Density Control over MBD2 Receptor-Coated Surfaces Provides Superselective Binding of Hypermethylated DNA.

Using the biomarker hypermethylated DNA (hmDNA) for cancer detection requires a pretreatment to isolate or concentrate hmDNA from nonmethylated DNA. Affinity chromatography using a methyl binding domain-2 (MBD2) protein can be used, but the relatively low enrichment selectivity of MBD2 limits its clinical applicability. Here, we developed a superselective, multivalent, MBD2-coated platform to improve the selectivity of hmDNA enrichment. The multivalent platform employs control over the MBD2 surface receptor density, which is shown to strongly affect the binding of DNA with varying degrees of methylation, improving both the selectivity and the affinity of DNAs with higher numbers of methylation sites. Histidine-10-tagged MBD2 was immobilized on gold surfaces with receptor density control by tuning the amount of nickel nitrilotriacetic acid (NiNTA)-functionalized thiols in a thiol-based self-assembled monolayer. The required MBD2 surface receptor densities for DNA surface binding decreases for DNA with higher degrees of methylation. Both higher degrees of superselectivity and surface coverages were observed upon DNA binding at increasing methylation levels. Adopting the findings of this study into hmDNA enrichment of clinical samples has the potential to become more selective and sensitive than current MBD2-based methods and, therefore, to improve cancer diagnostics.

An inkjet-printed polysaccharide matrix for on-chip sample preparation in point-of-care cell counting chambers.

On-chip sample preparation in self-contained microfluidic devices is a key element to realize simple, low-cost, yet reliable in vitro diagnostics that can be carried out at the point-of-care (POC) with minimal training requirements by unskilled users. To address this largely unmet POC medical need, we have developed an optimized polysaccharide matrix containing the reagents which substantially improves our fully printed POC CD4 counting chambers for the monitoring of HIV patients. The simply designed counting chambers allow for capillary-driven filling with unprocessed whole blood. We carefully tailored a gellan/trehalose matrix for deposition by inkjet printing, which preserves the viability of immunostains during a shelf life of at least 3 months and enables controlled antibody release for intense and homogeneous immunofluorescent cell staining throughout the complete 60 mm2 image area within 30 min. Excellent agreement between CD4 counts obtained from our fully printed CD4 counting chambers and the gold standard, flow cytometry, is demonstrated using samples both from healthy donors and HIV-infected patients.

All-printed cell counting chambers with on-chip sample preparation for point-of-care CD4 counting.

We demonstrate the fabrication of fully printed microfluidic CD4 counting chips with complete on-chip sample preparation and their applicability as a CD4 counting assay using samples from healthy donors and HIV-infected patients. CD4 counting in low-income and resource-limited point-of-care settings is only practical and affordable, if disposable tests can be fabricated at very low cost and all manual sample preparation is avoided, while operation as well as quantification is fully automated and independent of the skills of the operator. Here, we show the successful use of (inkjet) printing methods both to fabricate microfluidic cell counting chambers with controlled heights, and to deposit hydrogel layers with embedded fluorophore-labeled antibodies for on-chip sample preparation and reagent storage. The maturation process of gelatin after deposition prevents antibody wash-off during blood inflow very well, while temperature-controlled dissolution of the matrix ensures complete antibody release for immunostaining after the inflow has stopped. The prevention of antibody wash-off together with the subsequent complete antibody release guarantees a homogeneous fluorescence background, making rapid and accurate CD4 counting possible. We show the successful application of our fully printed CD4 counting chips on samples from healthy donors as well as from HIV-infected patients and find an excellent agreement between results from our method and from the gold standard, flow cytometry, in both cases.

Controlling Protein Surface Orientation by Strategic Placement of Oligo-Histidine Tags.

