Optimization of DNA-directed immobilization on mixed oligo(ethylene glycol) monolayers for immunodetection

Protein Adsorption on Mixed Self-Assembled Monolayers: Influence of Chain Length and Terminal Group

Mixed self-assembled monolayers (SAMs) are often used as highly tunable substrates for biomedical and biosensing applications. It is well documented, however, that mixed SAMs can be highly disordered at the molecular level and do not pack as closely or homogeneously as single-component SAMs, particularly when the chain lengths and head groups of the SAM thiol components are significantly different. In this study, we explore the impact of SAM structure and mixing ratio (-OH and -CH3 termini) on the weak physisorption behavior of bovine serum albumin (BSA), which adsorbs more readily to hydrophobic, methyl-terminated SAMs. Our results suggest that once the mixture includes 50% or more of the methyl terminus, the mixing ratio alone is a relatively good predictor of adsorption, regardless of the relative chain lengths of the thiols used in the mixture. This trend persists at any mixing ratio for SAMs where methyl- and hydroxyl-terminated groups are the same length or where the hydroxyl-terminated thiol is longer. The only variance observed is at low mixing ratios (<50% methyl-terminated) for a mixed SAM where the methyl-terminated component has a longer chain length. Relative protein adsorption increases on these mixtures, perhaps due to the disordered exposure of the excess alkane backbone. Taken together, however, we do not find significant evidence that varying chain lengths for mixed SAMs prepared on polycrystalline substrates and analyzed in air have an outsized influence on nanoscopic adsorption behavior, despite molecular-level disorder in the SAM itself.

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.

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.

Functionalizing gold with single strand DNA: novel insight into optical properties via combined spectroscopic ellipsometry and nanolithography measurements

We have studied the self-assembly of 22-base oligonucleotides bound by a short alkyl thiol linker (C6-ssDNA) on flat Au films. The self-assembled monolayer (SAM) was modified by addition of a spacer (mercaptohexanol, MCH). Molecular depositions were monitored in situ by spectroscopic ellipsometry (SE). SAMs were characterized in a liquid environment by coupling SE (difference spectra method) with Atomic Force Microscope (AFM) measurements. We exploited the biofilm thickness obtained by AFM nanolithography and imaging to solve the refractive index/thickness correlation in optical measurements on ultrathin molecular layers. The combined SE/AFM analysis provided reliable estimates of the thickness and the refractive index of the biofilm in the NIR region (650-1300 nm) and revealed new aspects of DNA molecular organization: exposure to MCH leads to an increase of both film thickness and refractive index, which points to a reorganization of C6-ssDNA film. We show that the contribution of the thiol/Au interface has to be included in the optical model to obtain a more reliable determination of the refractive index of the biofilm in a liquid. The careful, correlative characterization of the mixed C6-ssDNA/MCH SAM represents a key step towards the optimization of a robust detection scheme based on helix-helix hybridization.

Workshop, Cost-Effective and Streamlined Fabrications of Re-Usable World-To-Chip Connectors for Handling Sample of Limited Volume and for Assembling Chip Array

The world-to-chip interface is an essential yet intriguing part of making and employing microfluidic devices. A user-friendly connector could be expensive or difficult to make. We fabricated two ports of microfluidic chips with easily available materials including Teflon blocks, double adhesive films, coverslips, and transparency films. By using a mini grinder, coverslips were drilled to form small holes for the fluid passages between port and chip. Except for the double adhesive films, the resultant ports are durable and re-useable. The DK1 port, contains a mini three-way switch which allows users to handle fluid by a tube-connected pump, or by a manual pipette for the sample of trace amount. The other port, the DK2 port, provides secured tube-connections. Importantly, we invented a bridge made of craft cutter-treated transparency films and double adhesive films to mediate liquid flow between DK2 port and chip. With the use of a bridge, users do not need to design new ports for new chips. Also, individual chips could be linked by a bridge to form a chip array. We successfully applied DK1 port on a microfluidic chip where green fluorescent protein was immobilized. We used DK2 port on an array of fish chips where the embryos of zebra fish developed.

Photoinduced Cross-Linking of Short Furan-Modified DNA on Surfaces

We report for the first time the formation of site-specific interstrand cross-linked (ICL) surface-immobilized furan-modified DNA duplexes via singlet oxygen. ¹O₂, necessary for effecting furan-mediated ICL formation, was produced in situ using methylene blue or a zinc phthalocyanine derivative (TT1) as a photosensitizer. Via surface plasmon resonance spectroscopy, we show that surface ICL was achieved, and a robust link formed that enhances the stability of the 12-mer duplex even after surface regeneration. The described method represents a novel platform technology based on surfaces with addressable and stable DNA duplexes requiring only short oligonucleotides.

Nature inspires sensors to do more with less

The world is filled with widely varying chemical, physical, and biological stimuli. Over millennia, organisms have refined their senses to cope with these diverse stimuli, becoming virtuosos in differentiating closely related antigens, handling extremes in concentration, resetting the spent sensing mechanisms, and processing the multiple data streams being generated. Nature successfully deals with both repeating and new stimuli, demonstrating great adaptability when confronted with the latter. Interestingly, nature accomplishes these feats using a fairly simple toolbox. The sensors community continues to draw inspiration from nature's example: just look at the antibodies used as biosensor capture agents or the neural networks that process multivariate data streams. Indeed, many successful sensors have been built by simply mimicking natural systems. However, some of the most exciting breakthroughs occur when the community moves beyond mimicking nature and learns to use nature's tools in innovative ways.

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.

Improved DNA detection by utilizing electrically neutral DNA probe in field-effect transistor measurements as evidenced by surface plasmon resonance imaging

Intensive efforts have been focused on the development of ultrasensitive DNA biosensors capable of quantitative gene expression analysis. Various neutralized nucleic acids have been demonstrated as alternative and attractive probe for the design of a DNA chip. However, the mechanism of the improvements has not been clearly revealed. In this investigation, we used a newly developed neutral ethylated DNA (E-DNA), a DNA analog with the "RO-P-O" backbone (wherein R could be methyl, ethyl, aryl, or alkyl group) obtained from synthetic procedures, and a silicon nanowire (SiNW) field-effect transistor (FET) to evaluate the difference in DNA detection performance while using E-DNA and DNA as probes. It is demonstrated that using the E-DNA probe in the FET measurement could have a significantly enhanced effect upon the detection sensitivity. Surface plasmon resonance imaging (SPRi) was used to evidence the mechanism of the improved detection sensitivity. SPRi analysis showed the amounts of probe immobilization on the sensor surface and the hybridization efficiency were both enhanced with the use of E-DNA. Consequently, neutral ethylated DNA probe hold a great promise for DNA sensing, especially in the electrical-based sensor.