[Photoactivated analogues of the initiating substrates of RNA polymerase II based on arylazide derivatives of NTP gamma-amidophosphate: synthesis and chemical and photochemical reactions of functional groups].

Photoactivatable derivatives Ar-NH-(CH2)n-NHpppB (where Ar = p-azidophenyl (A1), 5-azido-2-nitrobenzoyl (A2), or 4-azido-2,3,5,6-tetrafluorobenzoyl (A3) group; B = Ado or Guo; n = 2, 3, or 4) were synthesized. The phosphoroamidate bond stability was found to depend on the structure of both the heterocyclic and the photoactivatable groups. The derivative with A3, Ado, and n=3 is hydrolyzed with regeneration of aryl azide and ATP, whereas the other derivatives are stable in aqueous solutions. The photoanalogues with A1 and A2, B = Ado, and n = 2 or 4 were found to behave as initiating substrates toward the RNA polymerase II from Saccharomyces cerevisiae under the conditions of specific transcription initiation and control of the adenovirus late promoter. The photolysis of N-(4-azidophenyl)-1,4-diaminobutane and N-(5-azido-2-nitrobenzoyl)-1,3-diaminopropane, two functional fragments of the photoaffinity reagents, in aqueous solutions was established to result in the formation of p-benzoquinone diimine and p-nitro-N-arylhydroxylamine derivatives, respectively. The arylhydroxylamine derivatives undergo a number of transformations in aqueous solution leading to nitroso derivatives. We concluded that it is these nitroso derivatives (products of nitrene transformation, rather than the nitrene itself) that may modify proteins with reagents containing p-nitrophenylazide fragment.

Photoaffinity labeling as an approach to study supramolecular nucleoprotein complexes.

The modern approaches for studying the detailed structure of nucleoprotein complexes involved in replication and transcription, based on the use of nucleic acids with photoreactive groups incorporated into definite positions of polynucleotide chain, are considered. Methods of preparation of photoreactive nucleic acids of this type are presented. Their use for positioning of RNA polymerase III and transcription factors as well as of the main participants of the replication machinery at the respective templates is described. A survey of the data concerning the amino acid residues modified in the course of photoaffinity labeling of proteins is also presented and some complications are discussed.

Direct cleavage of a DNA fragment by a bleomycin-oligonucleotide derivative.

Bleomycin A5 oligonucleotide derivative was used for direct cleavage of a DNA target. In the presence of Fe2+ ions and 2-mercaptoethanol, Blm-R-pd(CCAAACA) (I) damaged the target. pd(TGTTTGGCGAAGGA), with the yield of 80% , without affecting its own oligonucleotide tail. The sites of cleavage were T3-T5 and G6-G7. Unbound bleomycin A5 damaged the G6-G7-C8 site. Reagent I formed more stable complementary complexes with the target than parent oligonucleotide (ATm = 11 C).

Dynamic aspects of affinity labelling as revealed by alkylation and phosphorylation of pancreatic ribonuclease with reactive deoxyribodinucleotide derivatives.

Affinity labelling of pancreatic RNase with 4-(N-2-chloroethyl-N-methylamino)benzylamide and (N----P) N-methylimidazolide of d(pTpA) results in the formation of monomodified enzyme derivatives retaining partially enzymatic activity. These data together with some cases described in the literature are considered as suggesting the dynamic nature of the enzyme-reagent complex represented by a set of states differing in the probability of intra-complex reaction. In particular, modification may proceed in a low probability state with an especially favorable mutual orientation of reagent and some protein residue remote from the active site of the enzyme resulting in the removal of the covalently attached reagent moiety from the active center.

5'-derivatives of oligonucleotides as primers of DNA polymerization catalyzed by AMV reverse transcriptase and Klenow fragment of DNA polymerase 1.

