Dmitry V. Klinov

True molecular resolution in tapping-mode atomic force microscopy with high-resolution probes

True molecular resolution was demonstrated in tapping-mode atomic force microscopy study of polydiacetylene crystal using carbon probes with an extremity of ∼1 nm. Images of the bc plane of the crystal, which were obtained at ambient conditions, reproduce the crystallographic molecular arrangement. The image features directly correspond to the edges of the individual side groups of the polymer chains, which form the crystal surface. In the consecutive images, the molecular-size defects have been observed on this surface as an additional proof of the true molecular resolution achieved with the probes.

Thickness and low-temperature conductivity of DNA molecules

We argue that interaction between molecules and substrate is a key parameter which determines the conducting or insulating behavior of DNA molecules. In this letter, we show that strongly deformed DNA molecules deposited on a substrate, whose thickness is less than half the native thickness of the molecule, are insulating, whereas molecules keeping their native thickness are conducting down to very low temperature with a non-ohmic behavior characteristic of a 1D conductor with repulsive electron–electron interactions.

Observation of single-stranded DNA on mica and highly oriented pyrolytic graphite by atomic force microscopy

Atomic force microscopy was used to image single‐stranded DNA (ssDNA) adsorbed on mica modified by Mg2+, by 3‐aminopropyltriethoxysilane or on modified highly oriented pyrolytic graphite (HOPG). ssDNA molecules on mica have compact structures with lumps, loops and super twisting, while on modified HOPG graphite ssDNA molecules adopt a conformation without secondary structures. We have shown that the immobilization of ssDNA under standard conditions on modified HOPG eliminates intramolecular base‐pairing, thus this method could be important for studying certain processes involving ssDNA in more details.

Feasibility study of the optical imaging of a breast cancer lesion labeled with upconversion nanoparticle biocomplexes

Abstract. Innovative luminescent nanomaterials, termed upconversion nanoparticles (UCNPs), have demonstrated considerable promise as molecular probes for high-contrast optical imaging in cells and small animals. The feasibility study of optical diagnostics in humans is reported here based on experimental and theoretical modeling of optical imaging of an UCNP-labeled breast cancer lesion. UCNPs synthesized in-house were surface-capped with an amphiphilic polymer to achieve good colloidal stability in aqueous buffer solutions. The scFv4D5 mini-antibodies were grafted onto the UCNPs via a high-affinity molecular linker barstar:barnase (Bs:Bn) to allow their specific binding to the human epidermal growth factor receptor HER2/neu, which is overexpressed in human breast adenocarcinoma cells SK-BR-3. UCNP-Bs:Bn-scFv4D5 biocomplexes exhibited high-specific immobilization on the SK-BR-3 cells with the optical contrast as high as 10:1 benchmarked against a negative control cell line. Breast cancer optical diagnostics was experimentally modeled by means of epi-luminescence imaging of a monolayer of the UCNP-labeled SK-BR-3 cells buried under a breast tissue mimicking optical phantom. The experimental results were analyzed theoretically and projected to in vivo detection of early-stage breast cancer. The model predicts that the UCNP-assisted cancer detection is feasible up to 4 mm in tissue depth, showing considerable potential for diagnostic and image-guided surgery applications.

Polyglycine II Nanosheets: Supramolecular Antivirals?

Tetraantennary peptides [glycinen‐NHCH2]4C can form stable noncovalent structures by self‐assembly through intermolecular hydrogen bonding. The oligopeptide chains assemble as polyglycine II to yield submicron‐sized, flat, one‐molecule‐thick sheets. Attachment of α‐N‐acetylneuraminic acid (Neu5Acα) to the terminal glycine residues gives rise to water‐soluble assembled glycopeptides that are able to bind influenza virus multivalently and inhibit adhesion of the virus to cells 103‐fold more effectively than a monomeric glycoside of Neu5Acα. Another antiviral strategy based on virus‐promoted assembly of the glycopeptides was also demonstrated. Consequently, the self‐assembly principle offers new perspectives on the design of multivalent antivirals.

