On the Structure and Desorption Dynamics of DNA Bases Adsorbed on Gold: A Temperature-Programmed Study

DNA Molecular Computation Using the CRISPR-Mediated Reaction and Surface Growth of Gold Nanoparticles

DNA has emerged as a promising tool to build logic gates for biocomputing. However, prevailing methodologies predominantly rely on hybridization reactions or structural alterations to construct DNA logic gates, which are limited in simplicity and diversity. Herein, we developed simple and smart DNA-based logic gates for biocomputing through the DNA-mediated growth of gold nanomaterials without precise structure design and probe modification. Capitalizing on their excellent plasmonic properties, the surface growth of gold nanomaterials enables distinct wavelength shifts and unique shapes, which are modulated by the composition, length, and concentration of the DNA sequences. Combined with a CRISPR-mediated reaction, we constructed DNA circuits to achieve complicated biocomputing to modulate the surface growth of gold nanomaterials. By implementing logic functions controlled by input-mediated growth of gold nanomaterials, we established YES/NOT, AND/NAND, OR/NOR, XOR, and INHIBIT gates and further constructed cascade logic circuits, parity checker for natural numbers, and gray code encoder, which are promising for DNA biocomputing.

Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces

We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.

Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers

Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.

DNA Sensing Platforms: Novel Insights into Molecular Grafting Using Low Perturbative AFM Imaging

By using AFM as a nanografting tool, we grafted micrometer-sized DNA platforms into inert alkanethiol SAMs. Tuning the grafting conditions (surface density of grafting lines and scan rate) allowed us to tailor the molecular density of the DNA platforms. Following the nanografting process, AFM was operated in the low perturbative Quantitative Imaging (QI) mode. The analysis of QI AFM images showed the coexistence of molecular domains of different heights, and thus different densities, within the grafted areas, which were not previously reported using contact AFM imaging. Thinner domains corresponded to low-density DNA regions characterized by loosely packed, randomly oriented DNA strands, while thicker domains corresponded to regions with more densely grafted DNA. Grafting with densely spaced and slow scans increased the size of the high-density domains, resulting in an overall increase in patch height. The structure of the grafted DNA was compared to self-assembled DNA, which was assessed through nanoshaving experiments. Exposing the DNA patches to the target sequence produced an increase in the patch height, indicating that hybridization was accomplished. The relative height increase of the DNA patches upon hybridization was higher in the case of lower density patches due to hybridization leading to a larger molecular reorganization. Low density DNA patches were therefore the most suitable for targeting oligonucleotide sequences.

Accounting for Interaction Kinetics between Gold Nanoparticles and Aptamers Enables High-Performance Colorimetric Sensors

DNA aptamers have emerged as promising probes for challenging analytes that cannot be easily detected by conventional probes, including small-molecule targets. Among the different signal transduction approaches, gold nanoparticle (AuNP) aggregation assays have been widely used to generate a colorimetric response from aptamer-target interactions. This sensor design relies on the competition between the aptamer adsorbing to the AuNP surface versus interacting with the target, whereby target binding reduces the number of adsorbed aptamers that destabilizes AuNPs toward salt-induced aggregation, thereby inducing a color change. However, this thermodynamic framework overlooks the potential influence of interaction kinetics of different aptamer conformations with AuNP surfaces and with targets in solution or near surfaces. Here, we show that aptamers become more strongly adsorbed on AuNPs over time, and these trapped aptamers are less responsive toward the target analyte. By varying the sequence of addition in sensing assays, we demonstrate that these interaction kinetics have a significant effect on the sensor response and thereby produce an effective sensor for methamphetamine (meth) at biologically relevant levels in oral fluids. Along with underpinning new tools for assay development, this new knowledge also highlights the need for aptamer selection strategies that evolve aptamer sequences based on the functionality that they need to exhibit in an actual sensor.

