Selection of Aptamers for Use as Molecular Probes in AFM Detection of Proteins.

Currently, there is great interest in the development of highly sensitive bioanalytical systems for diagnosing diseases at an early stage, when pathological biomarkers are present in biological fluids at low concentrations and there are no clinical manifestations. A promising direction is the use of molecular detectors-highly sensitive devices that detect signals from single biomacromolecules. A typical detector in this class is the atomic force microscope (AFM). The high sensitivity of an AFM-based bioanalysis system is determined by the size of the sensing element of an atomic force microscope-the cantilever-the radius of the curvature of which is comparable to that of a biomolecule. Biospecific molecular probe-target interactions are used to ensure detection system specificity. Antibodies, aptamers, synthetic antibodies, and peptides can be used as molecular probes. This study has demonstrated the possibility of using aptamers as molecular probes for AFM-based detection of the ovarian cancer biomarker CA125. Antigen detection in a nanomolar solution was carried out using AFM chips with immobilized aptamers, commercially available or synthesized based on sequences from open sources. Both aptamer types can be used for antigen detection, but the availability of sequence information enables additional modeling of the aptamer structure with allowance for modifications necessary for immobilization of the aptamer on an AFM chip surface. Information on the structure and oligomeric composition of aptamers in the solution was acquired by combining small-angle X-ray scattering and molecular modeling. Modeling enabled pre-selection, before the experimental stage, of aptamers for use as surface-immobilized molecular probes.

Nucleoid-Associated Proteins HU and IHF: Oligomerization in Solution and Hydrodynamic Properties.

Structure and function of bacterial nucleoid is controlled by the nucleoid-associated proteins (NAP). In any phase of growth, various NAPs, acting sequentially, condense nucleoid and facilitate formation of its transcriptionally active structure. However, in the late stationary phase, only one of the NAPs, Dps protein, is strongly expressed, and DNA-protein crystals are formed that transform nucleoid into a static, transcriptionally inactive structure, effectively protected from the external influences. Discovery of crystal structures in living cells and association of this phenomenon with the bacterial resistance to antibiotics has aroused great interest in studying this phenomenon. The aim of this work is to obtain and compare structures of two related NAPs (HU and IHF), since they are the ones that accumulate in the cell at the late stationary stage of growth, which precedes formation of the protective DNA-Dps crystalline complex. For structural studies, two complementary methods were used in the work: small-angle X-ray scattering (SAXS) as the main method for studying structure of proteins in solution, and dynamic light scattering as a complementary one. To interpret the SAXS data, various approaches and computer programs were used (in particular, the evaluation of structural invariants, rigid body modeling and equilibrium mixture analysis in terms of the volume fractions of its components were applied), which made it possible to determine macromolecular characteristics and obtain reliable 3D structural models of various oligomeric forms of HU and IHF proteins with ~2 nm resolution typical for SAXS. It was shown that these proteins oligomerize in solution to varying degrees, and IHF is characterized by the presence of large oligomers consisting of initial dimers arranged in a chain. An analysis of the experimental and published data made it possible to hypothesize that just before the Dps expression, it is IHF that forms toroidal structures previously observed in vivo and prepares the platform for formation of DNA-Dps crystals. The results obtained are necessary for further investigation of the phenomenon of biocrystal formation in bacterial cells and finding ways to overcome resistance of various pathogens to external conditions.

Template-Directed Polymerization Strategy for Producing rGO/UHMWPE Composite Aerogels with Tunable Properties.

In this paper, we suggest a previously unknown template-directed polymerization strategy for producing graphene/polymer aerogels with elevated mechanical properties, preservation of the nanoscale pore structure, an extraordinary crystallite structure, as well as tunable electrical and hydrophobic properties. The suggested approach is studied using the reduced graphene oxide (rGO)/ultrahigh molecular weight polyethylene (UHMWPE) system as an example. We also develop a novel method of ethylene polymerization with formation of UHMWPE directly on the surface of rGO sheets prestructured as the aerogel template. At a UHMWPE content smaller than 20 wt %, composite materials demonstrate completely reversible deformation and good conductivity. An ultrahigh polymer content (more than 80 wt %) results in materials with pronounced plasticity, improved hydrophobic properties, and a Young's modulus that is more than 200 times larger than that of pure rGO aerogel. Variation of the polymer content makes it possible to tune the electro-conductive properties of the aerogel in the range from 4.8 × 10-6 to 4.9 × 10-1 S/m and adjust its hydrophobic properties. The developed approach would make it possible to create composite materials with highly developed nanostructural morphology and advanced properties controlled by the thickness of the polymer layer on the surface of graphene sheets.

Microphase separation of stimuli-responsive interpenetrating network microgels investigated by scattering methods.

Polymer stimuli-responsive microgels find their use in various applications. The knowledge of its internal structure is of importance for further improvement and expanding the scope. Interpenetrating network (IPN) microgels may possess a remarkable feature of strongly non-uniform inner architecture, even microphase separation, in conditions of a selective solvent. In this research, we, for the first time, use a combination of static light scattering (SLS) and small-angle X-ray scattering (SAXS) techniques to collect the structure factors of aqueous dispersions of poly(N-isopropylacrylamide)-polyacrylic acid IPN microgels on the broad scale ofqvalues. We study the influence of solvent quality on microgel conformations and show that in a selective solvent, such a system undergoes microphase separation: the sub-network in a poor solvent conditions forms dense small aggregates inside the large swollen sub-network in a good solvent. We propose the microstructured sphere model for the IPN microgel structure factor interpretation and perform additional analysis and verification through coarse-grained molecular dynamics computer simulations.