Controlling DNA orientation on mixed ssDNA/OEG SAMs

Bifunctional Protein TC1 Mediated One-Pot Strategy for Robust Immobilization of DNA with High Accessibility

Immobilizing DNA with high accessibility at the interface is attractive but challenging. Current methods often involve multiple chemical reactions and derivatives. In this study, an endonuclease, TC1, is introduced to develop a robust strategy for immobilizing DNA with enhanced accessibility. TC1 enables direct immobilization of DNA onto a solid support through self-catalytic DNA covalent coupling and robust solid adsorption capabilities. This method demonstrates high accessibility to target molecules, supported by the improved sensitivity of DNA hybridization and aptamer-target recognition assays. TC1-mediated DNA immobilization is a one-pot reaction that does not require chemical derivatives, making it promising for the development of high-performance DNA materials and technologies.

Surface immobilization strategies for the development of electrochemical nucleic acid sensors

Following the recent pandemic and with the emergence of cell-free nucleic acids in liquid biopsies as promising biomarkers for a broad range of pathologies, there is an increasing demand for a new generation of nucleic acid tests, with a particular focus on cost-effective, highly sensitive and specific biosensors. Easily miniaturized electrochemical sensors show the greatest promise and most typically rely on the chemical functionalization of conductive materials or electrodes with sequence-specific hybridization probes made of standard oligonucleotides (DNA or RNA) or synthetic analogues (e.g. Peptide Nucleic Acids or PNAs). The robustness of such sensors is mostly influenced by the ability to control the density and orientation of the probe at the surface of the electrode, making the chemistry used for this immobilization a key parameter. This exhaustive review will cover the various strategies to immobilize nucleic acid probes onto different solid electrode materials. Both physical and chemical immobilization techniques will be presented. Their applicability to specific electrode materials and surfaces will also be discussed as well as strategies for passivation of the electrode surface as a way of preventing electrode fouling and reducing nonspecific binding.

DNAzyme-Immobilizing Microgel Magnetic Beads Enable Rapid, Specific, Culture-Free, and Wash-Free Electrochemical Quantification of Bacteria in Untreated Urine

Rapid, ultrasensitive, and specific detection and identification of bacteria in unprocessed clinical specimens is critically needed to enable point-of-care diagnosis of infectious diseases. However, existing systems require sample processing and/or analyte enrichment for direct bacterial analysis in clinical samples, which significantly adds to the assay time and complexity. Herein, we integrate RNA-cleaving DNAzymes specific to Escherichia coli (E. coli) and programmed for electrochemical signal transduction, multifunctional microgel magnetic beads for immobilizing the DNAzyme into a hydrated and three-dimensional scaffold, and hierarchical electrodes for ultrasensitive electrochemical readout to achieve rapid bacterial analysis in undiluted and unprocessed urine collected from symptomatic patients suspected of having urinary tract infections (UTIs). The microgel magnetic bead assay enables highly efficient conjugation and hydration of the immobilized DNAzymes, resulting in low limits-of-detection of 6 CFU/mL in buffer and 138 CFU/mL in unprocessed urine with high specificity against multiple urinary pathogens within a 1 hour assay time. The assay successfully identifies which patients are infected with E. coli as the causative organism for their UTI symptoms, indicating the clinical relevance of this assay.

Beyond Sensitive and Selective Electrochemical Biosensors: Towards Continuous, Real-Time, Antibiofouling and Calibration-Free Devices

Nowadays, electrochemical biosensors are reliable analytical tools to determine a broad range of molecular analytes because of their simplicity, affordable cost, and compatibility with multiplexed and point-of-care strategies. There is an increasing demand to improve their sensitivity and selectivity, but also to provide electrochemical biosensors with important attributes such as near real-time and continuous monitoring in complex or denaturing media, or in vivo with minimal intervention to make them even more attractive and suitable for getting into the real world. Modification of biosensors surfaces with antibiofouling reagents, smart coupling with nanomaterials, and the advances experienced by folded-based biosensors have endowed bioelectroanalytical platforms with one or more of such attributes. With this background in mind, this review aims to give an updated and general overview of these technologies as well as to discuss the remarkable achievements arising from the development of electrochemical biosensors free of reagents, washing, or calibration steps, and/or with antifouling properties and the ability to perform continuous, real-time, and even in vivo operation in nearly autonomous way. The challenges to be faced and the next features that these devices may offer to continue impacting in fields closely related with essential aspects of people's safety and health are also commented upon.

