Oligoribonucleotides containing an aminoalkyl group at the N(4) atom of cytosine as precursors of new reagents for site-specific modifications of biopolymers

A solid-phase H-phosphonate procedure was developed for the synthesis of oligoribonucleotides containing aliphatic amino linkers with different lengths at the N(4) atom of cytosine. The hybridization properties of modified oligoribonucleotides were studied. Thermal stability of the RNA—RNA* and DNA—RNA* duplexes depends on the position of modified cytosine in the chain and the type of the duplex.     

Synchronous ultrasonic Doppler imaging of magnetic microparticles in biological tissues

We considered applicability of acoustic imaging technology for the detection of magnetic microparticles and nanoparticles inside soft biological tissues. Such particles are widely used for magnetically targeted drug delivery and magnetic hyperthermia. We developed a new method of ultrasonic synchronous tissue Doppler imaging with magnetic modulation for in vitro and in vivo detection and visualization of magnetic ultradisperse objects in soft tissues. Prototype hardware with appropriate software was produced and the method was successfully tested on magnetic microparticles injected into an excised pig liver.     

Investigation of surface oligonucleotide-binding proteins of eucaryotic cells by affinity modification with reactive oligonucleotide derivatives

Interactions between oligodeoxyribonucleotides (ODN) with different sequences and cell proteins were examined using the affinity modification by [³²P]-labeled reactive oligonucleotide derivatives. 3"-Terminal ribouridine oxidized with sodium periodate, 4-[(N-2-chloroethyl-N-methyl)amino]benzylamine, and the maleimide residue were used as reactive groups. All the compounds used are specific reagents. The set of the discovered nucleic acid-binding (NA-binding) proteins depends on the chemical properties of the affinity reagent. The presence of the hydrophobic group at the 5"-terminus of the ODN molecule is the key factor determining the variety of the discovered NA-binding proteins. The cells of different origin (A431, HeLa, KB, MCF-7, Hap-2, K562, Cos-7, NIH/3T3, human-lung primary epithelial cells, and porcine kidney primary cells) are characterized by the same set of NA-binding proteins whose affinity modifications depends on the conditions of incubation of oligonucleotides with the cells. Treatments of cells disturbing the integrity of the cellular membrane (scrapping, treatment with trypsin, or cell permeabilization with streptolysin O or saponin), disrupt interactions between NA-binding proteins from native cells and ODN.     

Direct C-nitration of cyclic α,β-unsaturated oximes under the action of sodium nitrite and acetic acid in methanol

Using a number of cyclic ,-unsaturated oximes of the terpene series and some simplest model compounds as examples, unsaturated oximes bearing a hydrogen atom at the -carbon atom were demonstrated to be converted into -hydroxyiminonitroalkenes under the action of sodium nitrite and acetic acid in methanol. In the case of the introduction of an alkyl substituent at the terminal carbon atom of the diene C=C—C=NOH fragment, the reaction performed under the same conditions gave rise exclusively to conjugated ketone (a deoximation product).     

A new simple and convenient method for preparation of oligonucleotides containing a pyrene or a cholesterol moiety

Russian Chemical Bulletin - A new simple and convenient approach to the synthesis of oligonucleotides containing pyrene or cholesterol moieties is described. The approach does not require a special...     

Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides

Continuous stacking hybridization of oligodeoxyribonucleotides with the stem of a preformed minihairpin structure of a DNA template was studied by thermal denaturation in solution. The thermodynamic parameters (H°, S°, and G°₃₇) were determined for the formation of all 16 possible types of coaxial stackings (or cooperative interactions) ^5" X*pY ^3"/^5" ZZ"3" (an asterisk stands for a nick) between the terminal complementary base pairs of two adjacent duplexes formed on a common DNA template. The maximum efficacy G°₃₇ of coaxial stacking (1 M NaCl, pH 7.4) was observed for the G*pC/GC interaction (–2.76 kcal mol^–1), whereas the minimum efficacy was observed for the T*pA/TA interaction (–0.85 kcal mol^–1). In the general case, the efficacy of the cooperative interaction at the X*pY/ZZ" junction does not correlate with the energy of formation of the corresponding unified XY/ZZ" dinucleotide pair in the structure of native DNA. The formation of a stack by the terminal oligonucleotide bases upon their continuous stacking hybridization makes the major and governing contribution to the energy of cooperative interaction.     

Spatial Structure of a DNA Duplex d(CGTTTATT)p-Net:d(AATAAACG) with an Unusual Localization of a Covalently Bound Netropsin (Net) Analog According to Two-Dimensional NMR Spectroscopy

Two-dimensional ¹H NMR (NOESY, COSY) spectroscopy was used to study the spatial structure of a DNA complex CGTTTATTp-Net:AATAAACG with a netropsin analog bound at the terminal 3-phosphate group in aqueous solution. The positions of the proton NMR signals of the duplex are compared with those for the unmodified duplex and the free ligand. A mean conformation of the duplex is constructed by the molecular mechanics technique using the obtained NMR limitations on the interproton distances. The data obtained indicate that the aromatic pyrrole rings of the netropsin analog are involved in a stacking interaction with the terminal AT base pair of the duplex; this is generally not typical of ordinary minor-groove netropsin type ligands.