Interactions of the Cocaine and Quinine Aptamer with Gold Nanoparticles under the Dilute Biosensor and Concentrated NMR Conditions

The cocaine aptamer was later found to bind quinine with an even higher affinity. In this work, we used a fluorescently labeled aptamer named MN4 to study its adsorption by gold nanoparticles (AuNPs), and the subsequent displacement by the nonlabeled aptamer and by quinine. Without washing, 14% of the preadsorbed MN4 strands were displaced by 4000-fold excess of free MN4, whereas no displacement was observed after washing, suggesting that washing removed weakly adsorbed aptamers. In a previous paper, rapid exchange was observed with NMR by directly mixing AuNPs and concentrated MN4, and our work has unified the dilute and concentrated aptamer conditions. The difference is attributable to the conformation of the adsorbed aptamer, where dilute aptamers are adsorbed in a collapsed state with a much higher affinity to AuNPs. In addition, the preadsorbed MN4 aptamer cannot be desorbed by adding quinine, indicating that direct desorption-based fluorescent sensors cannot be made. Finally, based on the similar color responses to both the aptamer and its nonbinding mutants, the label-free colorimetric detection method cannot be directly applied for the detection of quinine. This work indicated that different experimental conditions need to be carefully compared to have a unified understanding of aptamer/AuNP systems.

Metal nanoparticle alters adenine induced charge transfer kinetics of vitamin K3 in magnetic field

In this article, we highlight the alterations in the photoinduced electron transfer (ET) and hydrogen atom transfer (HAT) pathways between an anti-tumor drug vitamin-K3 (MQ) and a nucleobase adenine (ADN) in the presence of gold (Au) and iron (Fe) nanoparticles (NPs). Inside the confined micellar media, with laser flash photolysis corroborated with an external magnetic field (MF), we have detected the transient geminate radicals of MQ and ADN, photo-generated through ET and HAT. We observe that the presence of AuNP on the MQ-ADN complex (^AuMQ-ADN) assists HAT by limiting the ET channel, on the other hand, FeNP on the MQ-ADN complex (^FeMQ-ADN) mostly favors a facile PET. We hypothesize that through selective interactions of the ADN molecules with AuNP and MQ molecules with FeNP, a preferential HAT and PET process is eased. The enhanced HAT and PET have been confirmed by the escape yields of radical intermediates by time-resolved transient absorption spectroscopy in the presence of MF.

Sensing Adenosine and ATP by Aptamers and Gold Nanoparticles: Opposite Trends of Color Change from Domination of Target Adsorption Instead of Aptamer Binding

The 27 mer DNA aptamer for adenosine and adenosine 5'-triphosphate (ATP) is a popular model system for designing biosensors. Various strategies have been reported for label-free colorimetric detection using gold nanoparticles (AuNPs). It is generally accepted that free aptamers can protect AuNPs against salt-induced aggregation, whereas target-bound aptamers cannot. However, these studies only considered the aptamer binding to its target, and the adsorption of the aptamer on AuNPs, but none considered the adsorption of target molecules by AuNPs. We herein report that the adsorption of adenosine destabilized citrate-capped AuNPs with an apparent K_d of just 7.7 μM adenosine, whereas that of ATP stabilized the AuNPs because of the negative charges from the triphosphate group. The adsorbed ATP inhibited the adsorption of DNA. Using the aptamer and a nonbinding mutant, ATP and guanosine 5'-triphosphate (GTP) had the same colorimetric response, and so did adenosine and guanosine, regardless of the DNA sequence, indicating that the color change mainly reflected the adsorption of the nucleosides and nucleotides instead of aptamer binding. The related literature examples using this aptamer were classified into three types and individually analyzed, where the reported color changes can all be explained by the adsorption of target analytes.