Immobilization Techniques for Aptamers on Gold Electrodes for the Electrochemical Detection of Proteins: A Review

The development of reliable biosensing platforms plays a key role in the detection of proteins in clinically and environmentally derived samples for diagnostics, as well as for process monitoring in biotechnological productions. For this purpose, the biosensor has to be stable and reproducible, and highly sensitive to detect potentially extremely low concentrations and prevent the nonspecific binding of interfering compounds. In this review, we present an overview of recently published (2017–2019) immobilization techniques for aptamers on gold electrodes for the electrochemical detection of proteins. These include the direct immobilization of thiolated aptamers and the utilization of short linkers, streptavidin/biotin interaction, as well as DNA nanostructures and reduced graphene oxide as immobilization platforms. Applied strategies for signal amplification and the prevention of biofouling are additionally discussed, as they play a crucial role in the design of biosensors. While a wide variety of amplification strategies are already available, future investigations should aim to establish suitable antifouling strategies that are compatible with electrochemical measurements. The focus of our review lies on the detailed discussion of the underlying principles and the presentation of utilized chemical protocols in order to provide the reader with promising ideas and profound knowledge of the subject, as well as an update on recent discoveries and achievements.

Antifouling (Bio)materials for Electrochemical (Bio)sensing

(Bio)fouling processes arising from nonspecific adsorption of biological materials (mainly proteins but also cells and oligonucleotides), reaction products of neurotransmitters oxidation, and precipitation/polymerization of phenolic compounds, have detrimental effects on reliable electrochemical (bio)sensing of relevant analytes and markers either directly or after prolonged incubation in rich-proteins samples or at extreme pH values. Therefore, the design of antifouling (bio)sensing interfaces capable to minimize these undesired processes is a substantial outstanding challenge in electrochemical biosensing. For this purpose, efficient antifouling strategies involving the use of carbon materials, metallic nanoparticles, catalytic redox couples, nanoporous electrodes, electrochemical activation, and (bio)materials have been proposed so far. In this article, biomaterial-based strategies involving polymers, hydrogels, peptides, and thiolated self-assembled monolayers are reviewed and critically discussed. The reported strategies have been shown to be successful to overcome (bio)fouling in a diverse range of relevant practical applications. We highlight recent examples for the reliable sensing of particularly fouling analytes and direct/continuous operation in complex biofluids or harsh environments. Opportunities, unmet challenges, and future prospects in this field are also pointed out.

Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing

Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.

DNA self-assembly-driven positioning of molecular components on nanopatterned surfaces

We present a method for the specific, spatially targeted attachment of DNA molecules to lithographically patterned gold surfaces-demonstrated by bridging DNA strands across nanogap electrode structures. An alkanethiol self-assembled monolayer was employed as a molecular resist, which could be selectively removed via electrochemical desorption, allowing the binding of thiolated DNA anchoring oligonucleotides to each electrode. After introducing a bridging DNA molecule with single-stranded ends complementary to the electrode-tethered anchoring oligonucleotides, the positioning of the DNA molecule across the electrode gap, driven by self-assembly, occurred autonomously. This demonstrates control of molecule positioning with resolution limited only by the underlying patterned structure, does not require any alignment, is carried out entirely under biologically compatible conditions, and is scalable.

