Effects of psychogenic stress on some peripheral and central inflammatory markers in rats with the different level of excitability of the nervous system

Patients with post-stress pathologies display the signs of inflammation in the peripheral blood as well as in the brain. The mechanisms of such post-stress neuroimmune changes, their contribution to the behavior, the relationship of the intensity of inflammation with genetically determined features have not been clarified. The goal of this work was to evaluate the dynamics of post-stress inflammation in the blood and hippocampus of rats which differ in level of excitability of the nervous system. Rats of two strains (high/low excitability threshold) were subjected to stress according to the K. Hecht protocol and their behavior, neutrophil:lymphocyte ratio and the number of Iba+ cells in the hippocampus were analysed 24 hours, 7 and 24 days after stress exposure. Highly excitable animals show an increase in anxiety-like behavior, in the number of neutrophils compared to lymphocytes as well as in the number of Iba1+ cells in CA1, CA3 and DG areas of the hippocampus in response to stress. Thus, hereditary high excitability of the nervous system is a possible risk factor for the development of post-stress pathologies.

Antisense oligonucleotides for the arterial hypertension mechanisms study and therapy

Arterial hypertension is one of the most common chronic diseases in adults all over the world. This pathology can not only reduce patients’ life quality, but can also be accompanied by a number of complications. Despite the fact that there is a large group of antihypertensive drugs on the market, mainly representing different combinations of inhibitors of the renin-angiotensin system, adrenoreceptor blockers in combination with diuretics, there is no generally accepted “gold standard” for drugs that would not have side effects. The review discusses the main aspects of antisense oligonucleotides use in the context of arterial hypertension. It is well known that the medical implementation of antisense oligonucleotides aims to block the expression of particular genes involved in the pathology development, and a key advantage of this technique is a high selectivity of the effect. However, with the undoubted advantages of the method, there are difficulties in its application, related both to the properties of the oligonucleotides themselves (insufficient stability and poor penetration into cells), and to the variety of mechanisms of the origin of a particular pathology, arterial hypertension, in our case. The review provides a brief description of the main molecular targets for antisense treatment of hypertensive disease. The newest targets for therapy with oligonucleotides – microRNAs – are discussed. The main modifications of antisense nucleotides, designed to increase the duration of their effects and simplify the delivery of this type of drugs to the targets are discussed, in particular, combining antisense oligonucleotides with adenovirus-based expression vectors. Particular attention is given to antisense oligonucleotides in the complex with nanoparticles. The review discusses the results of the use of titanium dioxide (TiO2) containing antisense nanocomposites for the angiotensin converting enzyme in rats with stress induced arterial hypertension (ISIAH). It was shown that the use of antisense oligonucleotides continues to be a promising technique for studying the mechanisms of various forms of hypertensive disease and has a high potential for therapeutic use.

[Impact of Delivery Method on Antiviral Activity of Phosphodiester, Phosphorothioate, and Phosphoryl Guanidine Oligonucleotides in MDCK Cells Infected with H5N1 Bird Flu Virus]

We have previously described nanocomposites containing conjugates or complexes of native oligodeoxyribonucleotides with poly-L-lysine and TiO2 nanoparticles. We have shown that these nanocomposites efficiently suppressed influenza A virus reproduction in MDCK cells. Here, we have synthesized previously undescribed nanocomposites that consist of TiO2 nanoparticles and polylysine conjugates with oligonucleotides that contain phosphoryl guanidine or phosphorothioate internucleotide groups. These nanocomposites have been shown to exhibit antiviral activity in MDCK cells infected with H5N1 influenza A virus. The nanocomposites containing phosphorothioate oligonucleotides inhibited virus replication ~130-fold. More potent inhibition, i.e., ~5000-fold or ~4600-fold, has been demonstrated by nanocomposites that contain phosphoryl guanidine or phosphodiester oligonucleotides, respectively. Free oligonucleotides have been nearly inactive. The antiviral activity of oligonucleotides of all three types, when delivered by Lipofectamine, has been significantly lower compared to the oligonucleotides delivered in the nanocomposites. In the former case, the phosphoryl guanidine oligonucleotide has appeared to be the most efficient; it has inhibited the virus replication by a factor of 400. The results make it possible to consider phosphoryl guanidine oligonucleotides, along with other oligonucleotide derivatives, as potential antiviral agents against H5N1 avian flu virus.

Toward Gene Therapy of Hypertension: Experimental Study on Hypertensive ISIAH Rats

TiO₂-based nanocomposites were prepared to deliver oligonucleotides into cells. The nanocomposites were designed by the immobilization of polylysine-containing oligonucleotides on TiO₂-nanoparticles (TiO₂·PL-DNA). We showed for the first time the possibility of using the proposed nanocomposites for treatment of hypertensive disease by introducing them into hypertensive ISIAH rats developed as a model of stress-sensitive arterial hypertension. The mRNA of the gene encoding angiotensin I-converting enzyme (ACE1) involved in the synthesis of angiotensin II was chosen as a target. Administration (intraperitoneal injection and inhalation) of the nanocomposite showed a significant (by 20-30 mm Hg) decrease in systolic blood pressure when the nanocomposite contained the ACE1 gene-targeted oligonucleotide. When using the oligonucleotide with a random sequence, no effect was observed. Further development and improvement of the inhalation nanocomposite drug delivery to systemic hypertensive disease treatment promises new possibilities for clinical practice.

[Persistent infections in the children presenting with chronic ENT diseases: the potential of etiotropic therapy]

The objective of the present study that involved 176 children at the age varying from 2 to 12 years presenting with chronic ENT diseases was etiological diagnostics and etiotropic therapy of these pathologies taking into consideration the duration of the disease of less than one year (n=72), from 1 to 2 years (n=54), and over 2 years (n=50). The bacteriological method was employed to identify microflora from the upper respiratory tract and the molecular-biological methods for the detection of Epstein-Barr virus DNA, cytomegalovirus, and 6 types of human herpes virus in the blood and saliva. All the children were treated with the recombinant interferon preparations given for 1-1.5 months. For 41% of the children this treatment was combined with antibacterial therapy followed by immunocorrective therapy with interferon inducers (in 79.4% of the patients) or bacterial lysates (20.6%). The study revealed the predominant role of types 4, 5, and 6 type herpes viruses in the development of chronic ENT pathologies in the children with the gradual lowering of activity of these infections over 2 years. Staphylococcus aureus and Streptococcus pyogenes as well as fungi of the genus Candida were the commonest bacterial and fungal pathogenic agents isolated from the naso- and oropharynx of the children suffering from chronic ENT pathology.The effectiveness of etiotropic therapy was shown to decrease with time, from 78% during 1 year after the onset of the disease to 30% within the next 2 years.