We report oriented immobilization of proteins using the standard hexahistidine (His6)-Ni2+:NTA (nitrilotriacetic acid) methodology, which we systematically tuned to give control of surface coverage. Fluorescence microscopy and surface plasmon resonance measurements of self-assembled monolayers (SAMs) of red fluorescent proteins (TagRFP) showed that binding strength increased by 1 order of magnitude for each additional His6-tag on the TagRFP proteins. All TagRFP variants with His6-tags located on only one side of the barrel-shaped protein yielded a 1.5 times higher surface coverage compared to variants with His6-tags on opposite sides of the so-called ß-barrel. Time-resolved fluorescence anisotropy measurements supported by polarized infrared spectroscopy verified that the orientation (and thus coverage and functionality) of proteins on surfaces can be controlled by strategic placement of a His6-tag on the protein. Molecular dynamics simulations show how the differently tagged proteins reside at the surface in "end-on" and "side-on" orientations with each His6-tag contributing to binding. Also, not every dihistidine subunit in a given His6-tag forms a full coordination bond with the Ni2+:NTA SAMs, which varied with the position of the His6-tag on the protein. At equal valency but different tag positions on the protein, differences in binding were caused by probing for Ni2+:NTA moieties and by additional electrostatic interactions between different fractions of the ß-barrel structure and charged NTA moieties. Potential of mean force calculations indicate there is no specific single-protein interaction mode that provides a clear preferential surface orientation, suggesting that the experimentally measured preference for the end-on orientation is a supra-protein, not a single-protein, effect.

Targeting protein-loaded CB[8]-mediated supramolecular nanocarriers to cells.

Supramolecular amphiphiles, consisting of ternary complexes of cucurbit[8]uril (CB[8]), an alkylated paraquat derivative and a tetraethylene glycol-functionalized azobenzene, self-assemble into vesicles of about 200 nm in diameter. The outer surface of the vesicles was functionalized with cell-targeting ligands. These vesicles were employed for loading and delivery of proteins into cells. Supramolecular amphiphile-derived vesicles show great promise as nanocarriers of functional molecules to be transferred into cells.

Temperature-Switch Cytometry-Releasing Antibody on Demand from Inkjet-Printed Gelatin for On-Chip Immunostaining.

Complete integration of all sample preparation steps in a microfluidic device greatly benefits point-of-care diagnostics. In the most simplistic approach, reagents are integrated in a microfluidic chip and dissolved upon filling with a sample fluid by capillary force. This will generally result in at least partial reagent wash-off during sample inflow. However, many applications, such as immunostaining-based cytometry, strongly rely on a homogeneous reagent distribution across the chip. The concept of initially preventing release (during inflow), followed by a triggered instantaneous and complete release on demand (after filling is completed) represents an elegant and simple solution to this problem. Here, we realize this controlled release by embedding antibodies in a gelatin layer integrated in a microfluidic chamber. The gelatin/antibody layer is deposited by inkjet printing. Maturation of this layer during the course of several weeks, due to the ongoing physical cross-linking of gelatin, slows down the antibody release, thereby reducing antibody wash-off during inflow, and consequently helping to meet the requirement for a homogeneous antibody distribution in the filled chamber. After inflow, complete antibody release is obtained by heating the gelatin layer above its sol-gel transition temperature, which causes the rapid dissolution of the entire gelatin/antibody layer at moderate temperatures. We demonstrate uniform and complete on-chip immunostaining of CD4 positive (CD4+) T-lymphocytes in whole blood samples, which is critical for accurate cell counts. The sample preparation is realized entirely on-chip, by applying temperature-switched antibody release from matured gelatin/antibody layers.

Controlled antibody release from gelatin for on-chip sample preparation.

A practical way to realize on-chip sample preparation for point-of-care diagnostics is to store the required reagents on a microfluidic device and release them in a controlled manner upon contact with the sample. For the development of such diagnostic devices, a fundamental understanding of the release kinetics of reagents from suitable materials in microfluidic chips is therefore essential. Here, we study the release kinetics of fluorophore-conjugated antibodies from (sub-) µm thick gelatin layers and several ways to control the release time. The observed antibody release is well-described by a diffusion model. Release times ranging from ∼20 s to ∼650 s were determined for layers with thicknesses (in the dry state) between 0.25 µm and 1.5 µm, corresponding to a diffusivity of 0.65 µm(2) s(-1) (in the swollen state) for our standard layer preparation conditions. By modifying the preparation conditions, we can influence the properties of gelatin to realize faster or slower release. Faster drying at increased temperatures leads to shorter release times, whereas slower drying at increased humidity yields slower release. As expected in a diffusive process, the release time increases with the size of the antibody. Moreover, the ionic strength of the release medium has a significant impact on the release kinetics. Applying these findings to cell counting chambers with on-chip sample preparation, we can tune the release to control the antibody distribution after inflow of blood in order to achieve homogeneous cell staining.

Oriented protein immobilization using covalent and noncovalent chemistry on a thiol-reactive self-reporting surface.