Molecular Crowding Effects on Microgel-Tethered Oligonucleotide Probes

Microgel tethering is a nontraditional method with which to bind oligonucleotide hybridization probes to a solid surface. Microgel-tethering physically positions the probes away from the underlying hard substrate and maintains them in a highly waterlike environment. This paper addresses the question of whether molecular crowding affects the performance of microgel-tethered molecular beacon probes. The density of probe-tethering sites is controlled experimentally using thin-film blends of biotin-terminated [PEG-B] and hydroxyl-terminated [PEG-OH] poly(ethylene glycol) from which microgels are synthesized and patterned by electron beam lithography. Fluorescence measurements indicate that the number of streptavidins, linear DNA probes, hairpin probes, and molecular beacon probes bound to the microgels increases linearly with increasing PEG-B/PEG-OH ratio. For a given tethering-site concentration, more linear probes can bind than structured probes. Crowding effects emerge during the hybridization of microgel-tethered molecular beacons but not during the hybridization of linear probes, as the tethering density increases. Crowding during hybridization is associated with conformational constraints imposed by the close proximity of closed and hybridized structured probes. The signal-to-background ratio (SBR) of hybridized beacons is highest and roughly constant for low tethering densities and decreases at the highest tethering densities. Despite differences between microgel tethering and traditional oligonucleotide surface-immobilization approaches, these results show that crowding defines an optimum tethering density for molecular beacon probes that is less than the maximum possible, which is consistent with previous studies involving various linear and structured oligonucleotide probes.

Controlled DNA Patterning by Chemical Lift-Off Lithography: Matrix Matters

Nucleotide arrays require controlled surface densities and minimal nucleotide-substrate interactions to enable highly specific and efficient recognition by corresponding targets. We investigated chemical lift-off lithography with hydroxyl- and oligo(ethylene glycol)-terminated alkanethiol self-assembled monolayers as a means to produce substrates optimized for tethered DNA insertion into post-lift-off regions. Residual alkanethiols in the patterned regions after lift-off lithography enabled the formation of patterned DNA monolayers that favored hybridization with target DNA. Nucleotide densities were tunable by altering surface chemistries and alkanethiol ratios prior to lift-off. Lithography-induced conformational changes in oligo(ethylene glycol)-terminated monolayers hindered nucleotide insertion but could be used to advantage via mixed monolayers or double-lift-off lithography. Compared to thiolated DNA self-assembly alone or with alkanethiol backfilling, preparation of functional nucleotide arrays by chemical lift-off lithography enables superior hybridization efficiency and tunability.

Surface functionalisation of carbon for low cost fabrication of highly stable electrochemical DNA sensors

An alternative strategy for surface tethering of DNA probes, where highly reactive glassy carbon (GC) substrates are prepared via electrochemical hydrogenation and electrochemical/chemical chlorination is reported. Thiolated DNA probes and alkanethiols were stably immobilised on the halogenated carbon, with electrochemical chlorination being milder, thus producing less damage to the surface. Electrochemical DNA sensors prepared using this surface chemistry on carbon with electrochemical chlorination providing an improved performance, producing a highly ordered surface and the use of lateral spacers to improve steric accessibility to immobilised probes was not required.

Emerging technologies for hybridization based single nucleotide polymorphism detection

Detection of single nucleotide polymorphisms (SNPs) is a crucial challenge in the development of a novel generation of diagnostic tools. Accurate detection of SNPs can prove elusive, as the impact of a single variable nucleotide on the properties of a target sequence is limited, even if this sequence consists of only a few nucleotides. New, accurate and facile strategies for the detection of point mutations are therefore absolutely necessary for the increased adoption of point-of-care molecular diagnostics. Currently, PCR and sequencing are mostly applied for diagnosing SNPs. However these methods have serious drawbacks as routine diagnostic tools because of their labour intensity and cost. Several new, more suitable methods can be applied to enable sensitive detection of mutations based on specially designed hybridization probes, mutation recognizing enzymes and thermal denaturation. Here, an overview is presented of the most recent advances in the field of fast and sensitive SNP detection assays with strong potential for integration in point-of-care tests.