[Eficient inhibition of human influenza A virus by oligonucleotides electrostatically fixed on polylysine-containing TiO2 nanoparticles]

Antiviral activity of TiO2 * PL * DNA nanobiocomposites was studied on the MDCK cell culture infected with influenza A virus (subtype H3N2). DNA fragments in the nanocomposites are electrostatically bound to titanium dioxide nanoparticles pre-covered with polylysine. It was shown that TiO2 * PL * DNA(v3') nanocomposite bearing the DNA(v3') fragment targeted to the 3'-end of the noncoding region of segment 5 of viral RNA specifically inhibited the virus reproduction with the efficiency of 99.8 and 99.9% (or by factors of~400 and 1000) at a low concentration of DNA(v3') in nanocomposite (0.1 and 0.2 µM, respectively). The TiO2 * PL * DNA(r) nanocomposite containing oligonucleotide noncomplementary to viral RNA or the oligonucleotide unbound to the nanoparticles show very low antiviral activity (inhibition by factors of~3.5 and 1.3, respectively).

[Effect of activity of NMDA-receptors on process of methylation of histone H3 and on its asymmetry in hippocampal pyramidal neurons of rats with different threshold of excitability of the nervous system under normal and stress conditions]

Process of methylation of histone H3 for lysine 4 (H3K4) was studied in hippocampal pyramidal neurons of rats--intact and submitted to emotional-painful stress with active and inactivated channels of NMDA-receptors with taking into account the interhemisphere lateralization and in connection with the genetically determined level of excitability of the animals' nervous system. There were revealed interstrain differences in the basal level of the H3K4 methylation whose direction depends on structural-functional peculiarities of hippocampal fields and lateralization. Under action of stress the direction of the observed changes in the degree of the H3K4 methylation depended on the functional state of channels of NMDA-receptors. On the background of active receptors the proportion of immunopositive cells predominantly increased. In the CA1 field those changes were not connected to excitability and lateralization, whereas in the CA3 field it had a complex character and depended on those two factors. At inactivation of channels of NMDA-receptors the portion of immunopositive nuclei as a result of the stress action, on the contrary, predominantly decreased; interstrain specificity of these changes was connected to lateralization, while its direction in different hippocampal fields was different. Action of the short-time emotional-painful stress did not lead to a change of shape of interhemisphere asymmetry at active state of receptors, whereas at inactivation of receptors it changes depending on the structural-functional organization of hippocampus and on excitability of the nervous system.

[TiO2-DNA nanocomposites capable of penetrating into cells]

Methods of noncovalent immobilization of DNA fragments onto titanium dioxide nanoparticles (TiO2) were developed, which led to TiO2-DNA nanocomposites capable of penetrating through cell membranes. TiO2 nanoparticles of different forms (amorphous, anatase, brookit) with enhanced agglomeration stability were synthesized. The particles were characterized by X-ray diffraction, small angle X-ray scattering, infrared spectroscopy and atomic force microscopy. Three approaches to the preparation of nanocomposites are described: (1) sorption of polylysine-containing oligonucleotides onto TiO2-nanoparticles, (2) the electrostatic binding of oligonucleotides to TiO2 nanoparticles bearing immobilized polylysine, and (3) sorption of oligonucleotides on TiO2 nanoparticles in the presence of cetavlon. All three methods provide an efficient and stable immobilization of DNA fragments onto nanoparticles, which leads to nanocomposites with a density for an oligonucleotide up to 40 nmol/mg. It is shown that DNA fragments in nanocomposites retain their ability to form complementary complexes and can be delivered into cells without transfection agents and other methods of exposure.

[Design of deoxyribozymes for inhibition of influenza A virus]

Influenza A viruses take a significant place in human and animal pathology causing epidemics and epizootics. Therefore, the development of new antiflu drugs has become more and more urgent. Deoxyribozymes can be considered as promising antiviral agents due to their ability to efficiently and highly specifically cleave RNA molecules. In this study, a number ofgenomic sequences of the most relevant influenza A virus subtypes, H5N1, H3N2, and H1N1, were analyzed. Conservative regions were revealed in five the least variable segments of the fragmented viral RNA genome, and potential sites of their cleavage with "10-23" deoxyribozymes were determined. 46 virus-specific 33-mer deoxyribozymes with the general structure of 5'N8AGGCTAGCTACAACGAN9 were designed and synthesized. Screening of the antiviral activity of these agents in conjugation with lipofectin on the Madin-Darby Canine Kidney cells infected with highly pathogenic avian influenza virus A/chicken/Kurgan/05/2005 (H5N1) revealed 17 deoxyribozymes, which suppressed the titer of virus cytopathicity by more than 2.5 IgTCID50/mL (i.e. the virus neutralization index was more than 300), with five of them suppressing the virus titer by a factor of 1000 and more. The most active deoxyribozymes appeared to be specific to segment 5 of the influenza A virus genome, which encoded nucleoprotein (NP).