Discovery of and Insights into DNA "Codes" for Tunable Morphologies of Metal Nanoparticles

The discovery and elucidation of genetic codes has profoundly changed not only biology but also many fields of science and engineering. The fundamental building blocks of life comprises of four simple deoxyribonucleotides and yet their combinations serve as the carrier of genetic information that encodes for proteins that can carry out many biological functions due to their unique functionalities. Inspired by nature, the functionalities of DNA molecules have been used as a capping ligand for controlling morphology of nanomaterials, and such a control is sequence dependent, which translates into distinct physical and chemical properties of resulting nanoparticles. Herein, an overview on the use of DNA as engineered codes for controlling the morphology of metal nanoparticles, such as gold, silver, and Pd-Au bimetallic nanoparticles is provided. Fundamental insights into rules governing DNA controlled growth mechanisms are also summarized, based on understanding of the affinity of the DNA nucleobases to various metals, the effect of combination of nucleobases, functional modification of DNA, the secondary structures of DNA, and the properties of the seed employed. The resulting physical and chemical properties of these DNA encoded nanomaterials are also reviewed, while perspectives into the future directions of DNA-mediated nanoparticle synthesis are provided.

Nanoparticle Ligand Exchange and Its Effects at the Nanoparticle-Cell Membrane Interface

The nanoparticle (nano)-cell membrane interface is one of the most important interactions determining the fate of nanoparticles (NPs), which can stimulate a series of biological events, allowing theranostic and other biomedical applications. So far, there remains a lack of knowledge about the mechanisms governing the nanoparticle-cell membrane interface, especially the impact of ligand exchange, in which molecules on the nanosurface become replaced with components of the cell membrane, resulting in unique interfacial phenomena. Herein, we describe a family of gold nanoparticles (AuNPs) of the same core size (∼13 nm core), modified with 12 different kinds of surface ligands, and the effects of their exchangeable ligands on both nanoparticle-supported lipid bilayers (SLBs) and nanoparticle-natural cell membrane interfaces. The ligands are categorized according to their molecular weight, charge, and bonding modes (physisorption or chemisorption). Importantly, we found that, depending on the adsorption affinity and size of ligand molecules, physisorbed ligands on the surface of NPs can be exchanged with lipid molecules. At a ligand exchange-dominated interface, the AuNPs typically aggregated into an ordered monolayer in the lipid bilayers, subsequently affecting cell membrane integrity, NP uptake efficiency, and the NP endocytosis pathways. These findings advance our understanding of the underlying mechanisms of the biological effects of nanoparticles from a new point of view and will aid in the design of novel, safe, and effective nanomaterials for biomedicine.

Adsorption Mechanisms of Nucleobases on the Hydrated Au(111) Surface

The solution environment is of fundamental importance in the adsorption of molecules on surfaces, a process that is strongly affected by the capability of the adsorbate to disrupt the hydration layer above the surface. Here we disclose how the presence of interface water influences the adsorption mechanism of DNA nucleobases on a gold surface. By means of metadynamics simulations, we describe the distinctive features of a complex free-energy landscape for each base, which manifests activation barriers for the adsorption process. We characterize the different pathways that allow each nucleobase to overcome the barriers and be adsorbed on the surface, discussing how they influence the kinetics of adsorption of single-stranded DNA oligomers with homogeneous sequences. Our findings offer a rationale as to why experimental data on the adsorption of single-stranded homo-oligonucleotides do not straightforwardly follow the thermodynamics affinity rank.

Influence of amine and thiol modifications at the 3' ends of single stranded DNA molecules on their adsorption on gold surface and the efficiency of their hybridization

Adsorption of molecules of DNA (deoxyribonucleic acid) or modified DNA on gold surfaces is often the first step in construction of many various biosensors, including biosensors for detection of DNA with a particular sequence. In this work we study the influence of amine and thiol modifications at the 3' ends of single stranded DNA (ssDNA) molecules on their adsorption on the surface of gold substrates and on the efficiency of hybridization of immobilized DNA with the complementary single stranded DNA. The characterization of formed layers has been carried out using infrared spectroscopy and atomic force microscopy. As model single stranded DNA we used DNA containing 20 adenine bases, whereas the complementary DNA contained 20 thymine bases. We found that the bands in polarization modulation-infrared reflection-adsorption spectroscopy (PM-IRRAS) spectra of layers formed from thiol-modified DNA are significantly narrower and sharper, indicating their higher regularity in the orientation of DNA on gold surface when using thiol linker. Also, hybridization of the layer of thiol-modified DNA containing 20 adenine bases with the respective DNA containing thymine bases leads to formation of much more organized structures than in the case of unmodified DNA or DNA with the amine linker. We conclude that the thiol-modified ssDNA is more promising for the preparation of biosensors, in comparison with the amine-modified or unmodified ssDNA. We have also found that the above-mentioned modifications at the 3' end of ssDNA significantly influence the IR spectrum (and hence the structure) of polycrystalline films formed from such compounds, even though adsorbed fragments contain less than 5% of the DNA chain. This effect should be taken into account when comparing IR spectra of various polycrystalline films formed from modified and unmodified DNA.