We report the fabrication of a patterned protein array using three orthogonal methods of immobilization that are detected exploiting a fluorogenic surface. Upon reaction of thiols, the fluorogenic tether reports the bond formation by an instantaneous rise in (blue) fluorescence intensity providing a means to visualize the immobilization even of nonfluorescent biomolecules. First, the covalent, oriented immobilization of a visible fluorescent protein (TFP) modified to display a single cysteine residue was detected. Colocalization of the fluorescence of the immobilized TFP and the fluorogenic group provided a direct tool to distinguish covalent bond formation from physisorption of proteins. Subsequent orthogonal immobilization of thiol-functionalized biomolecules could be conveniently detected by fluorescence microscopy using the fluorogenic surface. A thiol-modified nitrilotriacetate ligand was immobilized for binding of hexahistidine-tagged red-fluorescing TagRFP, while an appropriately modified biotin was immobilized for binding of Cy5-labeled streptavidin.

Immobilization of Ferrocene-Modified SNAP-Fusion Proteins.

The supramolecular assembly of proteins on surfaces has been investigated via the site-selective incorporation of a supramolecular moiety on proteins. To this end, fluorescent proteins have been site-selectively labeled with ferrocenes, as supramolecular guest moieties, via SNAP-tag technology. The assembly of guest-functionalized SNAP-fusion proteins on cyclodextrin- and cucurbit[7]uril-coated surfaces yielded stable monolayers. The binding of all ferrocene fusion proteins is specific as determined by surface plasmon resonance. Micropatterns of the fusion proteins, on patterned cyclodextrin and cucurbituril surfaces, have been visualized using fluorescence microscopy. The SNAP-fusion proteins were also immobilized on cyclodextrin vesicles. The supramolecular SNAP-tag labeling of proteins, thus, allows for the assembly of modified proteins via supramolecular host-guest interaction on different surfaces in a controlled manner. These findings extend the toolbox of fabricating supramolecular protein patterns on surfaces taking advantage of the high labeling efficiency of the SNAP-tag with versatile supramolecular moieties.

Directed supramolecular surface assembly of SNAP-tag fusion proteins.

Supramolecular assembly of proteins on surfaces and vesicles was investigated by site-selective incorporation of a supramolecular guest element on proteins. Fluorescent proteins were site-selectively labeled with bisadamantane by SNAP-tag technology. The assembly of the bisadamantane functionalized SNAP-fusion proteins on cyclodextrin-coated surfaces yielded stable monolayers. The binding of the fusion proteins is specific and occurs with an affinity in the order of 10(6) M(-1) as determined by surface plasmon resonance. Reversible micropatterns of the fusion proteins on micropatterned cyclodextrin surfaces were visualized by using fluorescence microscopy. Furthermore, the guest-functionalized proteins could be assembled out of solution specifically onto the surface of cyclodextrin vesicles. The SNAP-tag labeling of proteins thus allows for assembly of modified proteins through a host-guest interaction on different surfaces. This provides a new strategy in fabricating protein patterns on surfaces and takes advantage of the high labeling efficiency of the SNAP-tag with designed supramolecular elements.

Patterning of peptide nucleic acids using reactive microcontact printing.

PNAs (peptide nucleic acids) have been immobilized onto surfaces in a fast, accurate way by employing reactive microcontact printing. Surfaces have been first modified with aldehyde groups to react with the amino end of the synthesized PNAs. When patterning fluorescein-labeled PNAs by reactive microcontact printing using oxygen-oxidized polydimethylsiloxane stamps, homogeneous arrays were fabricated and characterized using optical methods. PNA-patterned surfaces were hybridized with complementary and mismatched dye-labeled oligonucleotides to test their ability to recognize DNA sequences. The stability and selectivity of the PNA-DNA duplexes on surfaces have been verified by fluorescence microscopy, and the melting curves have been recorded. Finally, the technique has been applied to the fabrication of chips by spotting a PNA microarray onto a flat PDMS stamp and reproducing the same features onto many slides. The chips were finally applied to single nucleotide polymorphism detection on oligonucleotides.

An on-bead assay for the identification of non-natural peptides targeting the androgen receptor-cofactor interaction.

