Probing DNA–peptide interaction forces at the single-molecule level

Molecular Recognition of Proteins through Quantitative Force Maps at Single Molecule Level

Intermittent jumping force is an operational atomic-force microscopy mode that produces simultaneous topography and tip-sample maximum-adhesion images based on force spectroscopy. In this work, the operation conditions have been implemented scanning in a repulsive regime and applying very low forces, thus avoiding unspecific tip-sample forces. Remarkably, adhesion images give only specific rupture events, becoming qualitative and quantitative molecular recognition maps obtained at reasonably fast rates, which is a great advantage compared to the force–volume modes. This procedure has been used to go further in discriminating between two similar protein molecules, avidin and streptavidin, in hybrid samples. The adhesion maps generated scanning with biotinylated probes showed features identified as avidin molecules, in the range of 40–80 pN; meanwhile, streptavidin molecules rendered 120–170 pN at the selected working conditions. The gathered results evidence that repulsive jumping force mode applying very small forces allows the identification of biomolecules through the specific rupture forces of the complexes and could serve to identify receptors on membranes or samples or be applied to design ultrasensitive detection technologies.

Microstructure arrays of DNA using topographic control

DNA is a common biomaterial in nature as well as a good building block for producing useful structures, due to its fine feature size and liquid crystalline phase. Here, we demonstrate that a combination of shear-induced flow and microposts can be used to create various kinds of interesting microstructure DNA arrays. Our facile method provides a platform for forming multi-scale hierarchical orientations of soft- and biomaterials, using a process of simple shearing and controlled evaporation on a patterned substrate. This approach enables potential patterning applications using DNA or other anisotropic biomaterials based on their unique structural characteristics.

Quantitative Evaluation of Viral Protein Binding to Phosphoinositide Receptors and Pharmacological Inhibition

There is significant interest in developing analytical methods to characterize molecular recognition events between proteins and phosphoinositides, which are a medically important class of carbohydrate-functionalized lipids. Within this scope, one area of high priority involves quantitatively evaluating drug candidates that pharmacologically inhibit protein-phosphoinositide interactions. As full-length proteins are often difficult to produce, establishing methods to study these interactions with shorter, bioactive peptides would be advantageous. Herein, we report an atomic force microscopy (AFM)-based force spectroscopic approach to detect the specific interaction between an amphipathic, α-helical (AH) peptide derived from the hepatitis C virus NS5A protein and its biological target, the phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P₂] phosphoinositide receptor. After optimization of the peptide tethering strategy and measurement parameters, the binding specificity of AH peptide for PI(4,5)P₂ receptors was comparatively evaluated across a panel of phosphoinositides and the influence of ionic strength on AH-PI(4,5)P₂ binding strength was tested. Importantly, these capabilities were translated into the development of a novel experimental methodology to determine the inhibitory activity of a small-molecule drug candidate acting against the AH-PI(4,5)P₂ interaction, and extracted kinetic parameters agree well with literature values obtained by conventional biochemical methods. Taken together, our findings provide a nanomechanical basis for explaining the high binding specificity of the NS5A AH to PI(4,5)P₂ receptors, in turn establishing an analytical framework to study phosphoinositide-binding viral peptides and proteins as well as a broadly applicable approach to evaluate candidate inhibitors of protein-phosphoinositide interactions.

Control of Periodic Zigzag Structures of DNA by a Simple Shearing Method

A periodic zigzag structure of DNA material is successfully fabricated by a simple shearing method. The periodicity of the pattern can be finely controlled by combining the mechanical shearing method with topographic patterns of microchannels. The resultant zigzag patterns can be used as a template to control the alignment of rod-like liquid crystals due to its highly regular periodicity.

AFM-based force spectroscopy for bioimaging and biosensing

AFM-based force spectroscopy shows wide bio-related applications especially for bioimaging and biosensing.

Single-Molecule Force Spectroscopy of an Artificial DNA Duplex Comprising a Silver(I)-Mediated Base Pair

Single-molecule force spectroscopy measurements of a DNA duplex comprising an artificial metal-mediated base pair are reported. The measurements reveal that DNA duplexes comprising one central imidazole:imidazole mispair rupture at lower forces than a related duplex with canonical base pairs only. In contrast, DNA duplexes with one central imidazole-Ag(+)-imidazole base pair (formed by the addition of Ag(+) to the aforementioned duplex with the mispair) rupture at higher forces. These measurements indicate for the first time that the increase in thermal stability of a nucleic acid duplex that is observed upon the formation of a metal-mediated base pair is accompanied by a concomitant mechanical stabilization. In fact, the mechanical stabilization even exceeds the thermal one. This result indicates that nucleic acids with metal-mediated base pairs should be ideal building blocks for rigid functionalized DNA nano-objects.

Spatial recognition and mapping of proteins using DNA aptamers

Atomic force microscopy-based adhesion force measurements have emerged as a powerful tool for the biophysical analyses of biological systems. Such measurements can now be extended to detection and mapping of biomolecules on surfaces via integrated imaging and force spectroscopy techniques. Critical to these experiments is the choice of the biomolecular recognition probe. In this study, we demonstrate how oligonucleotide aptamers can be used as versatile probes to simultaneously image and spatially locate targets on surfaces. We focus on two structurally distinct proteins relevant to the clotting cascade - human α-thrombin and vascular endothelial growth factor. Via AFM-recognition mapping using specific DNA aptamers on a commercially available instrument, we show a clear consistency between height and force measurements obtained simultaneously. Importantly, we are able to observe changes in binding due to changes in the external microenvironment, which demonstrate the ability to study fluctuating biological systems in real time. The aptamer specificity and the ability to distinguish their targets are shown through positive and negative controls. It is therefore possible to generate high resolution maps to spatially and temporally identify proteins at the molecular level on complex surfaces.

