Here we review the applications of atomic force microscopy to the study of samples of biological origin. Emphasis is given to provide the reader with information on the broad range of different biophysical applications that, to date, such a technique can deal with. After recalling briefly the operating principles of an atomic force microscope, the broad field of bio-imaging applications is faced (DNA, DNA-protein interaction, proteins, lipid membranes, cells); thereafter, the use of the atomic force microscope to measure forces is introduced and force mapping on living cells is discussed. This section is followed by the description of the use of force curves in assessing single-molecule inter-and intramolecular interactions. A paragraph on the perspectives of the technique in biophysical applications concludes the paper. We hope that this review can help the reader in appreciating how atomic force microscopy contributes to the current explosive growth of nanobiosciences, where biology, chemistry and physics merge.

Self-assembly of proteins, peptides, DNA, and other biomolecules to semiconductor quantum dots (QD) is an attractive bioconjugation route that can circumvent many of the problems associated with covalent chemistry and subsequent purification. Polyhistidine sequences have been shown to facilitate self-assembly of proteins and peptides to ZnS-overcoated CdSe QDs via complexation to unoccupied coordination metal sites on the nanocrystal surface. We describe the synthesis and characterization of a thiol-reactive hexahistidine peptidic linker that can be chemically attached to thiolated-DNA oligomers and mediate their self-assembly to CdSe-ZnS core-shell QDs. The self-assembly of hexahistidine-appended DNA to QDs is probed with gel electrophoresis and fluorescence resonance energy transfer techniques, and the results confirm high-affinity conjugate formation with control over the average molar ratio of DNA assembled per QD. To demonstrate the potential of this reactive peptide linker strategy, a prototype QD-DNA-dye molecular beacon is self-assembled and tested against both specific and nonspecific target DNAs. This conjugation route is potentially versatile, as altering the reactivity of the peptide linker may allow targeting of different functional groups such as amines and facilitate self-assembly of other nanoparticle-biomolecule structures.

This review is intended to account for the experimental and theoretical achievements obtained in a period of about 15 years on the investigation of the electron transport through single redox metalloproteins by scanning probe techniques. A highly focussed research effort has been deployed by the scientists active in this particular field towards measuring and interpreting electronic current signals flowing via blue copper, redox metalloproteins (e.g. azurin). The field has taken a remarkable advantage of the use of electrochemically assisted scanning tunnelling microscope (EC-STM) which has allowed to probe single molecule signals under full control of all the potential values involved in the experiments. This experimental activity has both triggered more comprehensive theoretical interpretations and has been, in its turn, stimulated by theoreticians to test always new predictions. The authors hope to have succeeded in providing the reader with a valuable appraisal of this fascinating field.

Supported lipid bilayers composed of 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) and 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) were assembled by the vesicle fusion technique on mica and studied by temperature-controlled atomic force microscopy. The role of different physical parameters on the main phase transition was elucidated. Both mixed (POPE/POPG 3:1) and pure POPE bilayers were studied. By increasing the ionic strength of the solution and the incubation temperature, a shift from a decoupled phase transition of the two leaflets, to a coupled transition, with domains in register, was obtained. The observed behavior points to a modulation of the substrate/bilayer and interleaflet coupling induced by the environment and preparation conditions of supported lipid bilayers. The results are discussed in view of the role of different interactions in the system. The influence of the substrate on the lipid bilayers, in terms of interleaflet coupling, can also help us in understanding the possible effect that submembrane elements like the cytoskeleton might have on the structure and dynamics of biomembranes.

We are presenting a photography-derived methodology to achieve the photoreduction of Ag+-DNA complexes. lambda-Phage DNA was first loaded with silver ions, then irradiated with UV light at 254 nm. The DNA bases acted as light sensitizers, promoting the in situ reduction of Ag+ and the formation of metallic silver clusters. Three different approaches will illustrate this procedure, and silver nanoparticle chains will be grown along a DNA template in a rapid and specific way.

Metalloproteins are redox molecules naturally shuttling electrons with high efficiency between molecular partners. As such, they are candidates of choice for bioelectronics. In this work, we have used bacterial metalloprotein azurin, hosted in a nanometer gap between two electrically biased gold electrodes, to demonstrate an electrochemically gated single-molecule transistor operating in an aqueous environment. Gold-chemisorbed azurin shows peaks in tunneling current upon changing electrode potential and a related variation in tunneling barrier transparency which can be exploited to switch an electron current through it. These results suggest the wet approach to molecular electronics as a viable method for exploiting electron transfer of highly specialized biomolecules.

The usual biophysical approach to the study of biological membranes is that of turning to model systems. From these models, general physical principles ruling the lateral membrane structure can be obtained. A promising model system is the supported lipid bilayer (SLB) which could foresee the simultaneous investigation of the structure and physical properties of lipid bilayers reconstituted with membrane proteins. A complete exploitation of the model system to retrieve biologically relevant information requires an in-depth knowledge of the possible effect that experimental parameters could have on the behavior of the SLB. Here we used atomic force microscopy (AFM) to study the effect of different types of substrates on the behavior of SLBs as far as their main phase transition is concerned. We found that different substrates (mica and silicon oxide) can affect in dissimilar ways the interleaflet coupling of the bilayer, which might represent a sort of lipid signaling allowing communication between receptors on the extracellular leaflet and cytoplasmic components. By decreasing the interaction between the SLB and the substrate the interleaflet coupling is preserved independently of the bilayer preparation strategy. Moreover, we investigated by time-lapse AFM an isothermal phase transition induced by a pH change on a SLB. We established that the presence of a pH gradient across the bilayer can weaken the strength of the interleaflet coupling which is present in symmetrical pH conditions.

We review the capabilities of Atomic Force Microscopy (AFM) in the study of phase transitions in Supported Lipid Bilayers (SLBs). AFM represents a powerful technique to cover the resolution range not available to fluorescence imaging techniques and where spectroscopic data suggest what the relevant lateral scale for domain formation might be. Phase transitions of lipid bilayers involve the formation of domains characterized by different heights with respect to the surrounding phase and are therefore easily identified by AFM in liquid solution once the bilayer is confined to a flat surface. Even if not endowed with high time resolution, AFM allows light to be shed on some aspects related to lipid phase transitions in the case of both a single lipid component and lipid mixtures containing sterols also. We discuss here the obtained results in light of the peculiarities of supported lipid bilayer model systems.