An efficient and rapid on-bead screening method was established to identify non-natural peptides that target the Androgen Receptor-cofactor interaction. Binding of the Androgen Receptor ligand binding domain to peptide sequences displayed on beads in a One-Bead-One-Compound format could be screened using fluorescence microscopy. The method was applied to generate and screen both a focussed and a random peptide library. Resynthesis of the peptide hits allowed for the verification of the affinity of the selected peptides for the Androgen Receptor in a competitive fluorescence polarization assay. For both libraries strong Androgen Receptor binding peptides were found, both with non-natural and natural amino acids. The peptides identified with natural amino acids showed great similarity in terms of preferred amino acid sequence with peptides previously isolated from biological screens, thus validating the screening approach. The non-natural peptides featured important novel chemical transformations on the relevant hydrophobic amino acid positions interacting with the Androgen Receptor. This screening approach expands the molecular diversity of peptide inhibitors for nuclear receptors.

Modulation of protein dimerization by a supramolecular host-guest system.

Two sets of cyan and yellow fluorescent proteins, monomeric analogues, and analogues with a weak affinity for dimerization were functionalized with supramolecular host-guest molecules by expressed protein ligation. The host-guest elements induce selective assembly of the monomeric variants into a supramolecular heterodimer. For the second set of analogues, the supramolecular host-guest system acts in cooperation with the intrinsic affinity between the two proteins, resulting in the induction of a selective protein-protein heterodimerization at a more dilute concentration. Additionally, the supramolecular host-guest system allows locking of the two proteins in a covalent heterodimer through the facilitated and selective formation of a reversible disulfide linkage. For the monomeric analogues this results in a strong increase of the energy transfer between the proteins. The protein heterodimerization can be reversed in a stepwise fashion. The trajectory of the disassembly process differs for the monomeric and dimerizing set of proteins. The results highlight that supramolecular elements connected to proteins can both be used to facilitate the interaction between two proteins without intrinsic affinity and to stabilize weak protein-protein interactions at concentrations below those determined by the actual affinity of the proteins alone. The subsequent covalent linkage between the proteins generates a stable protein dimer as a single species. The action of the supramolecular elements in concert with the proteins thus allows the generation of protein architectures with specific properties and compositions.

EDOT-type materials: planar but not rigid.

The geometrical, electronic and optical properties of alpha,alpha'-quater(3,4-ethylenedioxythiophene) (4EDOT) and alpha,alpha'-quater(thiophene) (4T) are studied by quantum-chemical calculations; the computed vibronic spectra at low and room temperature (RT) are compared to experiment. Our results suggest that the better resolved RT absorption spectrum of 4EDOT in comparison with 4T is not due to the molecule's rigid nature as commonly assumed but due to very similar out-of-plane modes in the electronic ground and first excited states of 4EDOT, with low frequencies indicative of its rather soft nature.

Donor-functionalized polydentate pyrylium salts and phosphinines: synthesis, structural characterization, and photophysical properties.

A series of donor-functionalized pyrylium salts have been prepared by classical condensation reactions which were further converted into the corresponding thienyl- and pyridyl-substituted polydentate lambda(3)-phosphinines by reaction with P(SiMe(3))(3). Further chemical modification of these phosphorus heterocycles with Hg(OAc)(2) in the presence of methanol resulted in the formation of lambda(5)-phosphinines. The photophysical properties of a selected series of thienyl- and pyridyl-functionalized pyrylium salts, lambda(3)- and lambda(5)-phosphinines, were investigated and the results compared and supported by theoretical calculations on the DFT level. Significant fluorescence was observed for the pyrylium salts and lambda(5)-phosphinines. In contrast, the heteroaromatic substituted lambda(3)-phosphinines show very little emission which is consistent with the low oscillator strength predicted by DFT calculations for this pi-->pi* transition. Furthermore, all three classes of compounds show readily observable phosphorescence in solution, which was determined by time-gated detection at low temperature.

Phosphorescent resonant energy transfer between iridium complexes.