Gold nanowire based electrical DNA detection using rolling circle amplification

We present an electrical sensor that uses rolling circle amplification (RCA) of DNA to stretch across the gap between two electrodes, interact with metal nanoparticle seeds to generate an electrically conductive nanowire, and produce electrical signals upon detection of specific target DNA sequences. RCA is a highly specific molecular detection mechanism based on DNA probe circularization. With this technique, long single-stranded DNA with simple repetitive sequences are produced. Here we show that stretched RCA products can be metalized using silver or gold solutions to form metal wires. Upon metallization, the resistance drops from TΩ to kΩ for silver and to Ω for gold. Metallization is seeded by gold nanoparticles aligned along the single-stranded DNA product through hybridization of functionalized oligonucleotides. We show that combining RCA with electrical DNA detection produces results in readout with very high signal-to-noise ratio, an essential feature for sensitive and specific detection assays. Finally, we demonstrate detection of 10 ng of Escherichia coli genomic DNA using the sensor concept.

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.

Surface plasmon resonance sensing of nucleic acids: a review

Biosensors based on surface plasmon resonance (SPR) have become a central tool for the investigation and quantification of biomolecules and their interactions. Nucleic acids (NAs) play a vital role in numerous biological processes and therefore have been one of the major groups of biomolecules targeted by the SPR biosensors. This paper discusses the advances of NA SPR biosensor technology and reviews its applications both in the research of molecular interactions involving NAs (NA-NA, NA-protein, NA-small molecule), as well as for the field of bioanalytics in the areas of food safety, medical diagnosis and environmental monitoring.

Intermixed terpyridine-functionalized monolayers on gold: nonlinear relationship between terpyridyl density and metal ion coordination properties

Aiming at the functionalization of surfaces with terpyridine anchors for the coordinative deposition of additional layers, mixed self-assembled monolayers (SAMs) were prepared from binary solutions of 12-(2,2':6',2″-terpyridine-4'-yl)dodecane-1-thiol (TDT) and 1-decanethiol (DT). The SAMs and the order of the constituting molecules were analyzed by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), and time-of-flight-secondary ion mass spectrometry (ToF-SIMS). The composition of the (TDT/DT)-SAMs and with it the surface density of terpyridyl groups correlates linearly with the relative concentrations of the two compounds in the solution used for depositing them. In marked contrast, the amount of terpyridine-coordinated Pd(II) ions significantly deviates from this trend with an optimum at a 1:3 ratio of TDT/DT. This indicates a major fraction of the terpyridines in TDT-rich SAMs not to be accessible for Pd(II) ion coordination. In agreement, NEXAFS spectroscopy reveals the alkyl backbones in TDT-rich SAMs not to be ordered, while they are preferentially upright oriented in the optimal 1:3-(TDT/DT)-SAMs. We interpret this in terms of terpyridine backfolding in TDT-rich SAMs, while they are located in accessible positions on top of the SAM in the 1:3-(TDT/DT)-SAM. While the alkyl backbones in the 1:3-(TDT/DT)-SAM are ordered, NEXAFS spectroscopy shows the terpyridyl groups not to have a preferential orientation in this SAM and thus retain enough flexibility to adjust to molecules that are deposited on top of the mixed SAM. In conclusion, the novel SAM does not undergo phase separation and consists predominantly of intermixed phases with adjustable surface density of quite flexible terpyridine anchor groups. The terpyridine-Pd(II) anchors are not only available for a future deposition of the next layer, but the metal ions also represent a sensitive probe for the accessibility of the terpyridyl groups.

Label-free capacitive DNA sensor using immobilized pyrrolidinyl PNA probe: effect of the length and terminating head group of the blocking thiols