[Kainate receptors in the hippocampus of rat strains with different levels of the nervous system excitability]

Glutamate receptors in the central nervous system play a significant role in the mechanisms of differential adaptation to the environmental conditions. However, structural and functional parameters of kainate receptors (KR) under normal conditions and during exposure to stress are not well characterized. Therefore, the aim of this research was to 1) study the distribution and the quantity of KR GluR 5/6/7 subunits; 2) examine their changes in the pyramidal cell layer of the hippocampus in rat strains with have genetically determined distinctions in the levels of nervous system excitability following the exposure to short-term emotional-painful stress; 3) estimate the sensitivity of hippocampal pyramidal neurons to the action of KR agonist -kainic acid. It was demonstrated that GluR 5/6/7 KR are localized mainly in the region of hippocampal CA2 area; in the animals with low excitability their quantity was greater than in those with high excitability. Short-term emotional-painful stress resulted in the increase of KR in hippocampal CA2 area only in highly excitable rats. Selective sensitivity of pyramidal neurons in different hippocampal fields to the action of kainic acid was demonstrated and it was found to depend on animal strain characteristics of of the nervous system excitability.

An examination of the ability of titanium dioxide nanoparticles and its conjugates with oligonucleotides to penetrate into eucariotis cells

In this study we examine the possibility that TiO₂ nanoparticles and their conjugates can penetrate into cultivated cells without any special transfection procedures. Oligonucleotides and their derivates were conjugated with the TiO₂ nanoparticles, which were obtained as colloidal solutions at a concentration of TiO₂ 0.3M by TiCl₄ hydrolysis. The electronic microscopy of various cell cultures (KCT, Vero, and MDCK) treated with nanoparticle solutions (20 µg/µl) showed that nanoparticles could enter the cells and accumulate in the vacuoles and phagosomes and form inclusions in cytoplasm. Thus, we demonstrated the penetration of TiO₂ nanoparticles and their oligonucleotide conjugates into intracellular space without any auxiliary operations. Most other researches used electroporation techniques for similar purposes [1, 2, 5].

[Synthesis of polyamine-containing oligonucleotides]

A simple and efficient method of synthesis of polyamine-oligonucleotide conjugates in high yields (up to 95%) was suggested. The terminal phosphate group of deprotected oligonucleotides was selectively activated with the redox pair triphenylphosphine-dipyridyl disulfide in the presence of a nucleophilic catalyst, and the activated oligonucleotide derivative was subjected to the reaction with a polyamine.

[Functionalized nanocomposite coating of a glass surface for oligonucleotide immobilization]

A new type of coating for manufacturing DNA chips was constructed of the basis of an organic-inorganic nanocomposite based on the polyvinylbutyral-tetraethoxysilane copolymer. The organosilicon composite was functionalized by introduction of ethanolamine vinyl ether copolymers, which contain amino groups and anchor vinyloxide units capable of reacting with silanol groups of the nanocomposite. The resulting coatings form a film on glass slides with a high surface density of amino groups (up to 700 groups/nm2) suitable for three-dimensional immobilization of oligonucleotides. The use of bifunctional reagents (e.g., phenylene diisothiocyanate) for the attachment of oligonucleotides bearing amino linkers to the amino-containing surface provides an immobilization density of 0.5-1.6 pmol/mm2. Immobilization with a higher density (10-12 pmol/mm2) was achieved for attachment to amino-containing glass slides upon the use of oligonucleotides containing selectively activated terminal phosphate groups. The activation of oligonucleotides was carried out with the triphenylphosphine-dithiodipyridine pair in the presence of dimethylaminopyridine N-oxide. The resulting DNA chips were shown to be useful in principle for DNA detection.

Analysis of interactions of DNA polymerase beta and reverse transcriptases of human immunodeficiency and mouse leukemia viruses with dNTP analogs containing a modified sugar residue

Substrate properties of various morpholinonucleoside triphosphates in the reaction of DNA elongation catalyzed by DNA polymerase beta, reverse transcriptase of human immunodeficiency virus (HIV-1 RT), and reverse transcriptase of Moloney murine leukemia virus (M-MuLV RT) were compared. Morpholinonucleoside triphosphates were utilized by DNA polymerase beta and HIV-1 reverse transcriptase as substrates, which terminated further synthesis of DNA, but were virtually not utilized by M-MuLV reverse transcriptase. The kinetic parameters of morpholinoderivatives of cytosine (MorC) and uridine (MorU) were determined in the reaction of primer elongation catalyzed by DNA polymerase beta and HIV-1 reverse transcriptase. MorC was a more effective substrate of HIV-1 reverse transcriptase and significantly less effective substrate of DNA polymerase beta than MorU. The possible use of morpholinonucleoside triphosphates as selective inhibitors of HIV-1 reverse transcriptase is discussed.

[Synthesis of oligodeoxyribonucleotide derivatives, containing perfluoroarylazide group at C8-atom of deoxyadenosine and their use in photomodification of DNA fragments]

Heptadeoxynucleotides were obtained that contained an aliphatic amino group in position 8 of the deoxyadenosine residue: ALNH2 CTTTCT, CTCALNH2 CTT, and ACACTCALNH2 where L = NH(CH2)n, n = 3, 5, or 7. A 4-azidotetrafluorobenzoyl residue was attached to the amino group in the oligonucleotides, and photomodification of a DNA target by the resulting reagents was carried out. It was shown that the length of the spacer influences the photomodification extent of the target; a spacer with n = 5 is optimum. The maximum modification extent (65%) was reached when a reagent containing a photoreactive group at the 5'-terminal deoxyadenosine residue was used.

[Interaction of short nucleotide derivatives with nucleic acids. III. photomodification of DNA targets using tandems of short nucleotide derivatives]

High efficiency was demonstrated for the photomodification of a DNA target by a 5'-p-azidotet-rafluorobenzoyl reagent based on a tetranucleotide and its 3'-phosphoestrone ester in the presence of a pair of flanking effectors. These effectors are oligonucleotide derivatives with N-(2-hydroxyethyl)phenazinium groups or those connected to cholesterol residues at the terminal phosphates.