The Km and Vmax values for d(pT)8 and its derivatives containing various 5'-end groups were estimated in the reaction of polymerization catalyzed with AMV-RT and FK. The change in affinity of modified primers was more pronounced in the case of AMV-RT than in the case of FK. Introducing in d(pT)8 of intercalators such as phenazinium, ethidium and daunomycin residues results in 2.7-, 8.7- and 11-fold increases in the primer affinity to AMV-RT, respectively. However, in the case of hemin and cholesterol derivatives the Km values were 3 and 5 times higher than those for d(pT)8. Compared to d(pT)8, the affinity of FK to all the above analogs was 2.3-3.6 times higher with the exception of cholesterol derivative to which it was 2.4-fold lower. The effect of the 5'-end residues on the Vmax values of d(pT)8 was small and ranged from 44% to 120% of that for d(pT)8. Therefore such reactive derivatives of oligonucleotides can be used as effective primers of AMV-RT and FK. Possible reasons for various effects of the 5'-end residues of the primer on its interaction with FK or AMV-RT in the presence of poly(A) are discussed.

Hydroxyl radical generation by oligonucleotide derivatives of anthracycline antibiotic and synthetic quinone.

For the first time the covalent binding of anticancer anthracycline drugs and their potential synthetic analogs to oligonucleotides of different sequences is proposed for obtaining site-specific DNA scission in systems in vitro and in vivo. New compounds such as daunomycin (Dm) and synthetic naphthoquinone (NQ), covalently bound to the heptadeoxynucleotide of pCCAAACA (Dm-pN7) and decadeoxythymidilate (pT10p-NQ), have been obtained. These oligonucleotide derivatives can form specific complexes with complementary oligonucleotide sequences; these compounds and their complementary complexes can be reduced by purified NADPH-cytochrome P-450 reductase. Using the spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO), it has been shown that in aerobic conditions Dm-pN7 and pT10p-NQ are capable of generating OH radicals with and without complementary oligonucleotides. The chemical stability of the compounds in redox reactions has been studied. Oligonucleotide derivatives of natural and synthetic quinones capable of generating OH radicals seem to be a promising tool for site-specific scission of DNA in solution and in cells.

Study of the chemical structures of the photo-cross-linking products between Tyr and the 5-azido-2-nitrobenzoyl residue.

Irradiation of N-(tyrosyl)-N'-(5-azido-2-nitrobenzoyl)-1,2-diaminoethane (I) initiates chemical reactions that lead to different products depending on the experimental conditions. All of these products are attributed to the reactions of triplet 4-nitrobenzoyl nitrene (4NBN). The reactions of triplet 4NBN with the tyrosyl residue result in the formation of two distinct products: compound II, which is unstable in aqueous solution, and the stable compound cyclo-[1-(4'-nitro-3'-benzoyl)-2-(aminotyrosyl)-N,N'-ethylenediami ne] (III). The formation of II is detected only in aerobic conditions. The unstable photoproduct II converts almost completely into compound III when its solution is concentrated. The photoproducts II and III have absorption spectra that are close to those of the photolabelled peptides. This finding is important for speculating about the chemical nature of the photomodification products of protein tyrosyl residues by the arylazide group.

p-Azidophenyl phosphate is a photoactivatable phosphorylating reagent and p-benzoquinone monoimine precursor.

p-Azidophenyl phosphate (I) has been exposed to ultraviolet light (lambda=313 nm) in aqueous solution with or without Lys. Analysis of the photoproducts by means of UV-VIS, IR, (1)H, (13)C and (31)P NMR spectroscopy has revealed that under irradiation of I inorganic phosphate (P(i)) is released, and p-benzoquinone monoimine (II) and p-benzoquinone (III) have appeared. The electrophilic nature of the intermediate results in a high tendency to react with lysine molecules, whereas the reaction with water is less favourable when I is irradiated in the presence of Lys. The product formed in this case is a phosphoramidate whose structure has been tentatively supported by (31)P NMR spectroscopy. These results imply that a p-azidophenyl phosphate is a highly potent aryl nitrene-precursor, which can be transformed easily into p-benzoquinone monoimine and is able to phosphorylate nucleophilic groups of amino acids. This finding is of great importance for the discussions about the chemical nature of protein photomodification products when p-azidophenyl phosphate derivatives are used as modifying reagents.

Long-lived reactive intermediate photogenerated from N-(5-azido-2-nitrobenzoyl)-N'-(D-biotinyl)-1,2-diaminoethane as an affinity reagent to streptavidin.

