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.

RNA DNA discrimination by the antitermination protein NusB.

The regulation of ribosomal RNA biosynthesis in Escherichia coli by antitermination requires binding of NusB protein to a dodecamer sequence designated boxA on the nascent RNA. The affinity of NusB protein for boxA RNA exceeds that for the homologous DNA segment by more than three orders of magnitude as shown by surface plasmon resonance measurements. DNA RNA discrimination by NusB protein was shown to involve methyl groups (i.e. discrimination of uracil versus thymine) and 2' hydroxyl groups (i.e. discrimination of ribose versus deoxyribose side-chains) in the RNA motif. Ligand perturbation experiments monitored by 1H15N correlation NMR experiments identified amide NH groups whose chemical shifts are affected selectively by ribose/deoxyribose exchange in the 5' and the central part of the dodecameric boxA motif respectively. The impact of structural modification of the boxA motif on the affinity for NusB protein as observed by 1H15N heterocorrelation was analysed by a generic algorithm.

Transcriptional regulation by antitermination. Interaction of RNA with NusB protein and NusB/NusE protein complex of Escherichia coli.

A recombinant heterodimeric NusB/NusE protein complex of Escherichia coli was expressed under the control of a synthetic mini operon. Surface plasmon resonance measurements showed that the heterodimer complex has substantially higher affinity for the boxA RNA sequence motif of the ribosomal RNA (rrn) operons of E.coli as compared to monomeric NusB protein. Single base exchanges in boxA RNA reduced the affinity of the protein complex up to 15-fold. The impact of base exchanges in the boxA RNA on the interaction with NusB protein was studied by (1)H,(15)N heterocorrelation NMR spectroscopy. Spectra obtained with modified RNA sequences were analysed by a novel generic algorithm. Replacement of bases in the terminal segments of the boxA RNA motif caused minor chemical shift changes as compared to base exchanges in the central part of the dodecameric boxA motif.

Crystal structures of the antitermination factor NusB from Thermotoga maritima and implications for RNA binding.

NusB is a prokaryotic transcription factor involved in antitermination processes, during which it interacts with the boxA portion of the mRNA nut site. Previous studies have shown that NusB exhibits an all-helical fold, and that the protein from Escherichia coli forms monomers, while Mycobacterium tuberculosis NusB is a dimer. The functional significance of NusB dimerization is unknown. We have determined five crystal structures of NusB from Thermotoga maritima. In three crystal forms the protein appeared monomeric, whereas the two other crystal forms contained assemblies, which resembled the M. tuberculosis dimers. In solution, T. maritima NusB could be cross-linked as dimers, but it migrated as a monomer in gel-filtration analyses, suggesting a monomer/dimer equilibrium with a preference for the monomer. Binding to boxA-like RNA sequences could be detected by gel-shift analyses and UV-induced cross-linking. An N-terminal arginine-rich sequence is a probable RNA binding site of the protein, exhibiting aromatic residues as potential stacking partners for the RNA bases. Anions located in various structures support the assignment of this RNA binding site. The proposed RNA binding region is hidden in the subunit interface of dimeric NusB proteins, such as NusB from M. tuberculosis, suggesting that such dimers have to undergo a considerable conformational change or dissociate for engagement with RNA. Therefore, in certain organisms, dimerization may be employed to package NusB in an inactive form until recruitment into antitermination complexes.

Oligolayer-coated nanoparticles: impact of surface topography at the nanobio interface.

