and down), the impedimetric device revealed a large differential change in the charge-transfer resistance (ΔR_ct) of ∼100 ohms for both spins. Nearly, a threefold increase in the ΔR_ct value to ∼270 ohms is observed when light with a wavelength of 532 nm is illuminated on the sample, owing to the amplified CISS effect. The yield of spin polarization as extracted from the Nyquist plot increases by a factor of more than 2 when exposed to light, going from 6% in the dark to 13% in the light. The impact of light on the CISS effect was further corroborated by the observation of the spin-dependent asymmetric quenching of photoluminescence (PL) in the same hybrid system. These observations are absent in the case of a noncomplementary QD-DNA system due to the absence of a helical structure in DNA. Based on this, we develop a spin-based DNA hybridization sensor and achieve a limit of detection of 10 fM. These findings open a practical path for the development of spin-based next-generation impedimetric DNA sensors and point-of-care devices.

Rapid and Unamplified Detection of SARS-CoV-2 RNA via CRISPR-Cas13a-Modified Solution-Gated Graphene Transistors

The disease caused by severe acute respiratory syndrome coronavirus, SARS-CoV-2, is termed COVID-19. Even though COVID-19 has been out for more than two years, it is still causing a global pandemic. Due to the limitations of sample collection, transportation, and kit performance, the traditional reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method has a long detection period and high testing costs. An increased risk of infection is inevitable, since many patients may not be diagnosed in time. The CRISPR-Cas13a system can be designed for RNA identification and knockdown, as a promising platform for nucleic acid detection. Here, we designed a solution-gated graphene transistor (SGGT) biosensor based on the CRISPR-Cas13a system. Using the gene-targeting capacity of CRISPR-Cas13a and gate functionalization via multilayer modification, SARS-CoV-2 nucleic acid sequences can be quickly and precisely identified without the need for amplification or fluorescence tagging. The limit of detection (LOD) in both buffer and serum reached the aM level, and the reaction time was about 10 min. The results of the detection of COVID-19 clinical samples from throat swabs agree with RT-PCR. In addition, the interchangeable gates significantly minimize the cost and time of device fabrication. In a nutshell, our biosensor technology is broadly applicable and will be suitable for point-of-care (POC) testing.

Rational Design of Porous Poly(ethylene glycol) Films as a Matrix for ssDNA Immobilization and Hybridization

Poly(ethylene glycol) (PEG) films, fabricated by thermally induced crosslinking of amine- and epoxy-terminated four-arm STAR-PEG precursors, were used as porous and bioinert matrix for single-stranded DNA (ssDNA) immobilization and hybridization. The immobilization relied on the reaction between the amine groups in the films and N-hydroxy succinimide (NHS) ester groups of the NHS-ester-decorated ssDNA. Whereas the amount of reactive amine groups in the films with the standard 1:1 composition of the precursors turned out to be too low for efficient immobilization, it could be increased noticeably using an excess (2:1) concentration of the amine-terminated precursor. The respective films retained the bioinertness of the 1:1 prototype and could be successfully decorated with probe ssDNA, resulting in porous, 3D PEG-ssDNA sensing assemblies. These assemblies exhibited high selectivity with respect to the target ssDNA strands, with a hybridization efficiency of 78–89% for the matching sequences and full inertness for non-complementary strands. The respective strategy can be applied to the fabrication of DNA microarrays and DNA sensors. As a suitable transduction technique, requiring no ssDNA labeling and showing high sensitivity in the PEG-ssDNA case, electrochemical impedance spectroscopy is suggested.

Self-Assembly of Hausmannite Mn3O4 Triangular Structures on Cocosin Protein Scaffolds for High Energy Density Symmetric Supercapacitor Application

Recent advances in using biological scaffolds for nanoparticle synthesis have proven to be useful for preparing various nanostructures with uniform shape and size. Proteins are significant scaffolds for generating various nanostructures partly because of the presence of many functional groups to recognize different chemistries. In this endeavor, cocosin protein, an 11S allergen, is prepared from coconut fruit and employed as a potential scaffold for synthesizing Mn₃O₄ materials. The interaction between protein and manganese ions is studied in detail through isothermal calorimetric titration. At increased scaffold availability, the Mn₃O₄ material adopts the exact hexamer structure of the cocosin protein. The electrochemical supercapacitive properties of the cocosin-Mn₃O₄ material are found to have a high specific capacitance of 751.3 F g^-1 at 1 A g^-1 with cyclic stability (92% of capacitance retention after 5000 CV cycles) in a three-electrode configuration. The Mn₃O₄//Mn₃O₄ symmetric supercapacitor device delivers a specific capacitance of 203.8 F g^-1 at 1 A g^-1 and an outstanding energy and power density of 91.7 W h kg^-1 and 899.5 W kg^-1, respectively. These results show that cocosin-Mn₃O₄ could be considered a suitable electrode for energy storage applications. Moreover, the cocosin protein to be utilized as a novel scaffold in protein-nanomaterial chemistry could be useful for protein-assisted inorganic nanostructure synthesis 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.

