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Biomedical subjects

Wolfgang Knoll

Publications and source records attributed to Wolfgang Knoll.

At least 19 recordsLinked to original sources
PubMed2005

Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers.

Surface plasmon field-enhanced fluorescence spectroscopy was employed to extensively investigate the hybridization behaviors of polymerase chain reaction (PCR) amplicons on a peptide nucleic acid (PNA) or DNA probe layer that was previously attached on a streptavidin-modified gold surface via biotin/streptavidin interaction. Despite the neutral backbone of PNA, the hybridization reactions were strongly influenced by the variation of ionic strength. The association rates exhibited a monotonic decrease with ionic strength increase and the maximum hybridization signal was achieved at an intermediate sodium concentration (approximately 100 mM). These effects were mainly ascribed to the electrostatic cross talk among the hybridized DNA molecules and the secondary structure of PCR amplicons. For the negatively charged DNA probes, the hybridization reaction was subjected additionally to the DNA/DNA electrostatic barrier, particularly in lower ionic strength range (e.g., 10 approximately 150 mM Na(+)). The electrostatic cross talk was shown to be largely reduced if the PNA probe layer was sufficiently diluted by following a strategic templated immobilization method. As a consequence, a pseudo-first-order kinetic model was applicable to describe the hybridization kinetics, and affinity constants were derived for evaluating the influence of single nucleotide polymorphisms (SNPs).

Biophysics↗
PubMed2005

Surface plasmon resonance spectroscopy and quartz crystal microbalance study of streptavidin film structure effects on biotinylated DNA assembly and target DNA hybridization.

Surface plasmon resonance (SPR) spectroscopy is employed for the study of biotinylated DNA assembly on streptavidin modified gold surfaces for target DNA hybridization. Two immobilization strategies are involved for constructing streptavidin films, namely, (1) physical adsorption on biotin-containing thiol treated surfaces through biotin-streptavidin links and (2) covalent attachment to 11-mercaptoundecanoic acid (MUA) treated surfaces through amine coupling. To understand the structural properties of the streptavidin films, a quartz crystal microbalance with energy dissipation monitoring (QCM-D) is used to monitor the streptavidin immobilization procedures. The simultaneously measured frequency (Deltaf) and dissipation factor (DeltaD) changes, together with the SPR angle shifts (Deltatheta), suggest that the streptavidin film assembled on the biotin-containing surface is highly rigid with a well-ordered structure while the streptavidin film formed through amine coupling is highly dissipative and less structured. The subsequent biotinylated DNA (biotin-DNA) assembly and target hybridization results show that the streptavidin film structure has distinct effects on the biotin-DNA binding amount. On the streptavidin matrix, not only the probe DNA density but also the strand orientation mediated by the streptavidin films has distinct effects on hybridization efficiency. Particularly, the molecularly ordered streptavidin films formed on the biotin-containing surfaces ensure a well-ordered DNA assembly, which in turn allows for a higher efficiency in target DNA capture and for a higher sensitivity in the hybridization analysis when compared to the biotin-DNA assembled on the less structured streptavidin films formed through amine coupling.

Base Sequence↗
PubMed2005

Surface plasmon resonance spectroscopy and quartz crystal microbalance study of MutS binding with single thymine-guanine mismatched DNA.

MutS is a DNA mismatch binding protein that recognizes heteroduplex DNA containing mispaired or unpaired bases. In this study, we employ a quartz crystal microbalance (QCM) and a surface plasmon resonance (SPR) device for the study of MutS binding with DNA containing a single Thymine-Guanine (T-G) mismatch at different sites. Multi-step surface binding reactions are involved in the study, including probe DNA immobilization on the sensor surface through biotin-streptavidin-biotin bridge chemistry, target DNA hybridization to form T-G heteroduplexes, and MutS recognition of the mutation sites. The QCM frequency (d f) and motional resistance (d R, an impedance parameter reflective of QCM damping), as well as the SPR angle shift (d q ) are recorded for the binding reactions. The combined SPR and QCM data collection and analysis allow for an assessment of not only the amount of bound biopolymer but provide also information on also the structural properties of the streptavidin, DNA and MutS/DNA complexes. The affinity of the MutS/T-G heteroduplex assembly is determined by both the QCM and SPR methods through titration of the surface bound DNA with increasing MutS concentration. It is found that if the T-G mismatch is in the center of the DNA fragment, the MutS/DNA complex is more stable than if the mismatch is located near the end of the fragment.