Directional affinity of a spherical Gold nanoparticle for the adsorption of DNA bases

In this work, the adsorption activities of different facets of a spherical gold nanoparticle (Au(111), Au(100) and Au(110)) for adenine (ADE) and cytosine (CYT) in two different environments including gas phase and in the presence of solvent (water) have been investigated, separately. It has been found that the adsorption energy (E_ad) and geometry of the DNA bases depend strongly on the kind of nanoparticle facet. The Au (110) facet showed the highest adsorption affinity for the ADE and CYT in both gas phase and water compared to Au(111) and Au(100) facets. Comparison of the E_ads of bases calculated in the gas phase with those obtained in the presence of water showed that the electrostatic field of solvent decreases the E_ads of bases, especially, for the Au (110) facet. The adsorption geometry of the CYT showed strong dependency on the kind of nanoparticle facet compared to ADE. Also, it has been shown that the direction and amount of charge transfer (CT) between the molecule and nanoparticle strongly depends on the kind of nanoparticle facet and environment. The CT is from the Au (111) facet to the ADE while the CT direction is reversed when the ADE is adsorbed on the Au (110) and Au (100) facets in the gas phase. The CT is from the CYT to three facets in the gas phase while its direction for the ADE and CYT adsorbed on Au (100) facet is reversed. The atoms in molecules (AIM) analysis has been employed to determine the bond paths (BPs) and bond critical points (BCPs) between the bases and facets. The infrared (IR) spectra of the bases adsorbed on the selected facets were calculated and compared with each other and with the spectra of the isolated bases. It was found that the symmetric and unsymmetric stretching of the NH of NH₂ group, C-H stretching of the rings and CO stretching of bases can be used for the discrimination of the selected facets.

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.

Electron Transfer in Spacer-Free DNA Duplexes Tethered to Gold via dA10 Tags

Electrical properties of DNA critically depend on the way DNA molecules are integrated within the electronics, particularly on DNA-electrode immobilization strategies. Here, we show that the rate of electron transport in DNA duplexes spacer-free tethered to gold via the adenosine terminal region (a dA₁₀ tag) is enhanced compared to the hitherto reported DNA-metal electrode tethering chemistries. The rate of DNA-mediated electron transfer (ET) between the electrode and methylene blue intercalated into the dA₁₀-tagged DNA duplex approached 361 s^-1 at a ca. half-monolayer DNA surface coverage Γ_DNA (with a linear regression limit of 670 s^-1 at Γ_DNA → 0), being 2.7-fold enhanced compared to phosphorothioated dA₅* tethering (6-fold for the C₆-alkanethiol linker representing an additional ET barrier). X-ray photoelectron spectroscopy evidenced dA₁₀ binding to the Au surface via the purine N, whereas dA₅* predominantly coordinated to the surface via sulfur atoms of phosphothioates. The latter apparently induces the DNA strand twist in the point of surface attachment affecting the local DNA conformation and, as a result, decreasing the ET rates through the duplex. Thus, a spacer-free DNA coupling to electrodes via dA₁₀ tags thus allows a perspective design of DNA electronic circuits and sensors with advanced electronic properties and no implication from more expensive, synthetic linkers.

An experimental and theoretical study of adenine adsorption on Au(111)

The parallel and upright adenine phases on Au(111) were studied by photoelectron and absorption spectroscopies in combination with density functional theory calculations.