Layer-by-layer coating of nanoparticles with a layer number in the single-digit range has gained increasing attention in the field of nanomedicinal research. However, the impact of using various polyelectrolytes on oligolayer formation and, more importantly, their influence on the interaction with the biological system has not often been considered in the past. Hence, we investigated the polyelectrolyte deposition profiles and resulting surface topographies of up to three polyelectrolyte layers on a flat gold sensor surface using three different polycations, namely, poly(ethylene imine) (PEI), poly(allylamine hydrochloride) (PAH), and poly(diallylammonium chloride) (PD), each in combination with poly(styrenesulfonate) (PSS). Surface plasmon resonance spectroscopy and atomic force microscopy revealed that the PEI/PSS pair in particular showed a so-called overshoot phenomenon, which is associated with partial polyelectrolyte desorption from the surface. This is also reflected by a significant increase in the surface roughness. Then, after having transferred the oligolayer assembly onto nanoparticles of ∼32 nm, we realized that quite similar surface topographies must have emerged on a curved gold surface. A major finding was that the extent of surface roughness contributes significantly to the fashion by which the oligolayer-coated nanoparticles interact with serum proteins and associate with cells. For example, for the PEI/PSS system, both the surface roughness and protein adsorption increased by a factor of ∼12 from the second to third coating layer and, at the same time, the cell association massively decreased to only one-third. Our study shows that surface roughness, along with other particle properties such as size, shape, zeta potential, and hydrophobicity, is another decisive factor for nanoparticles in a biological context, which has indeed been discussed previously but has not to date been investigated for oligolayers.

Studying cell-surface interactions in vitro: a survey of experimental approaches and techniques.

A better understanding of the interactions of animal (or human) cells with in vitro surfaces is the key to the successful development, improvement and optimization of biomaterials for biomedical or biotechnological purposes. State-of-the-art experimental approaches and techniques are a prerequisite for further and deeper insights into the mechanisms and processes involved in cell-surface adhesion. This chapter provides a brief but not complete survey of optical, mechanical, electrochemical and acoustic devices that are currently used to study the structural and functional properties of the cell-surface junction. Each technique is introduced with respect to the underlying principles before example data are discussed. At the end of the chapter all techniques are compared in terms of their strengths, limitations and technical requirements.

Imaging of G protein-coupled receptors in solid-supported planar lipid membranes.

This contribution summarizes first some of our efforts in imaging G-protein-coupled receptor (GPCR) functional inserted into planar tethered lipid bilayer membranes (tBLMs) as a novel platform for biophysical studies. The authors introduced recently a novel approach for the functional incorporation of membrane proteins, i.e., by their cell-free expression and in vitro reconstitution in the presence of tBLMs. By the combination of the corresponding coding DNA with the protein synthesis machinery of a cell-extract (in vitro transcription and translation), the authors observe spontaneous and vectorial insertions of an interesting example of the GPCR family into a tethered bimolecular lipid membrane: the olfactory receptor OR5. After synthesis, imaging of the surface area is performed and the resulting signals are analyzed in order to resolve quantity and lateral mobilities. Ligand-independent aggregation behavior of the GPCRs and quantitative analysis of the fluorescent signals are presented in this work.

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.

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.

Detection of point mutation and insertion mutations in DNA using a quartz crystal microbalance and MutS, a mismatch binding protein.

MutS protein is a mismatch binding protein that recognizes mispaired and unpaired base(s) in DNA. In this study, we incorporate the MutS protein-based mutation recognition into quartz crystal microbalance (QCM) measurements for DNA single-base substitution mutation and 1-4 base(s) insertion (or deletion) mutation detection. The method involves the immobilization of single-stranded probe DNA on a QCM surface, the hybridization of target DNA to form homoduplex or heteroduplex DNA, and finally the application of MutS protein for the mutation recognition. By measuring the MutS binding signal, DNA containing a T:G mismatch or unpaired base(s) is(are) discriminated against perfectly matched DNA at target concentrations ranging from 1nM to 5 microM. Furthermore, the QCM damping behavior upon MutS-DNA complex formation is studied using a Network Analyzer. The measured motional resistance changes per coupled MutS unit mass (deltaR/deltaf) are found to be indicative of the viscoelastic or structural properties of the bound protein, corresponding to different binding mechanisms. In addition, the deltaR/deltaf values vary remarkably when the MutS protein binds at different distances away from the QCM surface. Thus, these values can be used as a "fingerprint" for MutS mismatch recognition and also used to quantitatively locate the mutation site.