Conjugates of minor groove DNA binders with oligodeoxynucleotides: synthesis and properties

Oligodeoxynucleotide conjugates of netropsin (Nt) and distamycin A (Dst) were synthesized, and the thermal stability of several model DNA duplexes containing conjugates was studied. Two Dst residues conjugated at both ends of the oligonucleotide were needed for substantial increase in the melting temperature of the corresponding duplex (delta Tm > 30 degrees C). Two attached Dst residues had a greater effect on the Tm value than did two free molecules of Dst per duplex. In contrast to Dst, one Nt molecule linked to the oligonucleotide was enough to influence the thermal stability of the duplexes. Like Dst, the attached Nt appeared to stabilize duplexes much more than free Nt molecules. Attachment of Nt to either the 5'- or 3'-end of the different nonadeoxynucleotides containing 5' ...TTAAA... or 5' ...TATA... sites increased Tm of their duplexes by 21 degrees C-25 degrees C, whereas delta Tm for free Nt was 8 degrees C-15 degrees C (delta delta Tm = 10 degrees C-14 degrees C). The same phenomenon was shown for oligonucleotide phosphorothioates (delta Tm were 18 degrees C-22 degrees C and 9 degrees C-13 degrees C for attached and free Nt, respectively; delta delta Tm = 9 degrees C). This effect was even more pronounced for a hairpin oligonucleotide (delta delta Tm = 18 degrees C).

Recognition of the primers containing different modified nucleotide units by the Klenow fragment of DNA polymerase I from E coli

A comparison of Km values and maximal rates of extension (Vmax) for primers containing different modified bases or mismatches, and fully complementary primers of the same length catalyzed by the Klenow fragment of E coli DNA polymerase I was carried out. Base modifications include T-T dimers and apurinic sites. In the case of mismatch, the number of complementary bases from the 3'-terminus to the non-complementary nucleotide determines the efficiency of substrate incorporation, which is a measure of degree of interaction of the enzyme with its primer template. Differently, removal of one base in any position from the 3'-terminus of the primer is equivalent to shortening of the primer by one nucleotide unit, and decreases the affinity to the enzyme by 1.8-fold. Since apurinic sites fail to interfere with the efficiency of DNA synthesis, we suppose that the Klenow fragment of E coli DNA polymerase I does not participate in the correction of DNAs containing apurinic nucleotides units. Finally, the efficiency of elongation of the d(p primer was shown to decrease with an increase in T-T dimers in the primer. When the d(pT)10m primer contains about 2.6 T-T dimers per molecule, the efficiency of its elongation decreases by a factor of 8-18.

Site-specific photomodification of single-stranded DNA targets by arylazide and perfluoroarylazide derivatives of oligonucleotides

Highly efficient site-specific photomodification of single-stranded DNA targets was achieved with oligonucleotide reagents bearing aromatic azido groups (R (R1 = p-azidotetrafluorobenzoyl, R2 = 2-nitro-5-azidobenzoyl, R3 = p-azidobenzoyl) at either the terminal phosphate or at the C5 position of deoxyuridine at the end or inside of the oligonucleotide chain. The extent of modification strongly depends on the reagent type. It does not exceed 5% in the case of the reagent with R3. It was 25%-50% and 60%-70% for the reagents with R2 and R1 depending on the target structure. The reagent with perfluoroarylazido group R1 appeared to be most efficient. The extent of covalent adduct formation amounts to 70% for all reagents bearing a perfluoroarylazine group at the end of the oligonucleotide chain, independently of whether it was attached to the 3'- or 5'-phosphate or to the C5 of deoxyuridine. The reagents with the reactive group within the chain provided fewer cross-links (50%-55%). The reagents with R1 and R2 were found to be sensitive to the nucleotide structure of the target. Guanine and cytosine residues were modified preferentially when adjacent to the R1 or R2 group of the reagent, respectively.

Sequence-specific photomodification of single-stranded and double-stranded DNA fragments by oligonucleotide perfluoroarylazide derivative

A highly efficient, sequence-specific photomodification of single-stranded (ss) and double-stranded (ds) DNA fragments was carried out with a hexadecathymidilate derivative, R approximately p(T)16 (R-perfluoroarylazido group), using 27-base pair DNA fragments as a target [table: see text] The main points of modification were G7 and G24 of the A-rich strand of the ss target and G7 and G22 of the A-rich and T-rich strands, respectively, for the ds target. The extent of photomodification was 60%-77% for ss DNA and 10%-53% for ds DNA depending on the reaction conditions. Photomodification increased in buffer with a high ionic strength (1.0 M) and at low temperature (4 degrees C) when presumably the triplexes were more stable.

[Recognition of uracil in DNA by uracil-DNA-glycosylase from human placenta]

The affinity of different ligands (d(pA)n, d(pT)n, d(pA)nxd(pT)n, dU-containing oligonucleotides) to the uracil-DNA-glycosylase (UDG) from human placenta have been investigated. All used oligodeoxynucleotides were shown to be competitive inhibitors of uracil-DNA glycosylase toward to [3H]-uracil-DNA substrate. Minimal ligand capable to bind to the template site of the enzyme was shown to be nucleoside monophosphate (Ki(dTMP) = 30 mM, Ki(dAMP) = 10 mM). Ligand affinity increases by the factor f 1.28 and 1.36 (respectively for d(pT)n and d(pA)n) per added monomer unit according to the progression Ki[d(pN)n] = Ki(dNMP).(f)-g, where g- number of mononucleotide bases of the d(pA)n, d(pT)n. Linear dependences of -lgKi vs n have inflection point at n = 10. At n > 10 ligand affinity remain constant. Affinity of the complexes d(pA)n.d(pT)n were observed to have the analogues dependencies, but Ki was 3 fold lower than for d(pA)n with corresponding length. The Ki of duplexes containing noncomplementary residues have been determined. Insertion of dU-residues or other noncomplementary base into one of the chains of duplexes d(pA)n.d(pT)n leads to increasing of the affinity about 10-20 fold: d(pT)4(pU)(pT)5 x d(pA)10 (Ki = 6.0 MKM), d(pT)10 x d(pA)4(pU)(pA)5 (Ki = 3.0 MKM), d(pA)7(pU)(pA)7 x d(pT)7(pC)(pT)7(4.0 MKM), d(pA)7(pU)(pA)7 x d(pT)7(pG)(pT)7 (6.0 MKM), d(pA)7(pU)(pA)7 x d(pT)15 (7.0 MKM). On the basis of the data obtained the conclusion that UDG interacts with 10 mononucleotide units of DNA was reached. The contribution of 9 nonmodified base pairs of DNA into recognition of substrate containing modified base by the enzyme is about 3-4 orders of magnitude higher than the contribution of the modified base.