Selection and Screening of DNA Aptamers for Inorganic Nanomaterials

Searching for DNA sequences that can strongly and selectively bind to inorganic surfaces is a long-standing topic in bionanotechnology, analytical chemistry and biointerface research. This can be achieved either by aptamer selection starting with a very large library of ≈10¹⁴ random DNA sequences, or by careful screening of a much smaller library (usually from a few to a few hundred) with rationally designed sequences. Unlike typical molecular targets, inorganic surfaces often have quite strong DNA adsorption affinities due to polyvalent binding and even chemical interactions. This leads to a very high background binding making aptamer selection difficult. Screening, on the other hand, can be designed to compare relative binding affinities of different DNA sequences and could be more appropriate for inorganic surfaces. The resulting sequences have been used for DNA-directed assembly, sorting of carbon nanotubes, and DNA-controlled growth of inorganic nanomaterials. It was recently discovered that poly-cytosine (C) DNA can strongly bind to a diverse range of nanomaterials including nanocarbons (graphene oxide and carbon nanotubes), various metal oxides and transition-metal dichalcogenides. In this Concept article, we articulate the need for screening and potential artifacts associated with traditional aptamer selection methods for inorganic surfaces. Representative examples of application are discussed, and a few future research opportunities are proposed towards the end of this article.

Screening Criteria for Qualified Antibiotic Targets in Unmodified Gold Nanoparticles-Based Aptasensing

In designing unmodified gold nanoparticles-based aptasensing (uGA) assays for antibiotics, we find that some antibiotics can adsorb directly on gold nanoparticles (GNP) regardless of the presence of aptamers, which have been long overlooked in the past. Some adsorptions, however, would strongly disturb the charge distribution on the GNP surface, break up the static colloidal profile, and thus generate false positive colorimetric signals. To identify antibiotics qualified for uGA assays, we established two rational screening criteria for antibiotic targets relying on their oil-water partition coefficients (log P values) and net physiological charges: log P > 0 and charge ≤0. A good agreement of the GNP color change was obtained between the two criteria-based predictions and the actual tests using six representative antibiotics. The proposed criteria help to shed light on GNP-target interactions, which is significant for developing novel GNP-based colorimetric assays with high reliability.

Biomarkers of cigarette smoking and DNA methylating agents: Raman, SERS and DFT study of 3-methyladenine and 7-methyladenine

3-Methyladenine and 7-methyladenine are biomarkers of DNA damage from exposure to methylating agents. For example, the concentration of 3-methyladenine increases significantly in the urine of cigarette smokers. Surface-enhanced Raman spectroscopy (SERS) has shown much potential for detection of biomolecules, including DNA. Much work has been dedicated to the canonical nucleobases, with comparatively fewer investigations of modified DNA and modified DNA nucleobases. Herein, Raman spectroscopy and SERS are used to examine the adsorption orientations of 3-methyladenine and 7-methyladenine on Ag nanoparticles. Density functional theory (DFT) calculations at the B3LYP level are used to support the conclusions via simulated spectra of the nucleobases and of Ag⁺/nucleobase complexes. The results herein show that 7-methyladenine adsorbs upright via its N3 and N9 atoms side, similarly to adenine. 3-Methyladenine adsorbs in a very tilted or flat orientation on the Ag nanoparticles. These findings will be useful for future SERS or other nanoparticle-based bioanalytical assays for detection of these methyladenines or other modified nucleobases.

Electrochemical biosensing strategies for DNA methylation analysis

DNA methylation is one of the key epigenetic modifications of DNA that results from the enzymatic addition of a methyl group at the fifth carbon of the cytosine base. It plays a crucial role in cellular development, genomic stability and gene expression. Aberrant DNA methylation is responsible for the pathogenesis of many diseases including cancers. Over the past several decades, many methodologies have been developed to detect DNA methylation. These methodologies range from classical molecular biology and optical approaches, such as bisulfite sequencing, microarrays, quantitative real-time PCR, colorimetry, Raman spectroscopy to the more recent electrochemical approaches. Among these, electrochemical approaches offer sensitive, simple, specific, rapid, and cost-effective analysis of DNA methylation. Additionally, electrochemical methods are highly amenable to miniaturization and possess the potential to be multiplexed. In recent years, several reviews have provided information on the detection strategies of DNA methylation. However, to date, there is no comprehensive evaluation of electrochemical DNA methylation detection strategies. Herein, we address the recent developments of electrochemical DNA methylation detection approaches. Furthermore, we highlight the major technical and biological challenges involved in these strategies and provide suggestions for the future direction of this important field.