Base Pair Mismatch↗
PubMed2005

Synaptic plasticity in micropatterned neuronal networks.

Synaptic plasticity is thought to be of central importance for information processing by the nervous system. Additionally, specific neuronal connectivity patterns in the brain are implicated to play a role in the perception, processing and storage of incoming signals. Experimental control over connectivity within functional neuronal networks is therefore a promising approach in research on signal transduction and processing by the nervous system. A cell culture system is presented that allows experimental determination of neuronal connectivity patterns in an in vitro network. Rat embryonic cortical neurons were grown on patterns of extracellular matrix proteins applied to polystyrene substrates by microcontact printing. Cells comply well with the pattern and form synaptic connections along the experimentally defined pathways. Chemical synapses identified by double patch-clamp measurement showed paired pulse depression as well as frequency-dependent depression in response to trains of stimuli. This type of short-term plasticity has similarly been reported by others in brain slices. Thus, the system reproduces features central for neuronal information processing while the architecture of the network is experimentally manipulable. The ability to tailor the geometry of functional neuronal networks offers a valuable tool both for fundamental questions in neuroscientific research and a wide range of biotechnological applications.

Action Potentials↗
PubMed2004

Oriented attachment and membrane reconstitution of His-tagged cytochrome c oxidase to a gold electrode: in situ monitoring by surface-enhanced infrared absorption spectroscopy.

A novel concept is introduced for the oriented incorporation of membrane proteins into solid supported lipid bilayers. Recombinant cytochrome c oxidase solubilized in detergent was immobilized on a chemically modified gold surface via the affinity of its histidine-tag to a nickel-chelating nitrilo-triacetic acid (NTA) surface. The oriented protein monolayer was reconstituted into the lipid environment by detergent substitution. The individual steps of the surface modification, including (1) chemical modification of the gold support, (2) adsorption of the protein, and (3) reconstitution of the lipid bilayer, were followed in situ by means of surface-enhanced infrared absorption spectroscopy (SEIRAS) and accompanied by normal-mode analysis. The high surface sensitivity of SEIRAS allows for the identification of each chemical reaction process within the monolayer at the molecular level. Finally, full functionality of the surface-tethered cytochrome c oxidase was demonstrated by cyclic voltammetry after binding of the natural electron donor cytochrome c.

Electrochemistry↗
PubMed2004

Surface plasmon field-enhanced fluorescence spectroscopy in PCR product analysis by peptide nucleic acid probes.

Surface plasmon field-enhanced fluorescence spectroscopy (SPFS) was recently developed for PCR product analysis, which allowed for real-time monitoring of hybridization processes and for the detection of trace amounts of PCR products, with a detection limit of 100 fmol on the peptide nucleic acid (PNA) probe surface, and 500 fmol on the DNA probe surface. By selectively labeling the strands of PCR-amplified DNA, it was shown that the heat denaturation process in combination with the application of low-salt condition substantially reduced the interference from the antisense strands and thus simplified the surface hybridization. Furthermore, SPFS was demonstrated to be capable of quantitatively discriminating the difference induced by single nucleotide substitution, even within one minute of contact time.

Antisense Elements (Genetics)↗
PubMed2004

Assembly modulates dissociation: electrokinetic experiments reveal peculiarities of the charge formation at monolayer films.

Self-assembled monomolecular films of alkanethiols chemisorbed on gold were used as a two-dimensional model system to study the effects of spatial confinement of surface functional groups on their acid-base behaviour; reduction of the surface charge density by mixed assemblies revealed an increase of the acidity of carboxy groups; surfaces with low amounts of charged groups show the interplay of dissociation of functional groups and preferential adsorption of ions in terms of surface charge formation.

Journal Article↗
PubMed2004

Surface plasmon fluorescence immunoassay of free prostate-specific antigen in human plasma at the femtomolar level.

This study describes the development of a surface plasmon fluorescence spectroscopy (SPFS)-based sandwich immunoassay, for the detection of free prostate-specific antigen (f-PSA). The commercial CM5 chip (Biacore) was integrated into the SPFS-based assay making use of its three-dimensionally extended dextran architecture, which offers a large protein retention capacity and alleviates the metal-induced fluorescence quenching. The performance of the f-PSA assay was investigated in buffer and in human plasma, respectively. In the human plasma, the limit of detection of f-PSA was estimated to be approximately 80 fM for 40 min of contact time, which adequately meets clinical requirements.

