Victor V. Demin

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.

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.

Electron microscopy of two-dimensional crystals of mitochondrial ATP synthase

Two‐dimensional crystals of the mitochondrial ATP synthase up to 0.4 μm in size were obtained from the detergent‐lipid‐protein micelles by detergent dialysis. A projected map of the negatively stained crystal was calculated from electron microscopical images by the Fourier‐filtering procedure at about 2.8 nm resolution. The unit cell (with not more than two ATP synthase molecules) has the following parameters: a = 13.0 nm, b = 25.6 nm and γ = 86°. Two alternative models for the crystal structural organization were suggested, viz. with one or two protein molecules per unit cell.

[Effect of supporting substrates on the structure of DNA and DNA-trivaline complexes studied by atomic force microscopy].

Linear DNA, circular DNA, and circular DNA complexes with trivaline (TV), a synthetic oligopeptide, were imaged by atomic force microscopy (AFM) using mica as a conventional supporting substrate and modified highly ordered pyrolytic graphite (HOPG) as an alternative substrate. A method of modifying the HOPG surface was developed that enabled the adsorption of DNA and DNA–TV complexes onto this surface. On mica, both purified DNA and DNA–TV complexes were shown to undergo significant structural distortions: DNA molecules decrease in height and DNA–TV displays substantial changes in the shape of its circular compact structures. Use of the HOPG support helps preserve the structural integrity of the complexes and increase the measured height of DNA molecules up to 2 nm. AFM with the HOPG support was shown to efficiently reveal the particular points of the complexes where, according to known models of their organization, a great number of bent DNA fibers meet. These results provide additional information on DNA organization in its complexes with TV and are also of methodological interest, since the use of the modified HOPG may widen the possibilities of AFM in studying DNA and its complexes with various ligands.

Atomic force and electron microscopy of high molecular weight circular DNA complexes with synthetic oligopeptide trivaline.

Abstract Intramolecular compact structures formed by high molecular weight circular superhelical DNA molecules due to interaction with synthetic oligopeptide trivaline (1) were studied by atomic force and electron microscopy. Three DNA preparations were used: plasmids pTbo1, pRX10 and cosmid 27877, with sizes 6120 bp, 10500 bp and 44890 bp respectively. Plasmid pTbo1 and pRX10 preparations along with monomers contained significant amount of dimers and trimers. Main structures in all preparations observed were compact particles, which coincide in their appearance and compaction coefficient (3,5–3,7) with triple rings described earlier. The size and structure characteristics of triple rings and other compact particles on atomic force images in general coincide with those obtained by EM (2). AFM (3) images allow to get additional information about the ultrastructural organization and arrangement of DNA fibers within the compact structures. Along with triple rings in pTbo1 and pRX10—TVP complexes significant amount of compact structures were observed having the shape of two or three compact rings attached to each other by a region of compact fibre. Basing on the data of contour length measurements and the shape of the particles it was concluded that these structures were formed due to compaction of dimeric and trimeric circular DNA molecules. Structures consisting of several attached to each other triple rings were not found for pTbo1, pRX10 monomers or cosmid preparations—TVP complexes where only single triple rings were observed. The conclusion is made that initiation of compact fibre formation within the circular molecules depends on the primary structure and for dimeric or trimeric circular molecules two or three compaction initiation points are present, located in each monomer unit within one circular DNA molecule. The nucleotide sequence dependent compaction mechanism providing independent compaction of portions of one circular molecule can be of interest for understanding of DNA compaction processes in vivo.

Conductive AFM as Nano Tester for DNA Molecules

λ‐DNA molecules have been deposited on mica partially covered by a Pt film and visualized by AFM operating both in standard contact and spreading resistance (SRM) modes. Depend on procedure of deposition, DNA molecules have different apparent heights and contrast in spreading resistance mode. We demonstrate that the absence of conductivity is caused by a very large compression deformation of DNAs under deposition technique.