Colorimetric detection of cholic acid based on an aptamer adsorbed gold nanoprobe

Au NPs modified with aptamers of different densities will grow into varied nanostructures with colours changing from blue to red.

Quantification of nucleobases/gold nanoparticles interactions: energetics of the interactions through apparent binding constants determination

The interaction between AuNPs and adenine/thymine molecules is quantified by absorption spectroscopy and deconvolution methods; results are confirmed by DFT calculations.

Mechanism of adsorption of single and double stranded DNA on gold and silver nanoparticles: Investigating some important parameters in bio-sensing applications

The mechanism of adsorption of single and double stranded DNAs on colloidal gold and silver nanoparticles has been studied by measuring the resistance of the nanoparticles, surrounded by various oligonucleotides, against salt induced aggregation. It is shown that both single and double stranded DNAs can be adsorbed on the metal nanoparticles and the adsorption strength is determined by the interaction between various bases of DNA and the nanoparticles. By changing the salt concentration, the difference between adsorption of various DNA strands on the nanoparticles can be specified. The results indicate that a key parameter in success of a sensing assay of DNA hybridization is the salt concentration which should be greater than a minimum threshold depending on the nanoparticles characteristics. We have also investigated the interaction mechanism between various DNA bases with the metal nanoparticles. For both gold and silver nanoparticles, adenine has the highest and thymine has the lowest attachment to the nanoparticles. From surface enhanced Raman spectroscopy (SERS) data of various bases in the presence of gold nanoparticles, the probable interaction points in the bases with the nanoparticles have been determined, which are mainly the nitrogen sites of these oligonucleotides.

Surface Adsorption from the Exchange-Hole Dipole Moment Dispersion Model

The accurate calculation of intermolecular interaction energies with density functional theory requires methods that include a treatment of long-range, nonlocal dispersion correlation. In this work, we explore the ability of the exchange-hole dipole moment (XDM) dispersion correction to model molecular surface adsorption. Adsorption energies are calculated for six small aromatic molecules (benzene, furan, pyridine, thiophene, thiophenol, and benzenediamine) and the four DNA nucleobases (adenine, thymine, guanine, and cytosine) on the (111) surfaces of the three coinage metals (copper, silver, and gold). For benzene, where the experimental reference data is most precise, the mean absolute error in the computed absorption energies is 0.04 eV. For the other aromatic molecules, the computed binding energies are found to be within 0.09 eV of the available reference data, on average, which is well below the expected experimental uncertainties for temperature-programmed desorption measurements. Unlike other dispersion-corrected functionals, adequate performance does not require changes to the canonical XDM implementation, and the good performance of XDM is explained in terms of the behavior of the exchange hole. Additionally, the base functional employed (B86bPBE) is also optimal for molecular studies, making B86bPBE-XDM an excellent candidate for studying chemistry on material surfaces. Finally, the noncovalent interaction (NCI) plot technique is shown to detect adsorption effects in real space on the order of tenths of an eV.

