n-Decyl-NHpppA2'p5'A2'p5'A A phosphatase-resistant, active pppA2'p5'A2'p5'A analog

n-Decyl-NHpppA2'p5'A2'p5'A, a gamma-substituted, phosphatase-resistant pppA2'p5'A2'p5'A analog, gives similar rRNA degradation pattern in interferon-treated HeLa cell extracts--even at a concentration of 10(-9)M--as the natural compound does.     

Synthesis and biological activity of tubercidin analogues of ppp5'A2'p(5'A2'p)n5'A

A series of tubercidin (7-deazaadenosine) analogues of 2-5A of the general formula p5'(c7A)2'p[5'(c7A)-2'p]n5'(c7A) (n = 0-5) were prepared by lead ion catalyzed polymerization of the 5'-phosphoroimidazolidate of tubercidin. Through the corresponding imidazolidates, these oligonucleotide 5'-monophosphates were converted to the 5'-triphosphates. All reported structures were corroborated by enzyme digestion and 1H or 31P nuclear magnetic resonance. When evaluated for its ability to bind to the 2-5 A-dependent endonuclease of mouse L cells, the tubercidin analogue of trimeric 2-5A, namely, ppp5'(c7A)2'p5'(c7A)2'p5'(c7A), and the corresponding tetramer were bound as effectively as 2-5A itself; nonetheless, it and the corresponding tetramer, ppp5'-(c7A)2'p5'(c7A)2'p5'(c7A)2'p5'(c7A), failed to stimulate the 2-5A-dependent endonuclease as judged by its inability to inhibit translation in extracts of mouse L cells programmed with encephalomyocarditis virus RNA and to give rise to ribosomal RNA cleavage in the same cell system under conditions where 2-5A showed activity at 10(-9) M. The trimer, ppp5'(c7A)2'p5'(c7A)2'p5'(c7A), was an antagonist of 2-5A action in the L cell extract. In the lysed rabbit reticulocyte system, both the trimeric and tetrameric tubercidin 2-5A analogues were bound to the 2-5A-dependent endonuclease as well as 2-5A, but in this case, the tetramer triphosphate, ppp5'(c7A)2'p5'(c7A)2'p5'(c7A)2'p5'(c7A), was just as potent an inhibitor of translation as 2-5A tetramer triphosphate. Moreover, this inhibition was prevented by the established 2-5A antagonist p5'A2'p5'A2'p5'A.(ABSTRACT TRUNCATED AT 250 WORDS)     

A regiospecific synthesis of branched tetranucleotides: U3'p5'A2'p5'G 3'p5'U and U3'p5'A2'p5'G3'p5'C

An efficient strategy for the synthesis of branched nucleotides 14 and 15 has been developed using key intermediates 6 and 10.     

Cordycepin analogs of ppp5'A2'p5'A2'p5'A (2-5A) inhibit protein synthesis through activation of the 2-5A-dependent endonuclease

Analogs of the triphosphate 2'-5'-linked adenylate trimer (ppp5'A2'p5'A2'p5'A, called 2-5A) which contain 3'-deoxyadenosine (cordycepin) instead of adenosine either in positions one and two, or in all three positions, are 10-100-fold less potent than is parent 2-5A in inhibition of protein synthesis in intact cells, when utilizing calcium co-precipitation techniques to introduce the 5'-triphosphate oligonucleotides into the cells. That the inhibition of protein synthesis was a consequence of activation of the 2-5A-dependent endonuclease by the 3'-deoxyadenosine analogs of 2-5A was demonstrated in obtaining the ribosomal RNA cleavage pattern that is characteristic of endonuclease activation by parent 2-5A. Additional results (i.e. lack of activity by the dimer species ppp5'(3'dA)2'p5'-(3'dA) or the monomer 3'dA) as well as kinetic analysis both in intact cells and in cell-free extracts provided further evidence that the inhibition of protein synthesis observed with these 3'-deoxyadenosine 2-5A analogs was not due to their degradation to the antimetabolite monomer unit 3'-deoxyadenosine.     

Inhibition of cell-free protein synthesis by pppA2'p5'A2'p5'A: a novel oligonucleotide synthesized by interferon-treated L cell extracts

The oligonucleotide pppA^2′ p^5′ A^2′ p^5′ A is synthesized by extracts from interferon-treated mouse L cells in the presence of double-stranded RNA. This compound is a potent inhibitor of protein synthesis in cell-free systems prepared from L cells or rabbit reticulocytes.After an initial lag, rates of protein synthesis in vitro are severely depressed in the presence of the oligonucleotide, and polysomes become disaggregated. In the presence of high concentrations of emetine, an inhibitor of chain elongation, reticulocyte polysomes containing an average of 4–6 ribosomes per mRNA are partially degraded to structures containing 1–4 ribosomes after incubation with the oligonucleotide. The level of association of exogenous ³⁵S-Met-tRNA_f with initiation complexes is not decreased, and under some conditions is even increased, by the oligonucleotide.When RNA is extracted from control and inhibited reticulocyte lysates and assayed for active mRNA content by retranslation in a fresh mRNA-dependent system, the results show extensive loss of template activity in the material obtained from the incubations containing pppA^2′ p^5′ A^2′ p^5′ A. The data are consistent with a mechanism in which this inhibitor activates a nuclease which prevents mRNA from being utilized for protein synthesis. This mechanism is contrasted with that of the heme-controlled repressor, another potent inhibitor of translation, which causes extensive inhibition of Met-tRNA_f binding to initiation complexes, has no effect on polysome size in the presence of emetine and does not inactivate mRNA.     