Irradiation of a complex between N-(5-azido-2-nitrobenzoyl)-N'-(D-biotinyl)-1,2-diaminoethane (I) and streptavidin with light of 313 nm led to the covalent attachment of the photobiotin analogue I to the protein. Streptavidin could also be labelled in the dark with prephotolyzed I. These results indicate that a long-lived reactive intermediate was formed upon irradiation. Moreover, after cleavage of labelled streptavidin with proteinase K this intermediate appears to be covalently attached to the same peptide as the one obtained by direct photoaffinity labelling. An iminosulfurane II derived from the reaction of biotin sulfur atom with aryl nitrene is responsible for the dark-labelling reaction. The photoproduct II converts in an aqueous solution almost completely into N-(5-amino-2-nitrobenzoyl)-N'-(D-(S-oxo)biotinyl)-1,2-diaminoethane (the half-life of II is 10 days).

Photoanalogues of the initiation substrates of the RNA polymerase II, 5-azido-2-nitrobenzoyl derivatives of the ATP gamma-amidophosphate: the possible photoinduced degradation of the functional group to an N-arylhydroxylamine.

Photoanlogues of the initiation substrates of the RNA polymerase II, N3ArNH(CH2)(n)NHpppA where N3Ar is 5-azido-2-nitrobenzoyl group (n = 2 or 4) were synthesized, allowing the preparation of photoreactive oligonucleotides in situ by RNA polymerase II for application as photolabels. Photolysis of p-nitro-substituted aromatic azide in aqueous medium was investigated. Using the azoxy-coupling reaction it was possible to determine whether a nitrene or p-nitrophenyl hydroxylamine azoxy compound is the trappable intermediate that is generated at ambient temperature in aqueous solution.

[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]. / Vliianie razlichnykh zamestitelei, prisoedinennykh po 5'- i 3'-kontsampraimera, na ego initsiiruiushchie svoistva v reaktsii polimerizatsii, kataliziruemoi AMV-revertazoi.

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.

[Direct breaks in a single-stranded DNA fragment by a bleomycin-derived oligonucleotide]. / Priamye razryvy odnotsepochechnogo fragmenta DNK bleomitsinovym proizvodnym oligonukleotida.

A method for coupling bleomycin to oligonucleotides is suggested. The reaction was carried out between the amino group of the spermidine residue of the bleomycin A5 Cu(II)-complex (Cu(II)Blm-RH) and the 5'-phosphate group of the oligonucleotide pd(CCAAACA) (I) activated with a mixture of triphenylphosphine and 2,2'-dipyridyldisulphide in the presence of 4-N,N-dimethylaminopyridine-1-oxide. The resultant compound (Ia) (yield 70%) forms more stable complementary complexes than the parent oligonucleotide (delta Tm = 11 degrees C). When Cu(II) ion was removed from (Ia), compound (Ib) formed which effectively (80%) cleaved pd(TGTTTGGCGAAGGA). Neither pd(TCCTTCG) nor the oligonucleotide tail of the reagent (Ib) were destroyed under the cleavage conditions. Free Blm-RH and bleomycin bound in the reagent (Ib) damage different regions of the target.

[Cleavage of a double-stranded DNA target by bleomycin derivatives of oligonucleotides, forming a ternary complex]. / Rasshcheplenie dvukhtsepochechnoi DNK-misheni bleomitsinovymi proizvodnymi oligonukleotidov, obrazuiushchimi troinoi kompleks.

Hexadecathymidylate derivatives, containing covalently-bound antitumor antibiotic bleomycin A5, were shown to form a triple-helix complex with double-strand 30-bp DNA-target and to carry out within this complex complementary-addressed DNA modification. Fivefold excess of reagent in relation to target leads to non-specific cleavage mainly of pyrimidine-rich DNA strand. Total degrees of the target-strand cleavage by 5'- and 3'-bleomycin derivatives of hexadecathymidylate were 25 and 35% for purine-rich strand and 47 and 36% for pyrimidine-rich strand. Degrees of non-specific cleavage by 5'-bleomycin derivative of hexadecanucleotide that does not form triple-helix were 6 and 16% for purine- and pyrimidine-rich strands, respectively. Comparison of these data has shown that site-specific cleavage prevailed nonspecific one. Triplex of 5'-bleomycin derivative with DNA melted by 5 degrees C lower (m.p. 40 degrees C) than the similar triplex of hexadecathymidylate. Temperature lowering from 50 to 20 degrees C increases the DNA-cleavage degree according to the increase in the part of target molecules involved in triple-helix formation.

