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The review covers three independent blocks of research. The first one is discovery, isolation, and investigation of snake venom RNases and their use in studying RNA macrostructure. It has been established that snake venom RNases are not specific to the primary RNA structure but rather to the RNA helical conformation (double, single, or hybrid helix). Snake venom RNases hydrolyze RNA to short oligomers with the 5'-terminal phosphate. Analysis of the kinetics and products of tRNA hydrolysis exemplifies the use of snake venom RNases for deciphering RNA macrostructure. The second block is devoted to the principle formulated by the author for analyzing the primary structure of nucleic acids and describes the method of direct RNA sequencing that has been developed with author's participation. The third block describes the results of genotyping and etiologic control of epidemic influenza A viruses circulating in the Soviet Union in 1968 to 1992. The method for comparative analysis of genome sequences of viral isolates has made it possible to detect and characterize epidemic influenza virus strains that had emerged in the circulation as a result of reactivation of inactivated vaccines.

Investigations of the antigenic structure and genome of influenza A (H1N1) viruses isolated in the Mongolian People's Republic in 1982, 1983, 1986 and 1987 from children with acute respiratory diseases using monoclonal antibodies and nucleotide sequencing revealed 4 strains identical to the prototype strain A/PR/8/34 (H1N1), variant M. Sinai, and 8 strains closely similar to the epidemic strain A/USSR/90/77 (H1N1) in the antigenic structure and A/Leningrad/54 (H1N1) in the primary structure of HA.

In an attempt to develop a reliable system for DNA sequence analysis with multiple hybridization probes, oligonucleotides down to 8 bases long were covalently immobilized in a thin layer of polyacrylamide gel fixed on a glass plate. It was shown possible to detect single base changes in DNA by hybridization of the immobilized oligonucleotides with radioactively and fluorescently labeled DNA fragments. Moreover, it was found that dissociation temperatures of differently GC-rich duplexes could be equalized by appropriate choice of immobilized oligonucleotides concentrations. A model accounting for this phenomenon is presented. In order to make the system more compact, a rectangular matrix of 200 mm dots of immobilized oligonucleotides ("hybridization chip") was designed which offered the sensitivity of 20 attomoles per dot for fluorescent DNA fragment. The applications and perspectives of the approach are discussed.

A new technique of DNA sequencing by hybridization with oligonucleotide matrix (SHOM) which could also be applied for DNA mapping and fingerprinting, mutant diagnostics, etc., has been tested in model experiments. A dot matrix was prepared which contained 9 overlapping octanucleotides (8-mers) complementary to a common 17-mer. Each of the 8-mers was immobilized as individual dot in thin layer of polyacrylamide gel fixed on a glass plate. The matrix was hybridized with the 32P-labeled 17-mer and three other 17-mers differing from the first one by a single base change. The hybridization enabled us to distinguish perfect duplexes from those containing mismatches in 32 out of 35 cases. These results are discussed with respect to the applicability of the approach for sequencing. It was shown that hybridization of DNA with an immobilized 8-mer in the presence of a labeled 5-mer led to the formation of a stable duplex with the 5-mer only if the 5- and the 8-mers were in continuous stacking making a perfect nicked duplex 13 (5+8) base pairs long. These experiments and computer simulations suggest that continuous stacking hybridization may increase the efficiency of sequencing so that random or natural coding DNA fragments about 1000 bases long could be sequenced in more than 97% of cases. Miniaturized matrices or sequencing chips were designed, where oligonucleotides were immobilized within 100 x 100 micron dots disposed at 100 micron intervals. Hybridization of fluorescently labeled DNA fragments with microchips may simplify sequencing and ensure sensitivity of at least 10 attomoles per dot. The perspectives and limitations of SHOM are discussed.

The authors own results on the variety of the genomic primary structures in human influenza A viruses participating in the epidemic process, including the atypical viruses. The comparative studies revealed new trends in the HA gene antigenic drift on the late stages and the PB1 gene shift. Modifications occurring in the primary structure of the influenza A viruses native genomes during laboratory treatment (adaptation to new hosts, vaccine preparation, egg passaging) have been analyzed. Sequencing of several types of "antigenic anachronisms" revealed the direct links between some of such viruses and the anthropogenic pollution of the biosphere by vaccine strains. Modifications in the HA genes of influenza A viruses during the persistent infection have also been studied.