[Complementary-addressed photomodification of nucleic acids by arylazide and perfluoroarylazide oligonucleotide derivatives. III. Oligonucleotide reagents with a photoactive group at the end or inside the chain; tandem reagents]

Photomodification of target oligonucleotides with reagents bearing p-azidotetrafluorobenzamide group at various positions of the oligonucleotide address was investigated. The photoactive group was attached to the 5'- or 3'-terminal phosphate or at the C5-position of a deoxyuridine residue at the 5'-end or inside the oligonucleotide chain. The reagents with the internal photoactive group modified the target with 50-55% efficiency (fraction of covalent adducts reagent-target), whereas the derivatives with a terminal reactive group were more effective (70%). The main point of the modification was the guanosine residue of the target which located near to the photoactive group and was not involved into the duplex formation. Tandems of reagents which are complementary to neighbouring sites of the target modify predominantly the same guanosine residue, with up to 80% extent.

[Complementary-addressed photomodification of DNA-targets by arylazide and perfluoroarylazide oligonucleotide derivatives. IV. Photomodification of ss- and ds-DNA-fragments]

A highly efficient sequence-specific photomodification of single stranded (ss) and double stranded (ds) DNA fragments was carried out with hexadecathymidilate derivative, R-p(T)16(R--p-azidotetrafluorobenzamide) and 27-meric DNA fragments as a targets. [formula: see text] The main points of the modification were G7 and G24 for the ss target and G7 and G22 of purine- and pyrimidine-rich strands, respectively, for the ds DNA fragment. The photomodification extent was 60-77% for ss DNA and 10-53% for ds DNA depending on the reaction conditions: it increased in a buffer with a high ionic strength (1.0 M) and at a low temperature (4 degrees C) when the triplexes are more stable.

[Recognition of primers, containing noncomplementary nucleotides and units, lacking bases, by the Klenow fragment of Escherichia coli DNA polymerase I]

A comparison was carried out for the Km and maximal rates of conversion on (Vmax) with primers containing noncomplementary bases, as well as primers without several bases, and fully complementary primers of the same length. The number of complementary bases from the 3' end to the noncomplementary nucleotide was shown to determine the efficiency of interaction (and conversion) of the primers containing noncomplementary bases with enzyme. The DNA polymerase practically does not discriminate between the primers without one or two bases and the fully complementary primers. Elimination of one base in any position from the 3' end of the primer is equivalent to shortening of the primer by one nucleotide unit, and leads to a decrease in the affinity by a factor of 1.8. We suppose that DNA polymerase does not participate in primer mistake correction during the repair process if the DNA contains apurinic or apyrimidinic nucleotide units.

Oligonucleotide derivatives bearing reactive and stabilizing groups attached to C5 of deoxyuridine

Oligonucleotides bearing an aliphatic amino group at the C5-position of deoxyuridine (ULNH2TCCCA, TULNH2CCCA, ULNH2CCACTT, where L = -CH2-, -CH2OCH2CH2- or -CH2NHCOCH2CH2-) have been synthesized. The photoactive (p-azidotetrafluorobenzamido, 2-nitro-5-azidobenzamido, or p-azidobenzamido), alkylating [4-[N-(2-chloroethyl)-N-methylamino]benzyl], or intercalating [N-(2-hydroxyethyl)phenazinium] groups were attached to the amino linker of oligonucleotides. The Tm values were determined for the duplexes formed by the above oligonucleotide derivatives. The alkylating group does not change the melting temperature of the corresponding duplex. The duplex stability is increased a little in the case of photoactive groups. The influence of the phenazinium residue on the duplex stability strongly depends on its location in the oligonucleotide. The spacer length between the C5 atom of deoxyuridine and the photoactive or phenazinium group was shown to influence the complementary duplex stability.

[The effect of various substituents, joined through the 5'- and 3'-ends of the primer, initiating properties during the polymerization reaction, catalyzed by AMV-revertase]

We investigated the interaction of AMV reverse transcriptase and Klenow fragment with oligonucleotide derivatives carrying different 3'- or 5'-terminal reactive groups. It was shown that the attachment of phenazinium, ethidium, and daunomycin residues to the 5'-terminal phosphate stabilized the enzyme template primer complexes, while cholesterol and hemin residues generally decreased their stability. The increased stability in solution correlated to a certain extent with the increase in affinity of the modified primers to the enzyme template complex. Coupling of bulky R residues to the primers had a weak effect on the maximal rate of primer conversion, which is likely to be a result of the lack of strong contacts between the substituents and the enzyme, and steric obstacles hindering translocation of the primer enzyme complex. We analyzed the inhibitory effect of 23 oligonucleotide derivatives (both complementary and noncomplementary to the template) with modified 3'- and 5'-ends, and revealed several analogs inhibiting polymerization catalyzed by AMV reverse transcriptase by 70-100% at 0.1-1 microM concentrations of the reagents.

Reversible modification of cysteine residues of NADPH-cytochrome P-450 reductase

A reversible chemical modification of SH-groups of NADPH-cytochrome P-450 reductase is the subject of the present study. The enzyme was modified using first biradical RS-SR (R being the imidazolidine derivative) and a new affinity reductase inhibitor beta-cystamine adenosine diphosphate (ANSSN). These reagents were shown to be covalently bound to reductase SH-groups via the reaction of thiol-disulfide exchange resulting in the loss of reducing activity for cytochrome c. NADP+ protected reductase from inactivation and decreased the extent of the modification by RS-SR. The modification of reductase was reversible: the modified enzyme was partially reactivated with glutathione and dithiothreitol. The method proposed can be used to study both the reductase structure and the reversible inhibition of microsomal monooxygenase systems.