Role of Order in the Mechanism of Charge Transport across Single-Stranded and Double-Stranded DNA Monolayers in Tunnel Junctions

Deoxyribonucleic acid (DNA) has been hypothesized to act as a molecular wire due to the presence of an extended π-stack between base pairs, but the factors that are detrimental in the mechanism of charge transport (CT) across tunnel junctions with DNA are still unclear. Here we systematically investigate CT across dense DNA monolayers in large-area biomolecular tunnel junctions to determine when intrachain or interchain CT dominates and under which conditions the mechanism of CT becomes thermally activated. In our junctions, double-stranded DNA (dsDNA) is 30-fold more conductive than single-stranded DNA (ssDNA). The main reason for this large change in conductivity is that dsDNA forms ordered monolayers where intrachain tunneling dominates, resulting in high CT rates. By varying the temperature T and the length of the DNA fragments in the junctions, which determines the tunneling distance, we reveal a complex interplay between T, the length of DNA, and structural order on the mechanism of charge transport. Both the increase in the tunneling distance and the decrease in structural order result in a change in the mechanism of CT from coherent tunneling to incoherent tunneling (hopping). Our results highlight the importance of the interplay between structural order, tunneling distance, and temperature on the CT mechanism across DNA in molecular junctions.

All-in-One DNA Extraction Tube for Facilitated Real-Time Detection of Infectious Pathogens

An "all-in-one tube" platform is developed, where the genetic analysis involving DNA extraction, amplification, and detection can be performed in a single tube. The all-in-one tube consists of a polymerase chain reaction (PCR) tube in which the inner surface is conformally modified with a tertiary-amine-containing polymer to generate a strong electrostatic interaction with DNA. The all-in-one tube provides high DNA capture efficiency exceeding 80% from Escherichia coli O157: H7 pathogen at a wide range of DNA amount from 0.003 to 3 ng. Indeed, the use of the surface-functionalized PCR tube enables direct amplification and detection of the surface-captured DNA without the modification of standard real-time PCR instrument. Besides, this platform has sensitivity, selectivity, and reliability enough for accurate detection at the minimal infective dose of both gram-positive and negative pathogens. The all-in-one tube enables the direct molecular diagnosis, substantially reducing the labor-intensive pathogen detection steps while providing high compatibility with the currently established real-time PCR instruments, and illustrates its on-site applicability with convenience expandable to various genetic analyses including food safety testing, forensic analysis, and clinical diagnosis.

In situ monitoring of the influence of water on DNA radiation damage by near-ambient pressure X-ray photoelectron spectroscopy

Ionizing radiation damage to DNA plays a fundamental role in cancer therapy. X-ray photoelectron-spectroscopy (XPS) allows simultaneous irradiation and damage monitoring. Although water radiolysis is essential for radiation damage, all previous XPS studies were performed in vacuum. Here we present near-ambient-pressure XPS experiments to directly measure DNA damage under water atmosphere. They permit in-situ monitoring of the effects of radicals on fully hydrated double-stranded DNA. The results allow us to distinguish direct damage, by photons and secondary low-energy electrons (LEE), from damage by hydroxyl radicals or hydration induced modifications of damage pathways. The exposure of dry DNA to x-rays leads to strand-breaks at the sugar-phosphate backbone, while deoxyribose and nucleobases are less affected. In contrast, a strong increase of DNA damage is observed in water, where OH-radicals are produced. In consequence, base damage and base release become predominant, even though the number of strand-breaks increases further.

DNA-mediated biomineralization of calcium-deficient hydroxyapatite for bone tissue engineering

A random DNA duplex was utilized as the biotemplate to mediate the biomineralization of calcium-deficient hydroxyapatite with osteoconductive properties.

Microcantilever Array Biosensor for Simultaneous Detection of Carcinoembryonic Antigens and α-Fetoprotein Based on Real-Time Monitoring of the Profile of Cantilever

A microcantilever array biosensor based on a sandwich structure has been developed for simultaneously measuring two biomarkers carcinoembryonic antigen (CEA) and α-fetoprotein (AFP) via an optical readout technique-real-time monitoring of the profile of cantilever. First, the aptamers of CEA and AFP were self-assembled on their respective cantilevers. After the adsorption of the mixture of CEA and AFP, further specific interaction was performed via the addition of the antibodies specific to each target. The compressive stress on the cantilever was generated by the aptamer-antigen-antibody sandwich structure formed on the gold surface, resulting in cantilever bending. The profile of cantilever could be monitored in real time. The relationship between the deflection value at the 90% position of the cantilever and the target concentration served as a calibration curve, and the detection sensitivity was 1.3 ng/mL for CEA and 0.6 ng/mL for AFP, respectively. This work demonstrated the ability of simultaneously measuring two biomarkers via a microcantilever array biosensor, giving great potential for further application in detecting several targets simultaneously for early clinical diagnosis.