This paper reports, for the first time, the influence of the length and the terminating head group of blocking thiols on the sensitivity and specificity of a label-free capacitive DNA detection system using immobilized pyrrolidinyl peptide nucleic acid (acpcPNA) probes. A C-terminal lysine-modified acpcPNA was immobilized through four different alkanethiol self-assembled monolayers (SAMs), i.e., 3-mercaptopropionic acid (MPA), thioctic acid (TA), thiourea (TU) and mercaptosuccinic acid (MSA). The hybridization between the acpcPNA probes and the target DNA was directly measured using the capacitive system. Five blocking thiols of various lengths (C=3, 6, 8, 9 and 11), with the -OH terminating head group, i.e., 3-mercapto-1-propanol (3-MPL), 6-mercapto-1-hexanol (6-MHL), 8-mercapto-1-octanol (8-MOL), 9-mercapto-1-nonanol (9-MNL), 11-mercapto-1-undecanol (11-MUL) and another blocking thiol (C=11) with a -CH(3) terminating head group, and 1-dodecanethiol (1-DDT) were investigated. The blocking thiol with the same length as the total spacer of the immobilized acpcPNA gave the highest sensitivity and specificity with the -OH terminating head group providing a slightly better signal than the -CH(3) group. Under the optimized conditions, the immobilized acpcPNA probes provided a wide linear range for DNA detection (1.0 × 10(-11)-1.0 × 10(-8)M) with a very low detection limit in the picomolar range. The modified acpcPNA electrode could be reused through at least 58 cycles. The high sensitivity and very low detection limits are potentially useful for the analysis of ultra-trace levels of DNA in samples. Preliminary studies were also performed to see the effect of probe concentration and target length.

Enabling fiber optic serotyping of pathogenic bacteria through improved anti-fouling functional surfaces

Significant research efforts are continually being directed towards the development of sensitive and accurate surface plasmon resonance biosensors for sequence specific DNA detection. These sensors hold great potential for applications in healthcare and diagnostics. However, the performance of these sensors in practical usage scenarios is often limited due to interference from the sample matrix. This work shows how the co-immobilization of glycol(PEG) diluents or 'back filling' of the DNA sensing layer can successfully address these problems. A novel SPR based melting assay is used for the analysis of a synthetic oligomer target as well as PCR amplified genomic DNA extracted from Legionella pneumophila. The benefits of sensing layer back filling on the assay performance are first demonstrated through melting analysis of the oligomer target and it is shown how back filling enables accurate discrimination of Legionella pneumophila serogroups directly from the PCR reaction product with complete suppression of sensor fouling.

Highly sensitive disposable nucleic acid biosensors for direct bioelectronic detection in raw biological samples

The development of rapid, low-cost and reliable diagnostic methods is crucial for the identification and treatment of many diseases. Screen-printed gold electrodes (Au/SPEs), coated with a ternary monolayer interface, involving hexanedithiol (HDT), a specific thiolated capture probe (SHCP), and 6-mercapto-1 hexanol (MCH) (SHCP/HDT/MCH) are shown here to offer direct and sensitive detection of nucleic acid hybridization events in untreated raw biological samples (serum, urine and crude bacterial lysate solutions). The composition of the ternary monolayer was modified and tailored to the surface of the Au/SPE. The resulting SHCP/HDT/MCH monolayer has demonstrated to be extremely useful for enhancing the performance of disposable nucleic acid sensors based on screen-printed electrodes. Compared to common SHCP/MCH binary interfaces, the new ternary self-assembled monolayer (SAM) resulted in a 10-fold improvement in the signal (S)-to-noise (N) ratio (S/N) for 1 nM target DNA. The SHCP/HDT/MCH-modified Au/SPEs allowed the direct quantification of the target DNA down to 25 pM (0.25 fmol) and 100 pM (1 fmol) in undiluted/untreated serum and urine samples, respectively, and of 16S rRNA Escherichia coli (E. coli) corresponding to 3000 CFU μL(-1) in raw cell lysate samples. The new SAM-coated screen-printed electrodes also displayed favorable non-fouling properties after a 24h exposure to raw human serum and urine samples, offering great promise as cost-effective nucleic acid sensors for a wide range of decentralized genetic tests.