Human immunodeficiency virus type-1 reverse transcriptase copies very short templates: kinetic and crosslinking analysis

We describe in this article some properties concerning the cDNA elongation activity of human immunodeficiency virus type-1 (HIV-1) reverse transcriptase (RT). The kinetic parameters of the polymerization reaction catalyzed by HIV-1 RT, using short templates, were studied. Values of Km and Vmax were measured as a function of the oligoadenylate template length: the logarithm of Km increased linearly, with an incremental factor of 2.2, when the template length differs by one nucleotide. Using short templates, olig(A)n (n = 7-14) and primers shorter or longer than the template, HIV-1 reverse transcriptase was able to synthesize polymer products longer than 200 nucleotides. We showed that an oligonucleotide as short as (pA)3 was long enough to serve as template for cDNA synthesis by RT. In the binding of RT to template of different lengths (5 to 14 nucleotides long), two constants were determined differing in each case by a factor of about 10. The three recombinant forms of HIV-1 RT (p66/p51, p66/p66 and p51/p51) were crosslinked to a short template, (pA)14, in the presence of cis-aquahydroxydiamminoplatinum. The efficiency of crosslink of [32P](pA)14 template with each of the subunits of RT correlated well with the affinity of this template to the different forms of RT. In the case of p66/p51, the crosslink occurred mainly with the p66 subunit. These results confirm the important catalytic role of the p66 subunit in the heterodimeric human retroviral polymerase.

Affinity labeling and functional analysis of the primer binding domain of HIV-1 reverse transcriptase

Six affinity reagents containing chemically reactive groups, either on the phosphate residue at the 5'-end or on the 5'- or 3'-end internucleoside phosphate linkages of the oligothymidylate primers, were used to covalently modify the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). After covalent binding of these modified primer analogs to the enzyme, the addition of [alpha-32P]dTTP, in the presence of a complementary template, led to elongation of the primer. This reaction was catalyzed by the active site of the enzyme carrying the covalently bound primer. The relative efficiency of labeling of the p66/p51 heterodimer compared to the p66/p66 and p51/p51 homodimers of HIV-1 RT was in agreement with the previously determined affinity of the various enzyme forms toward different primers. The analogues preferentially modified the p66 subunit of the HIV-1 RT heterodimer. The labeling of all RT forms by synthetic primer analogues showed significant and specific competition by the natural primer of HIV-1 RT, tRNA(Lys). In addition, the kinetics of inactivation of RT by primer analogues was studied. The affinity of the enzyme to those derivatives in the presence of poly(A) template was about 5-10 times higher than in the absence of template. Moreover, the maximal rates of HIV-1 RT inactivation by analogues in the absence of template were 3-4 times higher. Our results suggest that the mechanism of oligonucleotide primer binding to HIV-1 RT is different in the presence or absence of template.(ABSTRACT TRUNCATED AT 250 WORDS)

Photomodification of RNA and DNA fragments by oligonucleotide reagents bearing arylazide groups

Photomodification of ribo- and deoxyribo-octanucleotides by oligonucleotide reagents (6- and 7-mers) bearing p-azidotetrafluorobenzamido and 2-nitro-5-azidobenzamido groups has been investigated. It is shown that the oligonucleotides with a perfluoroarylazide group were effective modifiers both of deoxyribo- and ribo-targets. Maximum extent of cross-linked product formation (70%) was obtained when the deoxyribo-octanucleotide was modified by a heptanucleotide reagent with a perfluoroarylazide group. Selectivity of the photomodification was also high (50% on the G-residue at a certain position).

Human immunodeficiency virus type 1 reverse transcriptase. Affinity labeling of the primer binding site

Affinity modification of the primer site of HIV1-RT was performed with an oligonucleotide derivative containing a photoreactive azido group at the 5' end of d(pT)10. The affinity of HIV1-RT for d(pT)10 and for its derivative was first estimated by measuring the Michaelis constants of these two oligonucleotides acting as primers in the retrotranscription of poly(rA). The enzyme was then inactivated under UV-irradiation at 303-365 nm in the presence of ArN3-d(U*T9); the dependence of the rate of inactivation on primer concentration was found to be consistent with the Km value. Last, selectivity of affinity modification was demonstrated through elongation of the covalently bound primer and selective protection of inactivation by d(pT)10 or tRNA(Lys).

Functional analysis of primers and templates in the synthesis of DNA catalyzed by human immunodeficiency virus type 1 reverse transcriptase

The kinetics of copying of poly(A).(dT)n, poly(A).(U)n, poly(dA).(dT)n and poly(A).(dT)9-U by reverse transcriptase of human immunodeficiency virus-1 (HIV-1) has been studied and the binding affinity of the enzyme, for template or primer, determined. Short oligonucleotides and dTTP served as primers in the HIV-1 reverse-transcriptase-dependent DNA synthesis. Km and Vmax were measured as functions of the primer chain length; the logarithm of the values of both Km and Vmax increased linearly up to 10. For longer primers (n = 11 to n = 24) the increase of those values changes very little. The enhanced affinity of the primers, (dT)n or (U)n due to the formation of one complementary pair, A.dT, dA.dT, A.U was estimated as a factor of 2. A specific property of HIV-1 reverse transcriptase compared with other DNA polymerases (procaryotes, eucaryotes, other retroviruses and archaebacteria) was its higher affinity to riboprimers as compared to deoxyriboprimers. Relative initial rates when copying poly(A) or poly(dA) templates using different primers and various conditions were compared; the optimal temperature for the reaction of polymerization with poly(A) or poly(dA) templates and (U)10, (dT)10 or (dT)9-U primers was determined. The maximal activity of the enzyme in the case of poly(A) and decanucleotide primers was found at temperatures between 27-31 degrees C. An increase in the primer length results in the stabilization of the template.primer duplex complexed to the enzyme, thus increasing to more than 40 degrees C the optimal temperature of polymerization. The activation energy (Ea) values of the polymerization reaction for different template.primer complexes were evaluated.