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.

Tailoring pore structures with optimal mesopores to remarkably promote DNA adsorption guiding the growth of active Mn3(PO4)2 toward sensitive superoxide biomimetic enzyme sensors

The great challenge in preparing a biomimetic enzyme sensor is to have sensitivity and selectivity equal to or better than its corresponding biological sensor. Porous electrodes possess a large surface area and are often used to greatly improve the sensor sensitivity. However, how to tailor the pore structure, especially the pore size distribution to further improve the sensitivity and selectivity of a biomimetic sensor, has not been investigated yet. The superoxide anion (O2˙-) plays essential roles in various biological processes and is of importance in clinical diagnosis and life science research. It is generally detected by the superoxide dismutase enzyme. Herein, we delicately tailor the pore structure of carbon nanofibers (CNFs) by pyrolysis to obtain an optimal mesopore structure for strong adsorption of DNA, followed by guiding the growth of Mn3(PO4)2 as a biomimetic enzyme toward highly sensitive detection of O2˙-. The Mn3(PO4)2-DNA/CNF sensor achieves the best sensitivity among the reported O2˙- sensors while possessing good selectivity. The enhancement mechanism is also investigated, indicating that the mesopore ratio of CNFs plays an essential role in the high sensitivity and selectivity due to their strong adsorption of DNA for guiding the growth of a large amount of uniform sensing components, Mn3(PO4)2, toward high sensitivity and selectivity. The biomimetic sensor was further used to in situ monitor O2˙- released from human keratinocyte cells and human malignant melanoma cells under drug stimulation, showing high sensitivity to real-time quantitative detection of O2˙-. This work provides a highly sensitive in situ real-time biomimetic O2˙- sensor for applications in biological research and diagnosis, while shedding light on the enhancement mechanism of the pore structure, especially the pore size distribution of a porous electrode for high performance sensing processes.

Substituted Aromatic-Facilitated Dissemination of Mobile Antibiotic Resistance Genes via an Antihydrolysis Mechanism Across an Extracellular Polymeric Substance Permeable Barrier

Mobile antibiotic resistance genes (ARGs) in environmental systems may pose a threat to public health. The coexisting substituted aromatic pollutants may help the ARGs cross the extracellular polymeric substance (EPS) permeable barrier into the interior of cells, facilitating ARG dissemination, but the mechanism is still unknown. Here, we demonstrated that a specific antihydrolysis mechanism of mobile plasmid in the extracellular matrix makes a greater contribution to this facilitated dissemination. Specifically, fluorescence microtitration with a Tb³⁺-labeled pUC19 plasmid was used to study the formation of substituted aromatic-plasmid complexes associated with ARG dissemination. Manipulations of the endA gene and an EPS confirmed that these forming complexes antagonize the EPS-mediated hydrolysis of the plasmid. Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and computational chemistry demonstrated that substituents alter the polarity of aromatic molecules, making the carbon at the 6-position of 1,3-dichlorobenzene as well as the labile protons (-NH₂/-OH) of m-phenylenediamine, aniline, and 2-naphthol interact with the deprotonated hydroxy group of the phosphate (P-O···H-C/N/O), mainly via hydrogen bonds. Linear correlations among ARG disseminations, association constants, and bonding energies highlight the quantitative dependency of ARG proliferation on a combination of functionalities templated by d-ribose-phosphate.

Y-shaped DNA-Mediated hybrid nanoflowers as efficient gene carriers for fluorescence imaging of tumor-related mRNA in living cells

Organic-inorganic hybrid nanomaterial has gained much attention due to its excellent performances in bioanalysis and biomedicine. However, the preparation of DNA-inorganic hybrid nanomaterial with suitable size for cell uptake remains a huge challenge. Herein, a moderate biomineralization strategy for synthesis of Y-DNA@Cu₃(PO₄)₂ (Y-DNA@CuP) hybrid nanoflowers is reported. Y-DNA with a loop structure is used as both the biomineralization template and the recognition unit for thymidine kinase 1 (TK1) mRNA. The Y-DNA probe can linearly response to TK1 mRNA target sequence in a range from 2 nM to 150 nM with the limit of detection as low as 0.56 nM. Interestingly, the presence of Y-DNA significantly decreases the size of Cu₃(PO₄)₂ (CuP) particles, which allows them suitable for intracellular applications as gene nanocarriers. Once inside the cells, the hybrid nanoflowers dissolve and release the Y-DNA probes. Then, the intracellular TK1 mRNA hybridizes with the loop region of Y-DNA, which dissociates the Cy3-labeled loop strand and turns on the red fluorescence. Through the real-time imaging of the intracellular TK1 mRNA, the assessment of tumor cells before and after the treatment of drugs including β-estradiol and tamoxifen is achieved.