A molecular analysis was made of genomes of influenza A (H1N1) virus strains, the causative agents of an epidemic in Leningrad, 1986. The primary structure of hemagglutinin gene of two of these strains, A/Leningrad/624/86 and A/Leningrad/621/86, was established, as well as partial primary structure of PB1 gene of certain current strains of the A (H1N1) subtype. A hypothesis of a "shift" of PB1 gene in 1950-1957 is suggested.

The hemagglutinin gene primary structure of influenza virus A/Riga/9977/86 (H3N2) belonging to the "Coen/84" antigenic subgroup was determined by primer sequencing. A comparative analysis confirmed that the reversions of amino acids in the late stages of the H3 influenza virus subtype antigenic drift became more frequent and the antigenic variants remained in epidemic circulation longer. The possible role of some mutations is discussed.

Electrophoresis in polyacrylamide gel of the reference influenza A/Victoria/35/72 (H3N2) virus and its persisting variants (PV) showed that the PV isolated on the 158th day from the moment of persistence modelling (PV158) had mutation in the gene of hemagglutinin (HA). This mutation is manifested by incomplete HA synthesis at 40 degrees C and increase of mobility of the light HA subunit (HA2). Analysis of nucleotide sequence of the greater part of HA gene of PV158 virus revealed 5 nucleotide substitutions four of which were significant. Three substitutions were found in Hal: 219 (Ser----Phe), 220 (Arg----Gly), 226 (Leu----Gln) and one in HA2: 156 (Thr----Asn). The importance of these mutations in the determination of the PV phenotype is discussed.

The composition of polyuridilic acid hydrolisis products with mol. weight 400.000--600.000 by endoribonuclease from cobra venom was studied. The molecular weight distribution of products formed at initial stages of hydrolysis was according to the regularities of accidental cleavage of phosphodiether linkages. The sufficient non-statistic regularities due to the high-molecular polynucleotide hydrolysis for the most part during further hydrolysis were observed out of the way of accumulation of oligonucleotides with a polymerity degree of about 15--20. As shown from the oligocytidilates hydrolysis, the velocity of process increased sufficiently with increasing substrate polymerity degree. The results obtained were used for preparation of polyuridilic fractions with a narrow range of molecular weight distribution.

The complete nucleotide sequence of the cloned full-length DNA copy of the influenza virus A/Kiev/59/79 (H1N1) neuraminidase gene has been determined. The comparison with the other neuraminidases reveals the differences in localization of antigenic determinants between N1 and N2 subtypes and divarication of evolutionary pathways of the modern H1N1-influenza viruses.

An analysis of kinetic differences in homopolyribonucleotides hydrolysis by cobra venom endoribonuclease was carried out. It was concluded that the rate and intensity of hydrolysis as well as the length of the linear parts of the kinetic curves are correlated with the content of the nucleotide units with the C3'-endo conformation in the substrates. The structure factor was shown to predominate in some cases over the temperature factor. Protamine sulfate inhibits the enzyme by blocking its phosphodiether bonds. Study on the effects of divalent metal ions demonstrated the possibility that the enzyme-Me2+ complex is functionally active and that the ion-free polyribonucleotides are true substrates.

The primary structure of hemagglutinin (HA) gene of Influenza virus A/USSR/90/77 (H1N1) variants after 3 and 11 passages has been determined. In the HA1 coding region of mice-adapted virus (11 passages) there are two amino acid substitutions: Thr 89----Ala and Asn 127----Asp. At the first stage of adaptation (3-rd passage) only a single mutation was detected: Asn 127----Asp. The adaptation is accompanied by the loss of specific carbohydrate attachment sites adjacent to the receptor-binding site located at HA1 subunit with a concomitant variation in antigenicity.

Reverse transcription afforded DNA-copies of the 3'-terminal sequence of mouse encephalomyocarditis virus RNA. Cloning of this cDNA in pBR 322 plasmid and sequencing of DNA of one of the clones established the structure (552 nucleotide residues) of the 3'-terminus of viral RNA. This region contains a non-translatable fragment (126 nucleotides) and also the fragment coding for the C-terminus of viral replicase.