Three-dimensional arrangement of short DNA oligonucleotides at surfaces via the synthesis of DNA-branched polyacrylamide brushes by SI-ATRP

Short DNA oligonucleotide branches are incorporated into acrylamide brushes via surface initiated atom transfer radical polymerization in an attempt to increase DNA surface density by building three-dimensional molecular architectures. ATR-FTIR as well as hybridization studies followed by SPR confirm the incorporation of the DNA sequences into the polymer backbone. MALDI-TOF analysis further suggests that six acrylamide monomer units are typically separating DNA branches present on a single brushes approximately 26 units long. This new approach offers a promising alternative to SAM-based nucleic acid and aptamer sensors and could enable the realization of more complex soft materials of controlled architecture capable of both recognition and signaling by including additional optically or electrochemically active moieties.

Detection of DNA hybridisation in a diluted serum matrix by surface plasmon resonance and film bulk acoustic resonators

Nanomolar quantities of single-stranded DNA products ~100 nucleotides long can be detected in diluted 1% serum by surface plasmon resonance (SPR) and film bulk acoustic resonators (FBARs). We have used a novel FBAR sensor in parallel with SPR and obtained promising results with both the acoustic and the optical device. Oligonucleotides and a repellent lipoamide, Lipa-DEA, were allowed to assemble on the sensor chip surfaces for only 15 min by dispensing. Lipa-DEA surrounds the analyte-binding probes on the surface and effectively reduces the non-specific binding of bovine serum albumin and non-complementary strands. In a highly diluted serum matrix, the non-specific binding is, however, a hindrance, and the background response must be reduced. Nanomolar concentrations of short complementary oligos could be detected in buffer, whereas the response was too low to be measured in serum. DNA strands that are approximately 100 base pairs long at concentrations as low as 1-nM could be detected both in buffer and in 1% serum by both SPR and the FBAR resonator.

Fe3O4 nanoparticles-enhanced SPR sensing for ultrasensitive sandwich bio-assay

Magnetic nanoparticles (MNPs) have been receiving increasing attention because of its great potentials in bioseparation. However, the separation products are difficult to be detected by general method due to their extremely small size. Here, we demonstrate that MNPs can greatly enhance the signal of surface plasmon resonance spectroscopy (SPR). Features of MNPs-aptamer conjugates as a powerful amplification reagent for ultrasensitive immunoassay are reported in this work for the first time. In order to evaluate the sensing ability of MNPs-aptamer conjugates as an amplification reagent, a sandwich SPR sensor is constructed by using thrombin as model analyte. Thrombin, captured by immobilized anti-thrombin aptamer on SPR gold film, is sensitively detected by SPR spectroscopy with a lowest detection limit of 0.017 nM after MNPs-aptamer conjugates is used as amplification reagent. At the same time, the excellent selectivity of the present biosensor is also confirmed by using three kinds of proteins (BSA, human IgM and human IgE) as controls. These results confirm that MNPs is a powerful sandwich element and an excellent amplification reagent for SPR based sandwich immunoassay and SPR has a great potential for the detection of MNPs-based bioseparation products.

Ternary monolayers as DNA recognition interfaces for direct and sensitive electrochemical detection in untreated clinical samples

Detection of specific DNA sequences in clinical samples is a key goal of studies on DNA biosensors and gene chips. Herein we present a highly sensitive electrochemical genosensor for direct measurements of specific DNA sequences in undiluted and untreated human serum and urine samples. Such genosensing relies on a new ternary interface involving hexanedithiol (HDT) co-immobilized with the thiolated capture probe (SHCP) on gold surfaces, followed by the incorporation of 6-mercapto-1-hexanol (MCH) as diluent. The performance of ternary monolayers prepared with linear dithiols of different lengths was systematically examined, compared and characterized by cyclic voltammetry and electrochemical impedance spectroscopy, with HDT exhibiting the most favorable analytical performance. The new SHCP/HDT+MCH monolayer led to a 80-fold improvement in the signal-to-noise ratio (S/N) for 1 nM target DNA in undiluted human serum over the common SHCP+MCH binary alkanethiol interface, and allowed the direct quantification of the target DNA down to 7 pM (28 amol) and 17 pM (68 amol) in undiluted/untreated serum and urine, respectively. It also displayed attractive antifouling properties, as indicated from the favorable S/N obtained after a prolonged exposure (24h) to untreated biological matrices. These attractive features of the SHCP/HDT+MCH sensor interface indicate considerable promise for a wide range of clinical applications.