Robust Covalent Coupling Scheme for the Development of FRET Aptasensor based on Amino-Silane-Modified Graphene Oxide

In recent years, numerous aptamers have been physisorbed on graphene oxide (GO) to develop fluorescence resonance energy transfer-based aptasensors using the fluorescence quenching property of GO. However, physisorbed aptasensors show poor signal reversibility and reproducibility as well as nonspecific probe displacement, and thereby are not suitable for many analytical applications. To overcome these problems when working with complex biological samples, we developed a facile and robust covalent surface functionalization technique for GO-based fluorescent aptasensors using a well-studied adenosine triphosphate binding aptamer (ABA). In the scheme, GO is first modified with amino-silane, and further with glutaraldehyde to create available carbonyl groups for the covalent attachment of a fluorophore and an amino dual modified ABA. The surface modification method was characterized by ζ-potential, X-ray photoelectron spectroscopy, and Fourier-transform infrared spectroscopy (FTIR). The linearity, sensitivity, selectivity, and reversibility of the resulting GO-based covalent aptasensor was determined and systematically compared with the physisorbed aptasensor. Although both sensors showed similar performance in terms of sensitivity and linearity, better selectivity and higher resistance to nonspecific probe displacement was achieved with the developed covalent ABA sensor. The surface modification technique developed here is independent of the aptamer sequence, and therefore could be used universally for different analytical applications simply by changing the aptamer sequence for the target biomolecule.

Quaternary Ammonium-Terminated Films Formed from Mixed Bidentate Adsorbates Provide a High-Capacity Platform for Oligonucleotide Delivery

The exposure of quaternary ammonium groups on surfaces allows self-assembled monolayers (SAMs) to serve as architectural platforms for immobilizing oligonucleotides. The current study describes the preparation of SAMs derived from four unique bidentate adsorbates containing two different ammonium termini (i.e., trimethyl- and triethyl-) and comparison to their monodentate analogs. Our studies found that SAMs derived from the bidentate adsorbates offered considerable enhancements in oligonucleotide binding when compared to SAMs derived from their monodentate analogs. The generated SAMs were analyzed using ellipsometry, X-ray photoelectron spectroscopy, contact angle goniometry, polarization modulation infrared reflection-absorption spectroscopy, and electrochemical quartz crystal microbalance. These analyses showed that the immobilization of oligonucleotides was affected by changes in the terminal functionalities and the relative packing densities of the monolayers. In efforts to enhance further the immobilization of oligonucleotides on these SAM surfaces, we explored the use of adsorbates having aliphatic linkers with systematically varying chain lengths to form binary SAMs on gold. Mixed monolayers with 50:50 ratios of adsorbates showed the greatest oligonucleotide binding. These studies lay the groundwork for oligonucleotide delivery using gold-based nanoparticles and nanoshells.

Minimal attachment of Pseudomonas aeruginosa to DNA modified surfaces

Extracellular deoxyribonucleic acid (eDNA) exists in biological environments such as those around medical implants since prokaryotic or eukaryotic cells can undergo processes such as autolysis, necrosis, and apoptosis. For bacteria, eDNA has been shown to be involved in biofilm formation and gene transfer and acts as a nutrient source. In terms of biofilm formation, eDNA in solution has been shown to be very important in increasing attachment; however, very little is known about the role played by surface immobilized eDNA in initiating bacterial attachment and whether the nature of a DNA layer (physically adsorbed or covalently attached, and molecular weight) influences biofilm formation. In this study, the authors shed light on the role that surface attached DNA plays in the early biofilm formation by using Si wafers (Si) and allylamine plasma polymer (AAMpp) coated Si wafers to adsorb and covalently immobilize salmon sperm DNA of three different molecular weights. Pseudomonas aeruginosa was chosen to study the bacterial interactions with these DNA functionalized surfaces. Characterization of surface chemistry and imaging of attached bacteria were performed via x-ray photoelectron spectroscopy (XPS), scanning electron microscopy, and epi-fluorescence microscopy. XPS results confirmed the successful grafting of DNA on the AAMpp and Si surfaces, and surprisingly the results showed that the surface attached DNA actually reduced initial bacterial attachment, which was contrary to the initial hypothesis. This adds speculation about the specific role played by DNA in the dynamics of how it influences biofilm formation, with the possibility that it could actually be used to make bacterial resistant surfaces.