Human placenta RNase inhibitor has been shown to suppress the interfering ribonucleases, virtually not affecting the RNase H activity. This allows the usage of the inhibitor in the course of site-specific cleavage of high molecular weight RNAs by ribonuclease H.

The genome of hepatitis A virus (HAV) isolated from spontaneously infected African vervet monkey (Cercopithecus aethiops) has been cloned and partially sequenced. Comparison of genome fragments (1248 and 162 bp) from the 3D (RNA polymerase) region with the corresponding parts of human HAV genomes revealed a high degree of heterogeneity: there were altogether 257 nucleotide changes leading to 44 substitutions in predicted amino acid sequence, i.e. 89% amino acid identity. This divergence is considered to be significantly greater than genomic variations usually found among human HAV strains, where amino acid identity in the 3D region is over 98%.

The complete nucleotide sequence of the cloned full-length DNA copy of A/Kiev/59/79 (H1N1) influenza virus hemagglutinin gene has been determined. The comparison with the other hemagglutinin structures reveals the divarication of evolutionary pathway of the H1N1-influenza viruses.

The binding has been studied of Escherichia coli RNA-polymerase to the fragments of lambda DNA obtained by digestion with restriction endonucleases BsuI, HindIII, BamHI, EcoRI and HindII + III. There are at least six sites of RNA-polymerase binding in the b2-region. In vitro transcription of those BsuI-fragments of the b2-region which contain six binding sites is rightward. Therefore, the fragments contain promoters rather than mere RNA-polymerase binding sites. One of the promoters of the b2 region named patt was calculated to be about 50 bp to the left of the att site. We postulate that this promoter might correspond to the hef-target which was described as important for the site-specific recombination.

The complete nucleotide sequence of the cloned full-length DNA copy of A/Kiev/59/79 (H1N1) influenza virus nucleoprotein gene has been determined. This strain is shown to be the natural recombinant that inherited its nucleoprotein gene from contemporary H3N2-influenza strains. The comparison with other NP-genes reveals the probable localization of antigenic determinants and phosphorylation site of the NP-protein.

The accessibility of single-stranded sequences in 16S RNA in free state and in ribonucleoprotein particles (RNP) to complementary binding with isoplith fractions of oligonucleotides was studied. RNP had different protein composition and corresponded to intermediate stages of E. coli 30S subunit assembly in vitro. Gel-filtration was used to detect the most strong binding. It was found that S4 essentially inhibited the hexamer binding to RNA. 'Core' proteins bound to 16S RNA strongly increased the shielding of single-stranded regions while 'split' proteins insignificantly changed the hexamer binding. Nevertheless evidence is presented that 'split' proteins might also interact directly with 16S RNA in the 30S subunit.

RNA polymerase of E. coli (EC 2.7.7.6) is able to bind certain oligoribonucleotides with the length greater than or equal to 5 from the corresponding isoplith mixtures (Knorre V.L., Vasilenko S.V., Salganik R.I., FEBS Letters 30, 229, 1973). It has been shown in this study that all pentaribonucleotides able to be bound by RNA polymerase can be extracted from the random mixture by the enzyme saturation procedure. Loosely and tightly bound pentaribonucleotides subfractions were isolated and each was separated by chromatography into 3-4 isopliths. Blocking of the enzyme SH groups by p-chloromercurium benzoate (10(-3) M) and denaturation by urea (6.3 M) prevent formation of the enzyme-pentaribonucleotides complexes. Complexes are destroyed by heat denaturation. Removal of sigma-subunit does not influence the enzyme capacity for pentaribonucleotides binding.

An evolutional tree of human influenza viruses of the H3N2-subtype is suggested on the basis of combined published primary structures of the hemagglutinin HA1-subunit. Possible differences between natural and sequenced structures are discussed. A tendency to reversions in the course of antigenic draft within the subtype has been revealed to support the hypothesis of limited antigenic evolution within a single subtype.

The DNA-copy of the major antigen (VP1) coding region of the FMDV A22 sero-type has been cloned and sequenced. A comparison of the respective amino acid sequence with those of other VP1 of A-serotype revealed considerable differences in the structure of antigenic determinants.

Complete nucleotide sequence of the cloned full-length DNA copy of the influenza virus A (H1N1) neuraminidase gene has been determined. The predicted amino acid sequence is compared with sequences of neuraminidases from other influenza virus strains. A section of the neuraminidase is found to be homologous to the chicken lysozyme catalytic centre.