Chemical modifications of atomic force microscopy tips

Atomic force microscopy (AFM) works by scanning a very tiny tip over a surface with great precision. The microscope tips can be chemically functionalized to improve the images obtained. Well-defined chemical functionalization of AFM tips is especially important for experiments, such as chemical force microscopy and single molecule recognition force microscopy, to examine specific interactions at the single molecular level. In this chapter, we present an overview of chemical modifications of tips that have been reported to date with regards to the proper fixation of probe molecules, focusing particularly on chemical procedures developed to anchor biological molecules on AFM tips.

Surface immobilization of DNA aptamers for biosensing and protein interaction analysis

To utilize aptamers as molecular recognition agents in biosensors and biodiagnostics, it is important to develop strategies for reliable immobilization of aptamers so that they retain their biophysical characteristics and binding abilities. Here we report on quartz crystal microbalance (QCM) measurements and atomic force microscope (AFM)-based force spectroscopy studies to evaluate aptasensors fabricated by different modification strategies. Gold surfaces were modified with mixed self assembled monolayers (SAMs) of aptamer and oligoethylene glycol (OEG) thiols (HS-C(11)-(EG)(n)OH, n=3 or 6) to impart resistance to nonspecific protein adsorption. By affinity analysis, we show that short OEG thiols have less impact on aptamer accessibility than longer chain thiols. Backfilling with OEG as a step subsequent to aptamer immobilization provides greater surface coverage than using aptamer and OEG thiol to form a mixed SAM in one-step. Immunoglobulin E and vascular endothelial growth factor (VEGF) were studied as target proteins in these experiments. Binding forces obtained by these strategies are similar, demonstrating that the biophysical properties of the aptamer on the sensors are independent from the immobilization strategy. The results present mixed SAMs with aptamers and co-adsorbents as a versatile strategy for aptamer sensor platforms including ultrasensitive biosensor design.

Ternary surface monolayers for ultrasensitive (zeptomole) amperometric detection of nucleic acid hybridization without signal amplification

A ternary surface monolayer, consisting of coassembled thiolated capture probe, mercaptohexanol and dithiothreitol, is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers. Remarkably low detection limits down to 40 zmol (in 4 μL samples) as well as only 1 CFU Escherichia coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3',5,5'-tetramethylbenzidine system. Such dramatic improvements in the detection limits (compared to those of common binary alkanethiol interfaces and to those of most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to nonspecific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration "backfillers" that leads to a remarkably low background noise even in the presence of complex sample matrixes. A wide range of surface compositions have been investigated, and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety, and forensic analysis.

Real-time PMIRRAS studies of in situ growth of C11Eg6OMe on gold and immersion effects

We studied the growth of self-assembling monolayers of C(11)Eg(6)OMe on gold under aqueous conditions. With the help of polarisation modulation infrared reflection absorption spectroscopy (PMIRRAS) we monitored the evolution of characteristic absorption modes in the fingerprint region (1050-1500 cm(-1)) during the later stages of the growth of the SAM. We observed a change from rather amorphous structure with mixed all-trans and helical conformation to an ordered structure with predominantly helical structure over time. Changes of mode positions, intensities and broadness can be described by a single exponential. In addition, we investigated the effect of hydration for SAMs with different degrees of crystallinity. To that end, we compared their spectra at certain ordering levels in contact with aqueous solution with the corresponding spectra in air. SAMs with a highly ordered crystalline structure in air show the same structure under aqueous conditions. However, SAMs which are still crystalline in air, but less perfect, show rather amorphous spectral features under aqueous conditions indicating a strong interaction with water. This implies that the ability of water to penetrate the EG moiety strongly depends on its structure which in turn is related inter alia to the surface coverage. Since the interaction with water plays an important role in the prevention of unspecific adsorption on oligo(ethylene glycols) this is important for its application. Our experiments also underline the importance of the in situ analysis of the film structure.