Geometry-dependent DNA-TiO2 immobilization mechanism: A spectroscopic approach

DNA nucleotides are used as a molecular recognition system on electrodes modified to be applied in the detection of various diseases, but immobilization mechanisms, as well as, charge transfers are not satisfactorily described in the literature. An electrochemical and spectroscopic study was carried out to characterize the molecular groups involved in the direct immobilization of DNA structures on the surface of nanostructured TiO₂ with the aim of evaluating the influence of the geometrical aspects. X-ray photoelectron spectroscopy at O1s and P2p core levels indicate that immobilization of DNA samples occurs through covalent (POTi) bonds. X-ray absorption spectra at the Ti2p edge reinforce this conclusion. A new species at 138.5eV was reported from P2p XPS spectra analysis which plays an important role in DNA-TiO₂ immobilization. The POTi/OTi ratio showed that quantitatively the DNA immobilization mechanism is dependent on their geometry, becoming more efficient for plasmid ds-DNA structures than for PCR ds-DNA structures. The analysis of photoabsorption spectra at C1s edge revealed that the molecular groups that participate in the C1s→LUMO electronic transitions have different pathways in the charge transfer processes at the DNA-TiO₂ interface. Our results may contribute to additional studies of immobilization mechanisms understanding the influence of the geometry of different DNA molecules on nanostructured semiconductor and possible impact to the charge transfer processes with application in biosensors or aptamers.

Surface-Modified Mesh Filter for Direct Nucleic Acid Extraction and its Application to Gene Expression Analysis

Rapid and convenient isolation of nucleic acids (NAs) from cell lysate plays a key role for onsite gene expression analysis. Here, this study achieves one-step and efficient capture of NA directly from cell lysate by developing a cationic surface-modified mesh filter (SMF). By depositing cationic polymer via vapor-phase deposition process, strong charge interaction is introduced on the surface of the SMF to capture the negatively charged NAs. The NA capturing capability of SMF is confirmed by X-ray photoelectron spectroscopy, fluorescent microscopy, and zeta potential measurement. In addition, the genomic DNAs of Escherichia Coli O157:H7 can be extracted by the SMF from artificially infected food, and fluorescent signal is observed on the surface of SMF after amplification of target gene. The proposed SMF is able to provide a more simplified, convenient, and fast extraction method and can be applied to the fields of food safety testing, clinical diagnosis, or environmental pollutant monitoring.

Ironing Out Genes in the Environment: An Experimental Study of the DNA-Goethite Interface

DNA fate in soil plays an important role in the cycling of genetic information in the environment. Adsorption onto mineral surfaces has great impact on this function. This study probes the kinetics, equilibrium behavior and bonding mechanisms associated with adsorption of DNA onto goethite, a common soil mineral. Surface sensitive ATR-FTIR and XPS approaches are applied to directly characterize the DNA-goethite interface. Adsorption kinetics follow a pseudo-first-order model, suggesting adsorption rate is surface limited. Adsorption rate constants increase with DNA concentration, ranging from 3.29 × 10^-3 to 3.55 × 10^-1 min^-1. Equilibrium adsorption, as monitored by ATR-FTIR and XPS, follows the Langmuir model, with a high affinity of DNA for goethite observed (K = 1.25 × 10³ and 9.48 × 10² mL/mg for ATR-FTIR and XPS, respectively). ATR-FTIR and XPS characterization of the structure of surface adsorbed DNA demonstrates inner-sphere coordination between backbone phosphate groups of DNA and goethite. Furthermore, adsorbed DNA retains a B-form, suggesting the DNA helix adsorbs on goethite without degradation or alteration to helical structure, despite binding of backbone phosphate groups. This work advances our understanding of the environmental behavior of DNA by characterizing the mechanism of adsorption onto a prominent soil mineral.

Nanoporous Gold Disks Functionalized with Stabilized G-Quadruplex Moieties for Sensing Small Molecules

We report label-free small molecule sensing on nanoporous gold disks functionalized with stabilized Guanine-quadruplex (G4) moieties using surface-enhanced Raman spectroscopy (SERS). By utilizing the unique G4 topological structure, target molecules can be selectively captured onto nanoporous gold (NPG) disk surfaces via π-π stacking and electrostatic attractions. Together with high-density plasmonic "hot spots" of NPG disks, the captured molecules produce a remarkable SERS signal. Our strategy represents the first example of the detection of foreign molecules conjugated to nondouble helical DNA nanostructures using SERS while providing a new technique for studying the formation and evolution of G4 moieties. The molecular specificity of G4 is known to be controlled by its unit sequence. Without losing generality, we have selected d(GGT)₇GG sequence for the sensing of malachite green (MG), a known carcinogen frequently abused illegally in aquaculture. The newly developed technique achieved a lowest detectable concentration at an impressive 50 pM, two orders of magnitude lower than the European Union (EU) regulatory requirement, with high specificity against potential interferents. To demonstrate the translational potential of this technology, we achieved a lowest detectable concentration of 5.0 nM, meeting the EU regulatory requirement, using a portable probe based detection system.