[Photoaffinity modification of amino acid derivatives of oligonucleotides in a complementary complex]. / Fotoaffinnaia modifikatsiia aminokislotnykh proizvodnykh oligonukleotidov v komplementarnom komplekse.

Intracomplex photochemical interaction of photoactive derivatives R-CONH(CH2)3NH-pGATACCAA, where R= p-azidotetrafluorophenyl (I) or 2-nitro-5-azidophenyl (II), and 5'-phospho-p-azidoanilide pGATACCAA (III) with a target - oligonucleotide *pGGTATCp (IV) and its derivatives *pGGTATCp-NH(CH2)3NHX, where X = H (V), Phe (VI), or Lys (VII), was studied. According to electrophoretic data, photoreagent (I) gives rise to a covalent photoadduct with compound (IV) as well as with derivatives (VI) and (VII). In the case of reagent (II), only targets (V) - (VII) including aliphatic amino groups participate in the photocoupling. Upon irradiation of the duplexes comprising photoreagent (III) and targets (V)-(VII), the process is accompanied by the cleavage of the reagent's oligonucleotide moiety off the photomodification product. A plausible mechanism of the cleavage is discussed.

[Catalytic cleavage of target DNA in a complementary complex by a bleomycin oligonucleotide derivative]. / Kataliticheskoe rasshcheplenie DNK-misheni bleomitsinovym proizvodmym oligonukleotida v sostave komplementarnogo kompleksa.

For the first time, reagents that are capable of catalytic site-specific cleavage of DNA were synthesized based on oligonucleotides. One molecule of reagent (Blm-R)pd(CCAAACA) containing bleomycin A5 residue (Blm-RH) could degrade three molecules of target DNA pd(TGTTTGGCGAAGGA). The reagent displayed maximum catalytic activity in a temperature range that was close to the melting temperature of the reagent-target DNA complex. The number of the target DNA molecules that could be degraded by the reagent was limited by the degradation of the antibiotic residue itself during the oxidative degradation of the target DNA. The reagent catalyzed the subsequent degradation of residues G7, T5, T4, and T3 of the target DNA at an equimolar reagent-target DNA ratio. When the tenfold excess of the target DNA was used, the reagent degraded primarily the single G7 residue of the target DNA by 30%.

[Active derivatives of oligonucleotides with a zwitterionic terminal phosphate group for design of affinity reagents and probes]. / Aktivnye proizvodnye oligonukleotidov s tsvitter-ionnoi kontsevoi fosfatnoi gruppoi dlia konstruirovaniia affinnykh reagentov i zondov.

Method of synthesis and isolation of oligonucleotide derivatives with a zwitterionic terminal phosphate group, containing N-methylimidazole (MeIm), 4-dimethylaminopyridine (DMAP) or 4-dimethylaminopyridine 1-oxide (DMAPO) residues has been developed. Mononucleotide derivatives were used to study the reactivity of these compounds to various nucleophiles and the dependence of hydrolysis rate on pH of solution. These compounds interact rapidly and quantitatively with aliphatic amines and much slower with water, aniline and methanol. MeIm derivatives are most active to nucleophiles, whereas the reactivity of DMAP derivatives is ca. 5 times lower and that of DMAPO derivatives is lower by 2 order of magnitude. This method of activating terminal phosphate group is promising for synthesis of various oligonucleotide phosphoramidates.

[Synthesis, structure and properties of rubomycin derivatives of mono- and oligonucleotides]. / Sintez, struktura i svoistva rubomitsinovykh proizvodnykh mono- i oligonukleotidov.

Daunomycin derivatives of pT(DT) and oligodeoxynucleotides were synthesized using reactive zwitter-ionic 4-N,N-dimethylaminopyridine derivatives of the terminal phosphate group. Daunomycin oligodeoxynucleotide analogues form more stable complementary complexes than the corresponding non-modified oligonucleotides. Both one- and two-dimensional (2D NOESY and 2D COSY) NMR spectra of DT were recorded and the proton signals assigned. From the detected cross-relaxation between H6 of thymidine and H1', H2', H2" of the carbohydrate residue of daunomycin it was concluded that, in DMSO, the DT molecule has a rather stable conformation, apparently due to the stacking interaction between the mononucleotide and daunomycin residues.