Dialysis, gel-chromatography on Sephadex G-75 (superfine) and chromatography on sulphoethylcellulose give high yield (68 per cent) of 162-fold purified ribonuclease from cobra venom. In ion-exchange chromatography, ribonuclease is eluted in two fractions. The fraction with the highest specific activity has a molecular weight of 15900 and is homogeneous in 15 per cent polyacrilamide gel electrophoresis at pH 8.9. Electrophoresis at pH 4.3 reveals a minor fast component of this fraction which also exhibits a ribonuclease activity. Sulphoethylcellulose chromatography fairly separates cobra venom phosphodiesterase and 5'-nucleotidase eluted as a single fraction in gel chromatography.

Complete nucleotide sequence of the cloned full-length DNA copy of the influenza virus A (H1N1) RNA segment 8 has been determined. A section of the hypothetical protein coded for by the negative strand of the segment 8 is found to be homologous to the trypsin catalytic centre.

Cobra (Naja oxiana) venom ribonuclease, which catalyses hydrolysis of polyribonucleotides to 5'-oligonucleotides, was used to obtain preparatively isoplit oligonucleotide fractions, containing 2-30 nucleotides. The yield of hydrolysis products varied depending on the degree of hydrolysis. Hydrolysis rates of different polynucleotides were studied. Hydrolysis rate of polyadenylic acid was 20 times as high as that for polyuridylic acid. Quantitative ratios of isoplit fractions did not vary significantly under similar degree of hydrolysis of polyadenylic and polyuridilic acids. Chromatography on QAE-Sepahdex in ammonium bicarbonate concentration gradient containing 15% dioxan was used to separate enzymatic hydrolysates of polynucleotides, which permitted to bring the fraction isolation to simple evaporation.

The nucleotide sequence of the cDNA for the viral RNA region coding for the main antigenic protein of the epidemic stomatitis virus of Asia 1 serotype has been identified. The amino acid sequences in the regions of VP1 protein antigenic determinants of the serotype Asia 1 virus and other serotypes viruses have been compared.

The sequence analysis of HA gene of passaged variants of A/USSR/2/85 influenza virus was carried out. It was shown that in the process of passage of virus in chick embryos the structure of HA gene was not changed. These data correlated with those obtained early during investigation of A/Leningrad/337/76 influenza virus by the oligonucleotide mapping.

Complete nucleotide sequence of the cloned full-length DNA copy of the influenza virus A (H1N1) RNA segment 5 has been determined. The degree of nucleotide difference between two variants of A/PR/8/34 strain is estimated. The possible secondary structure of the segment 5 is deduced from the nucleotide sequence of some clones.

Full-length DNA-copy of hemagglutinin gene RNA of influenza A virus strain A/Leningrad/54/1 was synthesized and cloned in E. coli plasmid pBR 327. Its primary structure was determined by a modified Maxam - Gilbert procedure. The nucleotide sequence of this gene was compared with sequences of analogous genes of influenza strains A/USSR/90/77 and A/PR/8/34. An addition of one nucleotide in non-translated region was found in the former.

Nucleotide sequence of the A/Kiev/59/79 influenza virus PB1 gene is reported, thus completing the full-genome primary structure of the recombinant between the virus and laboratory strain A/PR/8/34. The parental strain A/Kiev/59/79 (H1N1) is, in turn, shown to be a natural reassortant inheriting its genes of polymerase complex (PB1, PB2, NP and, in all probability, PA) from contemporary H3N2 influenza virus strains.

The kinetics of the reaction of periodate oxidized oligonucleotides with polyacrylhydrazide gel was studied. The rate of the reaction is proportional to (see article), where M is the molecular weight of the oligonucleotide for the permeable gels. The rate of the reaction with given oligonucleotide decrease as the number of crosslinks in the gel matrix increase; a dramatic decrease of the rate occurs when oligonucleotides become too large to penetrate into the matrix. The rate of the reactions with short oligonucleotides does not depend upon the viscosity of the medium. ESR method revealed a considerable decrease of the rotational mobility of oligonucleotides captured by the gel matrix. It has been shown also that an increase of the number of cross-links leads to a decrease of the rotational mobility of the gel chains.