Aptamer-aptamer linkage based aptasensor for highly enhanced detection of small molecules

The multi-target colorimetric aptasensors can be easily fabricated by using two different aptamer sequences. However, there have been no research reports about improvement or enhancing of colorimetric signals based on the aggregation properties of AuNPs. Herein, we report a simple and efficient method to control and enhance the function of the multi-target aptasensor using an aptamer-aptamer linkage method. The aptasensor was developed for highly sensitive multiple-target detection of small molecules. The extension of aptamer DNA sequences using this method resulted in the enhanced analytical sensitivity of this aptasensor in sensing applications for two small molecule targets. Furthermore, the mechanism of the interaction between DNA aptamer and AuNPs was studied by measuring the zeta potential to explain the enhancement of the sensitivity of this multi-target aptasensor. The limit of detection of this multi-target aptasensor was found to be 1 nM and 37 nM for kanamycin (KAN) and chlortetracycline (CHLOR), respectively. It is 25-fold lower than in the previous report using an AuNP-based sensor for defining the limit of detection (LOD) of KAN and five times lower than the LOD for CHLOR. This aptasensor has great potential in the simultaneous detection of a wide range of KAN and CHLOR concentrations.

Highly Hybridizable Spherical Nucleic Acids by Tandem Glutathione Treatment and Polythymine Spacing

Gold nanoparticle (AuNP)-templated spherical nucleic acids (SNAs) have been demonstrated as an important functional material in bionanotechnology. Fabrication of SNAs having high hybridization capacity to their complementary sequences is critical to ensure their applicability in areas such as antisense gene therapy and cellular sensing. The traditional salt-aging procedure is effective but tedious, requiring 1-3 days to complete. The rapid low-pH assisted protocol is efficient, but causes concerns related to nonspecific DNA adsorption to the AuNP core. To address these issues, we systematically compared the SNAs prepared by these two methods (salt-aging method and low-pH protocol). In terms of the number of complementary DNA that each SNA can bind and the average binding affinity of each thiolated DNA probe to its complementary strand, both methods yielded comparable hybridizability, although higher loading capacity was witnessed with SNAs made using the low-pH method. Additionally, it was found that nonspecific DNA binding could be eliminated almost completely by a simple glutathione (GSH) treatment of SNAs. Compared to conventional methods using toxic mercapto-hexanol or alkanethiols to remove nonspecific DNA adsorption, GSH is mild, cost-effective, and technically easy to use. In addition, GSH-passivated SNAs minimize the toxicity concerns related to AuNP-induced GSH depletion and therefore offer a more biocompatible alternative to previously reported SNAs. Moreover, rational design of probe sequences through inclusion of a polythymine spacer into the DNA sequences resulted in enhanced DNA loading capacity and stability against salt-induced aggregation. This work provides not only efficient and simple technical solutions to the issue of nonspecific DNA adsorption, but also new insights into the hybridizability of SNAs.

A reagentless DNA-based electrochemical silver(I) sensor for real time detection of Ag(I) - the effect of probe sequence and orientation on sensor response

Ag(I) is known to interact with cytosine (C) via the formation C-Ag(I)-C complexes. The authors have utilized this concept to design six electrochemical Ag(I) sensors using C-rich DNA probes. Alternating current voltammetry and cyclic voltammetry were used to analyze the sensors. The results show that the dual-probe sensors that require the use of both 5'- and 3'-thiolated DNA probes are not suitable for this application, the differences in probe orientation impedes formation of C-Ag(I)-C complexes. Sensors fabricated with DNA probes containing both thymine (T) and C, independent of the location of the alkanethiol linker, do not response to Ag(I) either; T-T mismatches destabilize the duplex even in the presence of Ag(I). However, sensors fabricated with DNA probes containing both adenine (A) and C are ideal for this application, owing to the formation of C-Ag(I)-C complexes, as well as other lesser known interactions between A and Ag(I). Both sensors are sensitive, specific and selective enough to be used in 50% human saliva. They can also be used to detect silver sulfadiazine, a commonly prescribed antimicrobial drug. With further optimization, this sensing strategy may offer a promising approach for detection of Ag(I) in environmental and clinical samples.

Cooperative hydrogen-bonding of the adenine–thymine pair as a strategy for lowering the limit of detection of thymine by surface-enhanced Raman spectroscopy

The formation of cooperative hydrogen bonds between the thymine–adenine pair was used to indirectly determine thymine by SERS, improving the limit of detection values up to two orders of magnitude.