[Effective complementarily-addressed photomodification of nucleic acids by oligonucleotide derivatives, containing aromatic azido groups]

Highly effective site-specific photomodification of a DNA-target was carried out with oligonucleotide reagents carrying aromatic azido groups. Oligonucleotide derivatives with a photoactive function R on the 5'-terminal phosphate and at C-5 atom of deoxyuridine were synthesized: R1NH(CH2)3NHpd(TCCACTT) and d(ULNHRCCACTT), where R1 is p-azidotetrafluorobenzoyl, R2 is 2-nitro, 5-azidobenzoyl, R3 is p-azidobenzoyl; LNH = -CH2NH-, -CH2OCH2CH2NH- or -CH2NHCOCH2CH2NH-. The prepared compounds form stable complementary complexes and effect site-specific photomodification of the target DNA. The modification of pentadecanucleotide d(TAAGTGGAGTTTGGC) with the reagents was investigated. Maximum extent of modification strongly depended on the reagent's type, the photoreagent with R1 being the most effective. Whatever the binding site was, this agent provided a 65-70% modification in all cases except LNH = -CH2NH-, when the yield was twice lower. For the reagents bearing R1 the modification sites were identified. Selective modification at the G9 residue was detected in the case of LNH = -CH2OCH2CH2NH- and when a photoactive group was linked to the terminal phosphate.

The affinity of the Klenow fragment of E. coli DNA-polymerase 1 to primers containing bases noncomplementary to the template and hairpin-like elements

The Km and Vmax values for a set of primers: d(pT)n (pC) (pT)m (n = 3-9, m = 0-7) and d(pT)4 (pCpG)k (pT)4 (k = 1-5) have been estimated. Poly(dA) was used as a template. The number of complementary bases from the 3' end to a noncomplementary ones was shown to determine the efficiency of interaction of d(pT)n (pC) (pT)m with the Klenow fragment. Oligonucleotides d(pT)4 (pCpG)k (pT)4, in solution forming duplexes containing hairpin-like elements, show a higher affinity to the enzyme than control d(pT)4, d(pT)8 and d(pT)n (pC) (pT)m primers. For example, the Km value (1.1 nM) for d(pT)4 (pCpG)5 (pT)4 is about 14,000 and 200 times lower than those for d(pT)4 and d(pT)8, respectively. Possible reasons for such an abnormally high affinity of the above primers are discussed.

The mechanism of recognition of templates by DNA polymerases from pro- and eukaryotes as revealed by affinity modification data

Pt(2+)-containing derivatives of oligodeoxyribonucleotides were used to evaluate the ligand affinity to the template sites of Klenow fragment of DNA polymerase I from E. coli and DNA polymerase alpha from human placenta. The values of Kd and Gibb's energy (delta G degree) for the complexes of oligodeoxyribonucleotides and their derivatives with the template sites of these enzymes were determined from the effects protecting the enzyme from inactivation by Pt(2+)-containing oligonucleotides. Kd and delta G degree values of the complexes made by DNA polymerases and orthophosphate, triethylphosphate, d(pC)n, d(pT)n, d(pG)n, d(pA)n (where n = 1-25), heterooligonucleotides of various length and structure, and oligothymidylates with partially and completely ethylated internucleotide phosphates were evaluated. The obtained data enabled us to suggest 19-20 mononucleotide units of the template to interact with the protein. Only one template internucleotide phosphate forms a Me(2+)-dependent electrostatic contact (delta G = -1.1...-1.7 kcal/mol) and a hydrogen bond (delta G = -4.4...-4.9 kcal/mol) with the enzyme. It is likely that the mononucleoside units of the template form hydrophobic contacts with the enzymes. The efficiency of such interaction changes with the hydrophobicity of the bases: C less than T less than G approximately A. For both homo- and heterooligonucleotides the contributions of nucleoside units to the affinity of the templates to the enzymes is due to the complementary interactions with the primers. A hypothetical model for the template-primer interaction with DNA polymerases is suggested.

[Complementary addressed alkylation of 16S rRNA of Escherichia coli by 2',3'-O-[4-N-methyl-N-(2-chloroethyl)-amino]benzylidene derivatives of oligodeoxyribonucleotides. V. Study of the factors affecting selectivity of modification]

We studied the effect of different factors (reagent concentration, temperature, presence of oligonucleotide-effector (3',5'-diphenazinium derivative of oligodeoxyribonucleotide) stabilizing duplex RNA.reagent) on the selectivity of the site-directed modification of 16S rRNA with 2,3'-O-[4-N-methyl-N-(2-chloroethyl)-amino]-benzylidene derivative of oligonucleotide p(dTTTGCTCCCC)rA (reagent I) under conditions of secondary structure stability. The constant of cooperative binding of the reagent and oligonucleotide-effector with 16s rRNA was determined. The temperature rise from 20 to 40 degrees C brought about a 1.5-fold increase in the relative extent of modification at the target site 771-781. In the presence of oligonucleotide-effector, which is a full complementary copy of the 782-789 fragment of 16S rRNA (reagent concentration is 1 x 10(-6) M), the selectivity of the RNA modification at the target site is doubled and a high level of the modification is retained. When the reagent concentration in the reaction mixture was decreased down to 1 x 10(-7) M, the same level of selectivity was achieved without the oligonucleotide-effector. Under these conditions, however, a drastic (20-fold) drop of the level of the 16S rRNA alkylation was observed.

[Reactivity of oligonucleotide derivatives, containing methylphosphonate groups. VI. Increase in the effectiveness of directed action of alkylating derivatives of oligonucleotide methylphosphonate analogs on nucleic acids in the presence of effectors--3',5'-bis-N-(2-hydroxyethyl)-phenazine derivatives of oligonucleotides]

Effectors for increasing the efficiency of DNA modification with the alkylating methylphosphonate analogues of oligodeoxyribonucleotides (MFAO) were suggested. Oligodeoxyribonucleotide d(pC5A8ACAATG) used as a target DNA treated with alkylating derivatives of octathymidylate having alternating methylphosphonate and phosphodiester internucleotide bonds (both Rp- and Sp-individual diastereoisomers of MFAO were used) and bearing alkylating 4-(N-methyl-N-2-chloroethylamino)benzyl phosphoramide residue at the 3'-end. The reactions were carried out in the presence of an effector, hexadeoxyribonucleotide derivative PhnNH(CH2)2NHpCATTGTpNH(CH2)2NHPhn bearing two N-(2-hydroxyethyl)phenazinium (Phn) residues at the 3'- and 5'-ends and being complementary to the part of the target DNA neighbouring with octaadenylate. It was shown that Tm of the duplex formed by the target DNA, octathymidylate and effector is by 7-13 degrees C higher than in the absence of the effector, thus considerably increasing the efficiency of the intracomplex alkylation of the target (e.g., at 40 degrees C, the increase for the reagent based on the Rp-isomer is sixfold). Specificity of the target DNA modification by the MFAO alkylating derivatives in the presence of effector is same as with reagents based on oligodeoxyribonucleotides with natural internucleotide bonds.