Surfactant-free nanoparticle–DNA complexes with ultrahigh stability against salt for environmental and biological sensing

A AuNP–DNA complex highly stable in extremely high ionic strength media, such as seawater, was obtained by inserting a few thymine bases into the DNA strands.

Direct force measurement of single DNA-peptide interactions using atomic force microscopy

The selective interactions between DNA and miniature (39 residues) engineered peptide were directly measured at the single-molecule level by using atomic force microscopy. This peptide (p007) contains an α-helical recognition site similar to leucine zipper GCN4 and specifically recognizes the ATGAC sequence in the DNA with nanomolar affinity. The average rupture force was 42.1 pN, which is similar to the unbinding forces of the digoxigenin-antidigoxigenin complex, one of the strongest interactions in biological systems. The single linear fit of the rupture forces versus the logarithm of pulling rates showed a single energy barrier with a transition state located at 0.74 nm from the bound state. The smaller koff compared with that of other similar systems was presumably due to the increased stability of the helical structure by putative folding residues in p007. This strong sequence-specific DNA-peptide interaction has a potential to be utilized to prepare well-defined mechanically stable DNA-protein hybrid nanostructures.

Analysis of DNA interactions using single-molecule force spectroscopy

Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

Nanoimaging for protein misfolding diseases

Misfolding and aggregation of proteins are widespread phenomena leading to the development of numerous neurodegenerative disorders such as Parkinson's, Alzheimer's, and Huntington's diseases. Each of these diseases is linked to structural misfolding and aggregation of a particular protein. The aggregated forms of the protein induce the development of a particular disease at all levels, leading to neuronal dysfunction and loss. Because protein refolding is frequently accompanied by transient association of partially folded intermediates, the propensity to aggregate is considered a general characteristic of the majority of proteins. X-ray crystallography, nuclear magnetic resonance, electron microscopy, and atomic force microscopy have provided important information on the structure of aggregates. However, fundamental questions, such as why the misfolded conformation of the protein is formed, and why this state is important for self-assembly, remain unanswered. Although it is well known that the same protein under pathological conditions can lead to the formation of aggregates with diverse biological consequences, the conditions leading to misfolding and the formation of the disease prone complexes are unclear, complicating any development of efficient prevention of the diseases. Misfolded states exist transiently, so answering these questions requires the use of novel approaches and methods. Progress has been made during the past few years, when recently developed ensemble methods and single-molecule biophysics techniques were applied to the problem of the protein misfolding. In this review, the impacts of these studies on the understanding of the mechanisms of the protein self-assembly into aggregates and on the development of treatments of the diseases are discussed.

Single-molecule experiments to elucidate the minimal requirement for DNA recognition by transcription factor epitopes

Interactions between proteins and DNA are essential for the regulation of cellular processes in all living organisms. In this context, it is of special interest to investigate the sequence-specific molecular recognition between transcription factors and their cognate DNA sequences. As a model system, peptide and protein epitopes of the DNA-binding domain (DBD) of the transcription factor PhoB from Escherichia coli are analyzed with respect to DNA binding at the single-molecule level. Peptides representing the amphiphilic recognition helix of the PhoB DBD (amino acids 190-209) are chemically synthesized and C-terminally modified with a linker for atomic force microscopy-dynamic force spectroscopy experiments (AFM-DFS). For comparison, the entire PhoB DBD is overexpressed in E. coli and purified using an intein-mediated protein purification method. To facilitate immobilization for AFM-DFS experiments, an additional cysteine residue is ligated to the protein. Quantitative AFM-DFS analysis proves the specificity of the interaction and yields force-related properties and kinetic data, such as thermal dissociation rate constants. An alanine scan for strategic residues in both peptide and protein sequences is performed to reveal the contributions of single amino acid residues to the molecular-recognition process. Additionally, DNA binding is substantiated by electrophoretic mobility-shift experiments. Structural differences of the peptides, proteins, and DNA upon complex formation are analyzed by circular dichroism spectroscopy. This combination of techniques eventually provides a concise picture of the contribution of epitopes or single amino acids in PhoB to DNA binding.

Past, present and future of atomic force microscopy in life sciences and medicine

To introduce this special issue of the Journal of Molecular Recognition dedicated to the applications of atomic force microscopy (AFM) in life sciences, this paper presents a short summary of the history of AFM in biology. Based on contributions from the first international conference of AFM in biological sciences and medicine (AFM BioMed Barcelona, 19-21 April 2007), we present and discuss recent progress made using AFM for studying cells and cellular interactions, probing single molecules, imaging biosurfaces at high resolution and investigating model membranes and their interactions. Future prospects in these different fields are also highlighted.

Scanning probe microscopy in the field of drug delivery

The scanning probe microscopes (SPMs) are a group of powerful surface sensitive instruments which when used complimentarily with traditional analytical techniques can provide invaluable, definitive information aiding our understanding and development of drug delivery systems. In this review, the main use of the SPMs (particularly the atomic force microscopy (AFM)) and their successes in forwarding drug delivery are highlighted and categorised into two interlinked sections namely, preformulation and formulation. SPM in preformulation concentrates on applications in pharmaceutical processes including, crystal morphology and modification, discriminating polymorphs, drug dissolution and release, solid state stability and interaction. The ability of the AFM to detect forces between different surfaces and at the same time to operate in liquids or controlled humidity and defined temperatures has also been particularly useful in the study of drug delivery. In formulation, the use of SPMs in different drug delivery systems is discussed in light of different host entry routes.