Investigation of the in situ generation of oxide-free copper nanoparticles using pulsed-laser ablation of bulk copper in aqueous solutions of DNA bases

The pulsed-laser ablation method was used as a facile and green approach to prepare oxide-free copper nanoparticles, and was performed by laser ablation of a copper target in aqueous solutions of the DNA bases.

Enhanced in vitro cytotoxicity and cellular uptake of DNA bases functionalized gold nanoparticles in HeLa cell lines

DNA base functionalized AuNPs are internalized to a greater extent with high cellular uptake and enhanced cytotoxicity in HeLa cells.

Tween 20-stabilized gold nanoparticles combined with adenosine triphosphate-BODIPY conjugates for the fluorescence detection of adenosine with more than 1000-fold selectivity

This study describes the development of a simple, enzyme-free, label-free, sensitive, and selective system for detecting adenosine based on the use of Tween 20-stabilized gold nanoparticles (Tween 20-AuNPs) as an efficient fluorescence quencher for boron dipyrromethene-conjugated adenosine 5'-triphosphate (BODIPY-ATP) and as a recognition element for adenosine. BODIPY-ATP can interact with Tween 20-AuNPs through the coordination between the adenine group of BODIPY-ATP and Au atoms on the NP surface, thereby causing the fluorescence quenching of BODIPY-ATP through the nanometal surface energy transfer (NSET) effect. When adenosine attaches to the NP surface, the attached adenosine exhibits additional electrostatic attraction to BODIPY-ATP. As a result, the presence of adenosine enhances the efficiency of AuNPs in fluorescence quenching of BODIPY-ATP. The AuNP-induced fluorescence quenching of BODIPY-ATP progressively increased with an increase in the concentration of adenosine; the detection limit at a signal-to-noise ratio of 3 for adenosine was determined to be 60nM. The selectivity of the proposed system was more than 1000-fold for adenosine over any adenosine analogs and other nucleotides. The proposed system combined with a phenylboronic acid-containing column was successfully applied to the determination of adenosine in urine.

eMethylsorb: rapid quantification of DNA methylation in cancer cells on screen-printed gold electrodes

A simple, sensitive and inexpensive electrochemical method has been reported to detect regional DNA methylation by using differential adsorption affinity of DNA bases to gold.

Surfactant-free nanoparticle–DNA complexes with ultrahigh stability against salt for environmental and biological sensing

A AuNP–DNA complex highly stable in extremely high ionic strength media, such as seawater, was obtained by inserting a few thymine bases into the DNA strands.

Interaction of Nucleic Acid Bases with the Au(111) Surface

The fate of an individual DNA molecule when it is deposited on a hard inorganic surface in a "dry" environment is unknown, while it is a crucial determinant for nanotechnology applications of nucleic acids. In the absence of experimental approaches that are able to unravel the three-dimensional atomic structure of the target system, here we tackle the first step toward a computational solution of the problem. By using first-principles quantum mechanical calculations of the four nucleobases on the Au(111) surface, we present results for the geometries, energetics, and electronic structure, in view of developing a force field that will enable classical simulations of DNA on Au(111) to investigate the structural modifications of the duplex in these non-native conditions. We fully characterize each system at the individual level. We find that van der Waals interactions are crucial for a correct description of the geometry and energetics. However, the mechanism of adsorption is well beyond pure dispersion interactions. Indeed, we find charge sharing between the substrate and the adsorbate, the formation of hybrid orbitals, and even bonding orbitals. Yet, this molecule-surface association is qualitatively distinct from the thiol adsorption mechanism: we discuss such differences and also the relation to the adsorption mechanism of pure aromatic molecules.

Pattern recognition analysis of proteins using DNA-decorated catalytic gold nanoparticles

A label-free protein analysis strategy is based on patterns of gold nanoparticle (AuNP) growth. AuNPs pretreated with different oligonucleotides are challenged with various proteins. After Au reduction, the colorimetric patterns are processed with linear discriminant analysis. This method discriminates different proteins, or one protein of different concentrations, in mixed samples or even serum and urine.