Novel thymine-functionalized MIL-101 prepared by post-synthesis and enhanced removal of Hg(2+) from water

A novel thymine-functionalized MIL-101 (MIL-101-Thymine) material was synthesized using a post-synthesis method to remove mercury at a high efficiency. MIL-101-Thymine was successfully prepared in this work and was confirmed by several characterization methods, such as (13)C nuclear magnetic resonance, X-ray diffraction, and infrared spectroscopy. The Hg(2+) adsorption agreed well with the Langmuir model, and the maximum adsorption capacity was 51.27mg/g. The adsorption rate fit with the pseudo-second-order kinetic model. Furthermore, MIL-101-Thymine exhibited excellent selectivity towards Hg(2+) over other cations, and the maximum value of the selective coefficient reached 947.34; this result is very likely due to the highly selective interactions of T-Hg(2+)-T in MIL-101-Thymine. The result of X-ray photoelectron spectroscopy also showed that Hg(2+) was coordinated with the N of thymine in MIL-101-Thymine. Moreover, the results of the thermogravimetric analysis and adsorption experiments showed that the Hg atom was two-coordinated with the thymine group. MIL-101-Thymine was used to remove trace Hg(2+) in real water samples, and satisfactory recoveries were obtained.

'Spotted Nanoflowers': Gold-seeded Zinc Oxide Nanohybrid for Selective Bio-capture

Hybrid gold nanostructures seeded into nanotextured zinc oxide (ZnO) nanoflowers (NFs) were created for novel biosensing applications. The selected 'spotted NFs' had a 30-nm-thick gold nanoparticle (AuNP) layer, chosen from a range of AuNP thicknesses, sputtered onto the surface. The generated nanohybrids, characterized by morphological, physical and structural analyses, were uniformly AuNP-seeded onto the ZnO NFs with an average length of 2-3 μm. Selective capture of molecular probes onto the seeded AuNPs was evidence for the specific interaction with DNA from pathogenic Leptospirosis-causing strains via hybridization and mis-match analyses. The attained detection limit was 100 fM as determined via impedance spectroscopy. High levels of stability, reproducibility and regeneration of the sensor were obtained. Selective DNA immobilization and hybridization were confirmed by nitrogen and phosphorus peaks in an X-ray photoelectron spectroscopy analysis. The created nanostructure hybrids illuminate the mechanism of generating multiple-target, high-performance detection on a single NF platform, which opens a new avenue for array-based medical diagnostics.

Immobilization of DNA aptamers via plasma polymerized allylamine film to construct an endothelial progenitor cell-capture surface

The endothelial progenitor cells (EPCs) capture stent has drawn increasing attentions and become one of the most promising concepts for the next generation vascular stent. In this regard, it is of great significance to immobilize a molecule with the ability to bind EPC for rapid in vivo endothelialization with high specificity. In this work, a facile two-step method aimed at constructing a coating with specific EPC capturing aptamers is reported. The processes involves as the first-step deposition of plasma polymerized allylamine (PPAam) on a substrate to introduce amine groups, followed by the electrostatic adsorption of a 34 bases single strand DNA sequence to the PPAam surface as a second step (PPAam-DNA). Grazing incidence attenuated total reflection Fourier transform infrared spectroscopy (GATR-FTIR) and X-ray photoelectron spectroscopy (XPS) confirmed the successful immobilization of the aptamers. Quartz crystal microbalance with dissipation (QCM-D) real time monitoring result shows that about 175 ng/cm(2) aptamers were conjugated onto the PPAam surface. The interactions between the modified surfaces and human umbilical vein endothelial cells (ECs), smooth muscle cells (SMCs), and murine induced EPCs derived from mesenchymal stem cells (MSCs) were also investigated. It was demonstrated that PPAam-DNA samples could capture more EPCs, and present a cellular friendly surface for the proliferation of both EPCs and ECs but no effect on the hyperplasia of SMCs. Also, the co-culture results of 3 types of cells confirmed that the aptamer could specifically bond EPCs rather than ECs and SMCs, suggesting the competitive adhesion advantage of EPCs to ECs and SMCs. These data demonstrate that the EPC aptamer has large potential for designing an EPC captured stent and other vascular grafts with targeted in situ endothelialization.

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.

