Molecular patterns of oligopeptide hydrocarbons on graphite

Atomic force microscopy investigation of DNA denaturation on a highly oriented pyrolytic graphite surface

Understanding of DNA interaction with carbonaceous surfaces (including graphite, graphene and carbon nanotubes) is important for the development of DNA-based biosensors and other biotechnological devices. Though many issues related to DNA adsorption on graphitic surfaces have been studied, some important aspects of DNA interaction with graphite remain unclear. In this work, we use atomic force microscopy (AFM) equipped with super-sharp cantilevers to analyze the morphology and conformation of relatively long DNA molecule adsorbed on a highly oriented pyrolytic graphite (HOPG) surface. We have revealed the effect of DNA embedding into an organic monolayer of N,N'-(decane-1,10-diyl)-bis(tetraglycinamide) (GM), which may "freeze" DNA conformation on a HOPG surface during drying. The dependence of the mean squared point-to-point distance on the contour length suggests that DNA adsorbs on a bare HOPG by a "kinetic trapping" mechanism. For the first time, we have estimated the unfolded fraction of DNA upon contact with a HOPG surface (24 ± 5 %). The obtained results represent a novel experimental model for investigation of the conformation and morphology of DNA adsorbed on graphitic surfaces and provide with a new insight into DNA interaction with graphite.

Characterization of the effect of chromium salts on tropocollagen molecules and molecular aggregates

Though the capability of chromium treatment to improve the stability and mechanical properties of collagen fibrils is well-known, the influence of different chromium salts on collagen molecules (tropocollagen) is not well characterized. In this study, the effect of Cr³⁺ treatment on the conformation and hydrodynamic properties of collagen was studied using atomic force microscopy (AFM) and dynamic light scattering (DLS). Statistical analysis of contours of adsorbed tropocollagen molecules using the two-dimensional worm-like chain model revealed a reduction of the persistence length (i.e., the increase of flexibility) from ≈72 nm in water to ≈56-57 nm in chromium (III) salt solutions. DLS studies demonstrated an increase of the hydrodynamic radius from ≈140 nm in water to ≈190 nm in chromium (III) salt solutions, which is associated with protein aggregation. The kinetics of collagen aggregation was shown to be ionic strength dependent. Collagen molecules treated with three different chromium (III) salts demonstrated similar properties such as flexibility, aggregation kinetics, and susceptibility to enzymatic cleavage. The observed effects are explained by a model that considers the formation of chromium-associated intra- and intermolecular crosslinks. The obtained results provide novel insights into the effect of chromium salts on the conformation and properties of tropocollagen molecules.

Ordered Assembly of DNA on Topological Insulator Bi2Se3 and Octadecylamine for a Sensitive Biosensor

Controlling the assembly of DNA in order on a suitable electrode surface is of great significance for biosensors and disease diagnosis, but it is full of challenges. In this work, we creatively assembled DNA on the surface of octadecylamine (ODA)-modified topological insulator (Tls) Bi₂Se₃ and developed an electrochemical biosensor to detect biomarker DNA of coronavirus disease 2019 (COVID-19). A high-quality Bi₂Se₃ sheet was obtained from a single crystal synthesized in our lab. A uniform ODA layer was coated in argon by chemical vapor deposition (CVD). We observed and analyzed the assembly and mechanism of single-strand DNA (ssDNA) and double-strand DNA (dsDNA) on the Bi₂Se₃ surface through atomic force microscopy (AFM) and molecular dynamics (MD) simulations. The electrochemical signal revealed that the biosensor based on the DNA/ODA/Bi₂Se₃ electrode has a wide linear detection range from 1.0 × 10^-12 to 1.0 × 10^-8 M, with the limit of detection as low as 5 × 10^-13 M. Bi₂Se₃ has robust surface states and improves the electrochemical signal-to-noise ratio, while the uniform ODA layer guides high-density ordered DNA, enhancing the sensitivity of the biosensor. Our work demonstrates that the ordered DNA/ODA/Bi₂Se₃ electrode surface has great application potential in the field of biosensing and disease diagnosis.

Single-molecule AFM study of hyaluronic acid softening in electrolyte solutions

Investigation of hyaluronic acid (HA) morphology and mechanical properties at a single-molecule level is important for the development of HA based biomaterials. We have developed the atomic force microscopy (AFM) based approach for quantitative characterization of conformation of HA molecules. HA molecules adsorbed on a modified graphitic surface form oriented linear segments. Conformation of HA molecules can be considered as two-dimensional quasi-projection of a three-dimensional conformation locally straightened by a substrate. The persistence length and Young's modulus of biomolecules estimated using wormlike chain model decrease from 15.7 to 9.9 nm, and from ∼21 to ∼13 GPa, respectively, when KCl concentration increases from 0 to 100 mM. The dependence of the persistence length on ionic strength supports the Odijk-Skolnick-Fixman model of polyelectrolyte stiffening in electrolyte solution. The obtained results represent a new insight into the conformation and mechanical characteristics of HA molecules and complement the characterization of this biopolymer by bulk methods.

Visualization of G-Quadruplexes, i-Motifs and Their Associates

The non-canonical structures formed by G- or C-rich DNA regions, such as quadruplexes and i-motifs, as well as their associates, have recently been attracting increasing attention both because of the arguments in favor of their existence in vivo and their potential application in nanobiotechnology. When studying the structure and properties of non-canonical forms of DNA, as well as when controlling the artificially created architectures based on them, visualization plays an important role. This review analyzes the methods used to visualize quadruplexes, i-motifs, and their associates with high spatial resolution: fluorescence microscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM). The key approaches to preparing specimens for the visualization of this type of structures are presented. Examples of visualization of non-canonical DNA structures having various morphologies, such as G-wires, G-loops, as well as individual quadruplexes, i-motifs and their associates, are considered. The potential for using AFM for visualizing non-canonical DNA structures is demonstrated.

Myeloperoxidase-induced fibrinogen unfolding and clotting

Due to its unique properties and high biomedical relevance fibrinogen is a promising protein for the development of various matrixes and scaffolds for biotechnological applications. Fibrinogen molecules may form extensive clots either upon specific cleavage by thrombin or in thrombin-free environment, for example, in the presence of different salts. Here, we report the novel type of non-conventional fibrinogen clot formation, which is mediated by myeloperoxidase and takes place even at low fibrinogen concentrations (<0.1 mg/ml). We have revealed fibrillar nature of myeloperoxidase-mediated fibrinogen clots, which differ morphologically from fibrin clots. We have shown that fibrinogen clotting is mediated by direct interaction of myeloperoxidase molecules with the outer globular regions of fibrinogen molecules followed by fibrinogen unfolding from its natural trinodular to a fibrillar structure. We have demonstrated a major role of the Debye screening effect in regulating of myeloperoxidase-induced fibrinogen clotting, which is facilitated by small ionic strength. While fibrinogen in an aqueous solution with myeloperoxidase undergoes changes, the enzymatic activity of myeloperoxidase is not inhibited in excess of fibrinogen. The obtained results open new insights into fibrinogen clotting, give new possibilities for the development of fibrinogen-based functional biomaterials, and provide the novel concepts of protein unfolding.