[New approach to the study of interaction of amino acid side groups with aryl azides]. / Novyi podkhod k izucheniiu vzaimodeistviia aminokislot po ikh bokovym radikalam s arilazidami.

A new approach to the study of the interaction of amino acid side chains with photoreactive aryl azides was proposed. This approach was based on the drawing together of the reacting groups by the attachment of the reacting compounds to complementary oligonucleotides. Cystamine, histamine, and 1,6-hexamethylenediamine mimicking the cystine, histidine, and lysine residues, respectively, were attached to the 3'-terminal phosphate of the oligonucleotide GGTATCp through a phosphamide bond and used as the targets for photomodification. Derivatives of the oligonucleotide pGATACCAA with the fragment N3C6H4NH- attached directly to its 5'-end by a phosphamide bond or through the spacer -(CH2)nNH- (where n is 2, 4, and 6) were used as photoreagents. Their derivatives containing the same spacer and the N3C6F4CO-NH(CH2)3NH- or 2-N3,5-NO2-C6H3CO-NH(CH2)3NH- residues were also used. The duplexes were photomodified by irradiation with 300-350 nm wavelength light. The maximal yields of the photo-cross-linking were from 22 to 68%. The reagents containing p-azidoaniline residue were found to be the most effective toward the targets. The maximum yields of the photomodification products modeling the side chains of cysteine and lysine were found to vary from 40 to 67% and to depend on the length and the structure of the spacers used. The duplex with the target bearing the imidazole residue (the histidine model) manifested a yield decreased to 25%. This fact was in a good agreement with the data of computer modeling that indicated an unfavorable mutual displacement of the imidazole residue and the photoreactive group.

[Highly-sensitive nonradioactive detection of the tick-borne encephalitis virus]. / Vysokochuvstvitel'naia neradioaktivnaia detektsiia virusa kleshchevogo éntsefalita.

The non-radioactive reverse dot-blot method was used for the detection of tick-borne encephalitis virus (TBEV) in clinical specimens. The method involves reverse transcription (RT) and polymerase chain reaction (PCR) using a pair of biotin-labelled oligonucleotide primers. These primers flank a region in the gene of the envelope protein E, which is more conserved than other regions, and initiate the polymerisation with RNAs of all the investigated strains. The amplified cDNA was captured from solution on a solid support using complementary oligonucleotides covalently bound to a polyamide membrane. The biotin labels of the resulting hybrids were visualized by means of the streptavidin-horseradish peroxidase conjugate. The detection limit of the test was about 10(3)-10(4) molecules of target RNA. The sensitivity was comparable to that obtained by dot-hybridization of PCR-product with 32P-labelled DNA probe. The method was used for the detection of RNA in specimens of tick and blood.

[Use of photo-anchoring of DNA probes for fluorescent in situ hybridization]. / Ispol'zovanie fotoprishivaemykh DNK-zondov dlia fluorestsentnoi gibridizatsii in situ.

A possibility was investigated to use photo-crosslinking DNA probes for fluorescent in situ hybridization (FISH). DNA probes were modified by incorporating photonucleotides in these, containing a photoreactive group (tetrafluorobenzazid) and capable of making covalent bonds with the examined DNA, when irradiated in 300-330 nm region. The photonucleotide was incorporated into the probe either by nick-translation, or upon elongation of the hybridized probe by the Kljonow fragment. It has been shown that the DNA probe, cross-linking to a chromosome as a result of covalent bonds, is not removed from the place of hybridization under consequent denaturating washing, which makes it possible to carry out the following DNA hybridization with selective conservation of signals obtained due to previous hybridization. This peculiarity of photo-linking DNA probes makes it possible to use them for the two-step DNA hybridization. To demonstrate this, preparations of human chromosomes were investigated. On the first step, chromosomal DNA was hybridized by means of DNA probe having nucleotide sequences of centromeric regions of chromosomes 13 and 21, the probe being linked to chromosomal DNA by the photonucleotide. Following the denaturation treatment of the preparation, and after the second chromosomal DNA hybridization with cosmid DNA, containing chromosome 13 DNA nucleotide sequence, the signal in chromosome 13 centromeric region was retained to serve a marker of this chromosome, thus fascilitating its easier identification following the hybridization of its DNA with cosmic DNA. The denaturation stability of photo-crosslinking probes opens some new possibilities in technology of DNA in situ hybridization.