Spectroscopic study of a DNA brush synthesized in situ by surface initiated enzymatic polymerization

We used a combination of synchrotron-based X-ray photoelectron spectroscopy (XPS) and angle-resolved near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to study the chemical integrity, purity, and possible internal alignment of single-strand (ss) adenine deoxynucleotide (poly(A)) DNA brushes. The brushes were synthesized by surface-initiated enzymatic polymerization (SIEP) on a 25-mer of adenine self-assembled monolayer (SAM) on gold (A25-SH), wherein the terminal 3'-OH of the A25-SH serve as the initiation sites for SIEP of poly(A). XPS and NEXAFS spectra of poly(A) brushes were found to be almost identical to those of A25-SH initiator, with no unambiguous traces of contamination. Apart from the well-defined chemical integrity and contamination-free character, the brushes were found to have a high degree of orientational order, with an upright orientation of individual strands, despite their large thickness up to ~55 nm, that corresponds to a chain length of at least several hundred nucleotides for individual ssDNA molecules. The orientational order exhibited by these poly(A) DNA brushes, mediated presumably by base stacking, was found to be independent of the brush thickness as long as the packing density was high enough. The well-defined character and orientational ordering of the ssDNA brushes make them a potentially promising system for different applications.

A novel graphene-DNA biosensor for selective detection of mercury ions

A novel electrochemical biosensor for sensitive and selective detection of mercury (II) ions (Hg²⁺) based on a DNA grafted graphene is proposed. Graphene oxide (GO) was reduced by dopamine, and then the single-strand probe DNA modified at the 5'-end with an alkylamino modifier (NH₂-ssDNA) was grafted on the reduced graphene oxide (RGO) surface via Michael addition reaction. In the presence of Hg²⁺, the target DNA with four thymine-thymine (T-T) mismatches would hybridize with the probe DNA on the glassy carbon electrode (GCE) through T-Hg²⁺-T coordination chemistry. The hybridization of the two oligonucleotides leads to the increase in the peak currents of [Ru(NH₃)₆]³⁺, which could be used for electrochemical sensing of Hg²⁺. The difference in the value of the peak currents of [Ru(NH₃)₆]³⁺ before and after DNA hybridization was linear with the concentration of Hg²⁺ in the range from 8.0×10⁻⁹ to 1.0×10⁻⁷ M with a linear coefficiency of 0.996. The detection limit was 5.0×10⁻⁹ M (S/N=3). The proposed electrochemical biosensor is rapid, convenient and low-cost for effective sensing of Hg²⁺. Particularly, the proposed method was applied successfully to the determination of Hg²⁺ in real environmental samples.

Sensitive Marker of the Cisplatin-DNA Interaction: X-Ray Photoelectron Spectroscopy of CL

The development of cisplatin and Pt-based analogues anticancer agents requires knowledge concerning the molecular mechanisms of interaction between such drugs with DNA. However, the binding dynamics and kinetics of cisplatin reactions with DNA determined by traditional approaches are far from satisfactory. In this study, a typical 20-base oligonucleotide (CGTGACAGTTATTGCAGGCG), as a simplified model representing DNA, was mixed with cisplatin in different molar ratios and incubation time. High-resolution XPS spectra of the core elements C, N, O, P, and Cl were recorded to explore the interaction between cisplatin and DNA. From deconvoluted Cl spectra we could readily differentiate the covalently bound chlorine from ionic chloride species in the cisplatin-oligo complexes, which displayed distinct features at various reaction times and ratios. Monitoring the magnitude and energy of the photoelectron Cl 2p signal by XPS could act as a sensitive marker to probe the interaction dynamics of chemical bonds in the reaction of cisplatin with DNA. At 37°C, the optimum incubation time to obtain a stable cisplatin-oligo complex lies around 20 hrs. This novel analysis technique could have valuable implications to understand the fundamental mechanism of cisplatin cytotoxicity and determine the efficiency of the bonds in treated cancer cells.

Chemical passivation processes for biofunctionalization schemes on semiconductor surfaces

In developing novel designs for semiconductor-based biosensors and for biofunctionalization of semiconductors in general, it is extremely important to be able to block the reaction sites present on a surface following the biomodification from further chemical transformations. This procedure is required both to protect the surface from oxidation and to allow for molecular-level control of the biomolecular interactions at the topmost layer. In this work, the biosensor model system is designed based on a single-strand biotin-modified thiol-DNA attached to the silicon substrate. The binding of this thiol-DNA to the surface is performed through the cross-linker sulfosuccinimidyl-4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (SSMCC) attached to the 11-amino-1-undecene monolayer on Si(111) surface. Streptavidin-coated gold nanoparticles are used to test the reactivity of the surface and to examine the role of passivation in the entire scheme. The passivation of the remaining surface reactive sites is achieved via a reaction with 1-octadecanethiol (ODT). This approach tests both the stability of the silicon/organic layer interface and the passivation of the biofunctionalized surface on top of the organic layer. Microscopy and spectroscopy studies are combined to interrogate this model system before and after surface passivation.