Humans↗
PubMed2004

Incorporation of integrins into artificial planar lipid membranes: characterization by plasmon-enhanced fluorescence spectroscopy.

An optimized peptide-tethered artificial lipid membrane system has been developed. Integrins (cell adhesion receptors) were functionally incorporated into this membrane model and integrin-ligand interactions were analyzed by surface plasmon-enhanced fluorescence spectroscopy (SPFS). The transmembrane receptors alpha(v)beta(3) and alpha(1)beta(1) of the integrin superfamily were incorporated into a lipid-functionalized peptide layer by vesicle spreading. Consecutive layer formations were monitored by surface plasmon spectroscopy (SPS). Orientation and accessibility of the membrane receptor alpha(v)beta(3) was reliably assessed by specific and reproducible binding of selective antibodies. Moreover, full retention of the functional properties of this receptor was verified by specific and reversible binding of natural ligands. Functional integrity of incorporated integrins was maintained over a time period of 72 h. The integrin/extracellular matrix ligand complexes, whose formations are known to depend on the presence of divalent cations, were lost upon addition of ethylenediaminetetraacetate. Therefore, regeneration of the surface for further binding experiments with minimized unspecific ligand association was possible. These results demonstrate that integrins can be functionally incorporated into peptide-tethered artificial membranes. In combination with the SPS/SPFS method, this artificial membrane system provides a reliable experimental platform for investigation of isolated membrane proteins under experimental conditions resembling those of their native environment.

Antibodies↗
PubMed2004

Multiplexed hybridization detection of quantum dot-conjugated DNA sequences using surface plasmon enhanced fluorescence microscopy and spectrometry.

In this study, the general suitability of quantum dot (QD)-DNA conjugates for the surface plasmon enhanced fluorescence spectroscopy technique is demonstrated. Furthermore, the QD-DNA system is transferred to the platform of surface plasmon enhanced fluorescence microscopy. Using this technique together with a microarray format, in which the sensor-bound single-stranded catcher probes are organized in individual surface spots, results in a simultaneous qualitative analysis of QD-conjugated analyte DNA strands as multicolor images. A clear decomposition of different QD(x)()-DNA(y)() mixtures can be achieved for sequential, as well as mixture injections. Besides this, the study describes the successful approach of measuring spectrally resolved surface plasmon enhanced fluorescence signals derived from catcher probe hybridized QD-DNA conjugates.

Base Sequence↗
PubMed2004

The protein-tethered lipid bilayer: a novel mimic of the biological membrane.

A new concept of solid-supported tethered bilayer lipid membrane (tBLM) for the functional incorporation of membrane proteins is introduced. The incorporated protein itself acts as the tethering molecule resulting in a versatile system in which the protein determines the characteristics of the submembraneous space. This architecture is achieved through a metal chelating surface, to which histidine-tagged (His-tagged) membrane proteins are able to bind in a reversible manner. The tethered bilayer lipid membrane is generated by substitution of protein-bound detergent molecules with lipids using in-situ dialysis or adsorption. The system is characterized by surface plasmon resonance, quartz crystal microbalance, and electrochemical impedance spectroscopy. His-tagged cytochrome c oxidase (CcO) is used as a model protein in this study. However, the new system should be applicable to all recombinant membrane proteins bearing a terminal His-tag. In particular, combination of surface immobilization and membrane reconstitution opens new prospects for the investigation of functional membrane proteins by various surface-sensitive techniques under a defined electric field.

Biomimetics↗
PubMed2004

Concentration of dye-labeled nucleotides incorporated into DNA determined by surface plasmon resonance-surface plasmon fluorescence spectroscopy.

A method for the accurate determination of the fraction of surface-attached DNA duplexes exhibiting a single-fluorophore-labeled nucleobase is introduced. The fluorescence signals obtained from surface plasmon field-enhanced fluorescence spectroscopy along with the optical properties of the sensor architecture determined by surface plasmon resonance were employed for the calculation. A Cy5-labeled nucleotide was incorporated into DNA at a well-defined position via template-directed DNA synthesis performed by a DNA polymerase. The sample-to-sample variations associated with the optical properties of the employed metal films caused a small variation in the strength of the evanescent field. This variation was accounted for by evanescent field integration over the DNA layers. The exponential-type relationship between the fraction of DNA with Cy5-dCTP incorporation at the surface and the mole fraction of the Cy5-dCTP in solution indicates the preferential incorporation of nonlabeled nucleotides by the DNA polymerase.