Inactivation of DNA polymerase by adenosine 2',3'-riboepoxide 5'-triphosphate allows estimation of the primers affinity

Template-primer dependent inactivation of human DNA polymerase alpha and Klenow fragment of E. coli DNA polymerase I by adenosine 2',3'-riboepoxide 5'-triphosphate was used for quantitative analysis of the Kd values for oligonucleotide primers of different length. The Kd values are smaller by a factor of 2.5 than the Km values for the same primers determined in the reaction of DNA polymerization in the case of DNA polymerase alpha. The Kd and Km values are nearly the same for Klenow fragment. Such approach to the determination of Km/Kd ratio can likely be used for detailed quantitative analysis of DNA polymerases.

[Dependence of 3'-5-exonuclease activity of a fragment of Klenow DNA polymerase I from Escherichia coli on the length and structure of the cleaved oligonucleotide]

The Km and vmax values for oligothymidylates d(pT)2-16 in reaction of 3'-5'-exonuclease hydrolysis catalyzed by Klenow fragment were measured in the absence and presence of poly(dA) template without the poly(dA), the Km values for oligonucleotides are slightly dependent on their length. The rate of oligothymidylates hydrolysis increases with their length and for d(pT)16 it is about 190-times higher than for d(pT)2. The addition on poly(dA) does not lead to an essential change of the Km values for d(pT)2-16, but raises the rate of d(pT)2-7 hydrolysis 2-17-fold and at the same time lowers the efficiency of d(pT)8-16 hydrolysis. The Km values for d(pC)10, d(pA)19 and d(pT)10 are nearly the same. However the velocity of d(pC)10 hydrolysis is approximately 1,2 and 7,8-times higher than for d(pA)10 and d(pC)10, respectively d(pC)10, d(pA)10 and d(pT)10 under conditions of interaction with the template-binding site raise the rate of hydrolysis of d(pT)2 combined with the exonuclease center, with various efficiency. Under similar conditions, d(pT)8, d(pT)10 and d(pT)16 as templates activated hydrolysis of d(pT)2. The dependence of the Klenow fragment exonuclease activity both on the length and structure of the template and on the length of the hydrolyzed oligonucleotide was suggested.

The influence of oligonucleotide-effector on the selectivity of sequence specific modification of 16 S rRNA

The influence of duplex stabilizing oligonucleotide-effector (oligonucleotide, carrying N-(2-hydroxyethyl)phenazinium residues on both ends), on selectivity of site-directed modification of E. coli 16 S rRNA (1542 nucleotides in length) under the conditions of its secondary structure stability was studied. The constant of cooperative binding of the reagent and the oligonucleotide-effector with 16 S rRNA was determined. The accuracy of modification was shown to double in the presence of 50 microM effector at 5 microM concentration of the reagent.

[The effect of bases noncomplementary to the template on the effectiveness of interaction between primers and avian myeloblastosis virus reverse transcriptase]

The comparison of the Km and vmax values for various primers was carried out. The primers were either completely complementary to the poly(A)-template or contained noncomplementary bases in different positions from the 3'-end. An increase of the Km and vmax values for primers containing noncomplementary bases was shown. The affinity of the AMV-revertase complex with poly(A)-template to d(pT)10 was shown to be higher by a factor of 93, 325, 338, 425, 95 and 15 than to d(pT)9(pC), d[(pT)2pC]3pT, d(pT)8pCpT, d(pT)7pC(pT)2, d(pT)4pC(pT)5 and d(pC)3(pT)7, respectively. The vmax values for the above primers were 1.2-1.5-fold higher than for d(pT)10. The decrease of the affinity of noncorrect primers to the enzyme was supposed to serve as a mechanism for mistakes correction when noncomplementary to the template mononucleotide units were added to the primer. More effective discrimination between right and wrong primers takes place if the noncomplementary base is in the second or third position from the 3'-end. The mistake correction is performed by dissociation of a wrong primer from the complexes with the enzyme and template. The data obtained for AMV-revertase are in accord with results for pro- and eukaryotic DNA polymerases and are in favour of a similar mechanism of mistake correction by all enzymes in the case of short primers.

[Complementary addressed alkylation of Escherichia coli 16S rRNA with 2',3'-O-[4-N-methyl-N-(2-chloroethyl)aminobenzylidene]m derivatives of oligodeoxyribonucleotides. IV. Determination of binding sites of 16S rRNA with benzylidene derivatives of d(pACCTTGTT)rA, d(pTTACGACT)rU, d(TTTGCTCCCC)rA]

By site-directed alkylation of 16S rRNA with benzylidene derivatives of d(pACCTTGTT)rA (II), d(pTTACGACT)rU (III), d(pTTTGCTCCCC)rA (IV) (reagents (II)--(IV] followed by the RNase H treatment a number of 16S rRNA fragments have been obtained. Hybridisation of these fragments with restriction fragments of plasmid pKK 3535, containing operon rrnB of E. coli rRNAs, led to the identification of all reagents' binding sites in 16S rRNA. Good correlation is found between estimated stability of non-perfect 16S rRNA.oligodeoxyribonucleotide duplexes and the level of modification of this site with alkylating derivative of the same oligodeoxyribonucleotide. With high concentration of the reagents (II)--(IV) ((2-5) x 10(-5) M) the site-directed alkylation proceeds not only at the desired site but also at other sites corresponding to non-perfect duplexes between 16S rRNA and the reagents. It should be noted that the modification mainly occurs in the non-perfect duplexes, carrying mismatched bases at the termini. Influence of the secondary structure of 16S rRNA on the site-directed modification is discussed.