Probing electron-induced bond cleavage at the single-molecule level using DNA origami templates

Low-energy electrons (LEEs) play an important role in nanolithography, atmospheric chemistry, and DNA radiation damage. Previously, the cleavage of specific chemical bonds triggered by LEEs has been demonstrated in a variety of small organic molecules such as halogenated benzenes and DNA nucleobases. Here we present a strategy that allows for the first time to visualize the electron-induced dissociation of single chemical bonds within complex, but well-defined self-assembled DNA nanostructures. We employ atomic force microscopy to image and quantify LEE-induced bond dissociations within specifically designed oligonucleotide targets that are attached to DNA origami templates. In this way, we use a highly selective approach to compare the efficiency of the electron-induced dissociation of a single disulfide bond with the more complex cleavage of the DNA backbone within a TT dinucleotide sequence. This novel technique enables the fast and parallel determination of DNA strand break yields with unprecedented control over the DNA's primary and secondary structure. Thus the detailed investigation of DNA radiation damage in its most natural environment, e.g., DNA nucleosomes constituting the chromatin, now becomes feasible.

Development of an electrochemical DNA biosensor with the DNA immobilization based on in situ generation of dithiocarbamate ligands

In this article, a simple and effective strategy for DNA immobilization on gold electrode surface is developed. The amine-modified oligonucleotide was firstly reacted with CS(2) and then in situ generated dithiocarbamate group functionalized probe DNA (DTC-DNA) was directly attached onto the gold surface by bidentate anchoring points. The DNA biosensor fabrication process was characterized by cyclic voltammetry and electrochemical impedance spectroscopy with the use of Fe(CN)(6)(3-/4-) as a redox indicator. The hybridization of DTC-DNA with complementary target DNA could be well distinguished with the use of Co(phen)(3)(3+) as an electrochemical indicator. The fabricated electrochemical DNA biosensor could achieve a detection limit of about 0.1nM toward complementary target DNA. Also, the current strategy is readily operated with less time consumed and lower cost compared with those commonly used strategies.

A guided mode resonance aptasensor for thrombin detection

Recent developments in aptamers have led to their widespread use in analytical and diagnostic applications, particularly for biosensing. Previous studies have combined aptamers as ligands with various sensors for numerous applications. However, merging the aptamer developments with guided mode resonance (GMR) devices has not been attempted. This study reports an aptasensor based home built GMR device. The 29-mer thrombin aptamer was immobilized on the surface of a GMR device as a recognizing ligand for thrombin detection. The sensitivity reported in this first trial study is 0.04 nm/μM for thrombin detection in the concentration range from 0.25 to 1 μM and the limit of detection (LOD) is 0.19 μM. Furthermore, the binding affinity constant (K_a) measured is in the range of 10⁶ M⁻¹. The investigation has demonstrated that such a GMR aptasensor has the required sensitivity for the real time, label-free, in situ detection of thrombin and provides kinetic information related to the binding.

Hybridization in ssDNA films--a multi-technique spectroscopy study

A combination of X-ray photoelectron spectroscopy (XPS), high-resolution XPS, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and sum-frequency-generation (SFG) spectroscopy was used to monitor two types of ssDNA films on Au(111) before and after hybridization. As probe systems, films of thiolated and block-oligonucleotides were used, taking thiolated thymine d(T) homo-oligonucleotides and thymine-adenine d(A-T) diblock-oligonucleotides as representative examples. In accordance with previous work, hybridization of the shorter and more densely packed thiolated ssDNA films produced fewer (if any) hybrids, whereas the longer and less densely packed layers exhibited a larger hybridization yield. The above effects were less pronounced in the case of the d(A-T) films where the hybridization yield of the less densely packed monolayers was significantly lower. This was presumably due to the formation of internal dimeric hybrids in the immobilization step of the probe molecules, resulting in the generation of fewer probe-target hybrids upon exposure to the target molecules. In all ssDNA films displaying a reasonable number of hybrids present, significant orientational changes were observed and could be monitored in detail. These results suggest that the given combination of spectroscopic techniques can be a valuable tool to gain molecular-level information about hybrids at interfaces.

Effect of morphology of thin DNA films on the electron stimulated desorption of anions

We present a comparison between the electron stimulated desorption (ESD) of anions from DNA samples prepared by lyophilization (an example of poorly organized or nonuniform films) and molecular self-assembly (well-ordered films). The lyophilization (or freeze- drying) method is perhaps the most frequently employed technique for forming DNA films for studies of low-energy electron (LEE) interactions leading to DNA damage; however, this technique usually produces nonuniform films with considerable clustering which may affect DNA configuration and enhance sample charging when the film is irradiated. Our results confirm the general validity of ESD measurements obtained with lyophilized samples, but also reveal limitations of lyophilization for LEE studies on DNA films. Specifically we observe some modulation of structures, associated with dissociative electron attachment, in the anion yield functions from different types of DNA film, confirming that conformational factors play a role in the LEE induced damage to DNA.