The mechanism for triplet energy transfer from the green-emitting fac-tris[2-(4'-tert-butylphenyl)pyridinato]iridium (Ir(tBu-ppy)3) complex to the red-emitting bis[2-(2'-benzothienyl)pyridinato-N,C3')(acetylacetonato)iridium (Ir(btp)2(acac)) phosphor has been investigated using steady-state and time-resolved photoluminescence spectroscopy. [2,2';5,'2' ']Terthiophene (3T) was also used as triplet energy acceptor to differentiate between the two common mechanisms for energy transfer, i.e., the direct exchange of electrons (Dexter transfer) or the coupling of transition dipoles (Förster transfer). Unlike Ir(btp)2(acac), 3T can only be active in Dexter energy transfer because it has a negligible ground state absorption to the 3(pi-pi*) state. The experiments demonstrate that in semidilute solution, the 3MLCT state of Ir(tBu-ppy)3 can transfer its triplet energy to the lower-lying 3(pi-pi*) states of both Ir(btp)2(acac) and 3T. For both acceptors, this transfer occurs via a diffusion-controlled reaction with a common rate constant (ken = 3.8 x 10(9) L mol-1 s-1). In a solid-state polymer matrix, the two acceptors, however, show entirely different behavior. The 3MLCT phosphorescence of Ir(tBu-ppy)3 is strongly quenched by Ir(btp)2(acac) but not by 3T. This reveals that under conditions where molecular diffusion is inhibited, triplet energy transfer only occurs via the Förster mechanism, provided that the transition dipole moments involved on energy donor and acceptor are not negligible. With the use of the Förster radius for triplet energy transfer from Ir(tBu-ppy)3 to Ir(btp)2(acac) of R0 = 3.02 nm, the experimentally observed quenching is found to agree quantitatively with a model for Förster energy transfer that assumes a random distribution of acceptors in a rigid matrix.

High-resolution electronic spectra of ethylenedioxythiophene oligomers.

The photophysical properties of a series of 3,4-ethylenedioxythiophene oligomers (OEDOT) with up to five repeat units are studied as function of conjugation length using absorption, fluorescence, phosphorescence, and triplet-triplet absorption spectroscopy at low temperature in a rigid matrix. At 80 K, a remarkably highly resolved vibrational fine structure can be observed in the all electronic spectra which reveals that the electronic structure of the oligomers strongly couples to two different vibrational modes (approximately 180 and approximately 50 meV). The energies of the 0-0 transitions in absorption, and fluorescence, phosphorescence, and triplet-triplet absorption all show a reciprocal dependence on the inverse number of repeat units. The triplet energies inferred from the phosphorescence spectra are accurately reproduced by quantum chemical DFT calculations using optimized geometries for the singlet ground state (S0) and first excited triplet state (T1). Using vibrational IR and Raman spectroscopy and quantum chemical DFT calculations for the normal modes in the ground state, we have been able to assign the vibrations that couple to the electronic structure to fully symmetric normal modes. The high-energy mode is associated with the well-known carbon-carbon bond stretch vibration, and the low-energy mode involves a deformation of the bond angles within the thiophene rings and a change of C-S bond lengths. Experimentally obtained Huang-Rhys parameters and theoretical normal mode deformations are used to analyze the geometry changes between T1 and S0 and to semiexperimentally predict the geometry in the S1 state for 2EDOT.

High anisotropy of the field-effect transistor mobility in magnetically aligned discotic liquid-crystalline semiconductors.

A magnetic field has been utilized for producing highly oriented films of a substituted hexabenzocoronene (HBC). Optical microscopy studies revealed large area HBC monodomains that covered the entire film, while wide-angle X-ray measurements showed that the HBC molecules are aligned with their planes along the applied field. On the basis of this method, solution-processed field-effect transistors (FET) have been constructed with charge carrier mobilities of up to 10(-3) cm2/V.s, which are significantly enhanced with respect to the unaligned material. Exceptionally high mobility anisotropies of 25-75 for current flow parallel and perpendicular to the alignment direction have been measured as a function of the channel length. Atomic force microscopy performed on the FET structures reveals fibril superstructures that are oriented perpendicularly to the magnetic field direction, consisting of molecular columns with a slippage angle of 40 degrees between the molecules. For channel lengths larger than 2.5 mum, the fibrils are smaller than the electrode spacing, which adversely affects the device performance.

Phosphorescence and triplet state energies of oligothiophenes.

The phosphorescence spectra of a series of small oligothiophenes (nT, n = 1-3) incorporating a variety of substituents, end cappers, and functional groups have been recorded for the first time using gated detection in combination with nanosecond excitation in frozen solution at 80 K. The vibrationally resolved emission spectra provide accurate estimates of the T(1) and S(1) levels, and the singlet-triplet energy gap. Theoretical quantum chemical calculations performed at the DFT (B3LYP/6-31G*) level reproduce all experimental trends accurately and provide quantitative description of the S(0)-T(1) energy difference. The geometry relaxation in the excited state shows that the "natural" size of the triplet exciton is about 3-4 thiophene units.