Visualization of fibrinogen αC regions and their arrangement during fibrin network formation by high‐resolution AFM

Fibrinogen has been intensively studied with transmission electron microscopy and x‐ray diffraction. But until now, a complete 3D structure of the molecule has not yet been available because the two highly flexible αC regions could not be resolved in fibrinogen crystals. This study was aimed at determining whether the αC regions can be visualized by high‐resolution atomic force microscopy.

Temperature-Controlled Assembly of High Ordered/Disordered Dodecylamine Layers on HOPG: Consequences for DNA Patterning

It is shown that temperature-controlled ordered layers of dodecylamine, self-assembled on highly oriented pyrolytic graphite (HOPG), are an appropriate substrate for aligning individual DNA molecules. High resolution atomic force microscopy (AFM) permits visualization of the lamellar structure of dodecylamine on HOPG. The DNA adsorbed on ordered dodecylamine layers is stretched and oriented along the lamellae, while DNA on disordered dodecylamine layers is found to be in a random conformation. Small DNA bubbles appear in the case of partially denaturated linear double stranded DNA (dsDNA) adsorbed on ordered layers of dodecylamine.

Comparison of the 'chemical' and 'structural' approaches to the optimization of the thrombin-binding aptamer.

Noncanonically structured DNA aptamers to thrombin were examined. Two different approaches were used to improve stability, binding affinity and biological activity of a known thrombin-binding aptamer. These approaches are chemical modification and the addition of a duplex module to the aptamer core structure. Several chemically modified aptamers and the duplex-bearing ones were all studied under the same conditions by a set of widely known and some relatively new methods. A number of the thrombin-binding aptamer analogs have demonstrated improved characteristics. Most importantly, the study allowed us to compare directly the two approaches to aptamer optimization and to analyze their relative advantages and disadvantages as well as their potential in drug design and fundamental studies.

High-Resolution Atomic Force Microscopy Study of Hexaglycylamide Epitaxial Structures on Graphite

Two types of hexaglycylamide (HGA) epitaxial lamellar structures coexisting on the surface of highly oriented pyrolytic graphite (HOPG) exposed to water solutions were studied by high-resolution atomic force microscopy (AFM). Lamellae are distinguished by growth direction and by morphology. The lamellae of the first type (L1) produced by depositions from more dilute solutions are close-packed with a period of ∼5.2 nm, twice the HGA molecular length, and form highly ordered domains morphologically similar to the lamellar domains of alkanes. The less-ordered lamellae of the second type (L2) appear at intermediate and large HGA concentrations and demonstrate variable lamellar width, morphological diversity, and a tendency to merge. The interlamellar separation in the domains of close-packed L2 lamellae varies with the discrete increment ∼2.5 nm; the most frequently observed value is ∼7.5-8.0 nm corresponding to the triple HGA molecular length. The growth directions of lamellae of each type have sixfold rotational symmetry indicating epitaxy with graphite; however, the rosettes of L1 and L2 lamellae orientations are misaligned by 30°. The molecular modeling of possible HGA epitaxial packing arrangements on graphite and their classification have been conducted, and the energetically preferable structures are selected. On this basis, the structural models of the L1 and L2 lamellae are proposed explaining the experimentally observed peculiarities as follows: (1) the L1 and L2 lamellae are respectively parallel and antiparallel β-sheets with two HGA molecules in the unit cell oriented normally to the lamellae boundaries, (2) HGA molecules in L1 and L2 lamellae have different orientations with respect to the graphite lattice, respectively along the directions <1120> and <1010>, (3) L1 lamella is the assembly of two hydrogen-bonded parallel β-sheets oriented head-to-head, (4) L2 lamellae are assemblies of several molecular rows (antiparallel β-sheets) cross-linked by hydrogen bonds. The AFM observations indicate that the covering of the hydrophobic graphite by the dense, closely packed, well-ordered monolayers of hydrophilic oligopeptide is possible.

High-resolution atomic force microscopy of DNA

A method using high resolution atomic force microscopy for imaging DNA has been elaborated. Using super-sharp probes and modified graphite as support for molecule adsorption, DNA molecule images were obtained whose resolution made possible the observation of their fine structure with repeated helical motifs. The method can be used to visualize individual spread molecules of single-stranded DNA.