Base Sequence↗
PubMed2004

Attomolar sensitivity in bioassays based on surface plasmon fluorescence spectroscopy.

With the aid of a dextran matrix, the metal-induced fluorescence loss of bound fluorophores can be greatly reduced, and the distance dependence of the fluorescence yield could be largely convoluted. This is optimized for the limit of detection assessment of surface plasmon fluorescence spectroscopy. The model system was designed as a direct assay with mouse IgG covalently immobilized to the carboxymethyl dextran matrix of a CM5 sensor chip from Biacore. Time-resolved ultratrace detection of fluorophore (Alexa-Fluor 647)-labeled rabbit anti-mouse antibody down to 500 aM (10-18 M) was accomplished, corresponding to a binding rate of approximately 10 molecules mm-2 min-1.

Animals↗
PubMed2004

Surface plasmon enhanced diffraction for label-free biosensing.

Surface plasmon enhanced evanescent field at a (noble) metal/dielectric interface can be employed to enhance the diffraction efficiency of surface grating structure composed of biomolecules. Based on a Kretschmann configuration, we realized a diffraction biosensor to monitor the dynamic interaction of biological molecules in a label-free way. It was demonstrated by the binding of an anti-biotin antibody to the biotin-functionalized region of a periodically patterned surface, which generated significant optical contrast to diffract the surface plasmon field. With the aid of the synchronic surface plasmon resonance signal, a quadratic dependence of diffraction signal on the amount of bound antibody was found, which coincides with the theoretical expectation. Time-dependent measurements were conducted to estimate the density of biotin thiols on the functional region.

Antibodies, Monoclonal↗
PubMed2004

Oligonucleotide hybridization studied by a surface plasmon diffraction sensor (SPDS).

A novel label-free biosensor concept based on surface plasmon-enhanced diffraction by micro- patterned interfaces was applied to the study of hybridization reactions of target DNA oligonucleotides (15mers and 75mers) from solution to probe DNA oligonucleotides attached via streptavidin to the sensor surface. The self-referencing and quadratic signal amplification mechanism of the sensor allowed highly sensitive detection of the hybridization process. Association and dissociation processes of DNA targets could be recorded in real time and used for the quantification of their binding affinities, which differ considerably with a single base pair mismatch. An equilibrium titration approach was also applied in order to obtain the binding affinities for 15mer targets, yielding similar affinity values. The hybridization efficiencies were found to be higher for the 15mers than for the 75mers, although the latter contained the same recognition sequences. The hybridization efficiency was shown to depend on the probe density and reached nearly 100% for the 15mer fully complementary targets at a probe density of approximately 1.2 x 10(12) molecules/cm2. Using the assay as an end-point determination method, the lowest detectable coverage of a 15mer oligonucleotide was at least approximately 1.1 x 10(11) molecules/cm2. The diffraction sensing concept offers a completely novel way to integrate a reference channel in large-scale, label-free screening applications, to improve the stability and to enhance the sensitivity of microarray read-out systems.

Base Pair Mismatch↗
PubMed2004

Impact of micropatterned surfaces on neuronal polarity.

Experimental control over cellular polarity in a neuronal network is a promising tool to study synapse formation and network behavior. We aimed to exploit a mechanism described by Stenger et al. [J. Neurosci. Methods 82 (1998) 167] to manipulate the direction of axonal versus dendritic outgrowth on a micropattern. The group had used laser ablation to create patterns of aminated silanes for cell attachment on a background of repellent fluorinated silanes. The pattern offered continuous adhesive pathways for axonal and interrupted pathways for dendritic outgrowth. By microcontact printing, we created similar patterns containing continuous and interrupted pathways consisting of extracellular matrix proteins on a background of polystyrene. Neuronal polarity was determined on the functional level through double patch clamp measurements, detecting synapses and their orientation. Although our pattern reproduced the properties that were assumed to be critical for the described effect, namely contrasting pathways of different adhesiveness, we failed to reproduce the above results. It is indicated that other qualities of alternative pathways than mere differences in adhesiveness are required to orient neuronal polarity in vitro. We suggest that the effect observed by Stenger et al. has to be attributed to less universal characteristics of the micropattern, e.g. to the specific chemical groups that were utilized.

Animals↗