Synthesis and breakdown of pppA2'p5'A2'p5'A and transient inhibiton of protein synthesis in extracts from interferon-treated and control cells.

Incubation of the mouse L-cell-free system with a concentration of pppA2'p5'A2'p5'A [(2'-5')An] just sufficient to inhibit protein synthesis results in formation of a high-molecular-weight, heatlabile inhibitor and enhanced ribonuclease activity and in the rapid breakdown of (2'-5')An to ATP. The (2'-5')An-enhanced ribonuclease activity is also unstable and in the absence of a (2'-5')-An-regenerating system inhibiton of protein synthesis is transient. Although interferon treatment enhances the synthesis of (2'-5')An, the rates of degradation of (2'-5')An and levels of activatible nuclease are similar in extracts prepared from control or interferon-treated cells. Interestingly, the sensitivity of different cell-free systems to (2'-5')An, varies with the source of the cell-free systems and with the methods used in their preparation. There is, however, no obvious correlation between the sensitivities of the system and the rate of breakdown of (2'-5')An. The significance of these results is discussed in relation to a possible control function for the (2'-5')An system in both interferon-treated and control cells.     

Mechanism of pppA(2'p5'A)n2'p5'AOH synthesis in extracts of interferon-treated HeLa cells

Treatment of HeLa cells with interferon results in the induction of an enzymatic activity designated 2'5'oligo(A) polymerase. The polymerase requires continuous presence of double-stranded RNA (dsRNA) for activity, since degradation of dsRNA abolishes synthesis of the oligomeric series pppA(2'p5'A)n. These oligonucleotides are formed initially at a constant rate with dimer synthesized faster than trimer, and the latter faster than tetramer. After 45 min, accumulation of the dimer declines whereas that of other oligomers still proceeds at a linear rate. These results suggest that an oligomer remains associated with the enzyme for possible consecutive additions of adenylate, since no significant accumulation of dimer precedes synthesis of trimer. The relative amounts of the different oligomers found at the end of a reaction may reflect an increasing probability of release as the oligomers are elongated. The accumulation of dimer, however, decreases when it becomes a substrate for adenylate addition; incorporation of isolated dimer into 2'5'-oligo(A) was directly shown. Other nucleotides with a blocked p5'A terminus, like A5'ppppp5'A and NADH, can serve as adenylate acceptors in the presence of dsRNA. The adenosine triphosphates 2'-dATP and 3'-dATP are not incorporated efficiently into 2'5'-oligo(A) and inhibit its synthesis.     

3-Deazaadenosine analogues of p5'A2'p5'A2'p5'A: synthesis, stereochemistry, and the roles of adenine ring nitrogen-3 in the interaction with RNase L

Sequence-specific 3-deazaadenosine (c(3)A)-substituted analogues of trimeric 2',5'-oligoadenylate, p5'A2'p5'A2'p5'A, were synthesized and evaluated for their ability to activate human RNase L (EC 3.1.2.6) aiming at the elucidation of the nitrogen-3 role in this biochemical process. Substitution of either 5'-terminal or 2'-terminal adenosine with c(3)A afforded the respective analogues p5'(c(3)A)2'p5'A2'p5'A and p5'A2'p5'A2'p5'(c(3)A) that were as effective as the natural tetramer itself as activators of RNase L (EC(50)=1nM). In contrast, p5'A2'p5'(c(3)A)2'p5'A showed diminished RNase L activation ability (EC(50)=10nM). The extensive conformational analysis of the c(3)A-substituted core trimers versus the parent natural core trimer by the (1)H and (13)C NMR, and CD spectroscopy displayed close stereochemical similarity between the natural core trimer and (c(3)A)2'p5'A2'p5'A and A2'p5'A2'p5'(c(3)A) analogues, thereby strong evidences for the syn base orientation about the glycosyl bond of the c(3)A residue of the latter were found. On the contrary, an analogue A2'p5'(c(3)A)2'p5'A displayed rather essential deviations from the spatial arrangement of the parent natural core trimer.     

Occurrence of a novel nucleotide, Zpp5'A2'p, in rat liver extracts

The nucleotide Zpp5'A2'p has been isolated from rat liver. Z stands for an unknown compound, probably a nucleoside. The preliminary structure of Zpp5'A2'p has been elucidated by treatment with phosphodiesterase and/or alkaline phosphatase and analysis of the products of the reaction by high pressure liquid chromatography. The following ultraviolet absorption spectral characteristics were determined at pH 7.0: Zpp5'A2'p (lambda max = 265 nm; A250/A260 = 0.76; A280/A260 = 0.83); Zp (lambda max = 280 nm; A250/A260 = 0.88; A280/A260 = 1.46). The molar extinction coefficient found for Zp, at 280 nm, was (7.5 + 0.9) X 10(3) M-1 cm-1. The base of Zp could correspond to an indole derivative.     

Only one 3'-hydroxyl group of ppp5' A2'p5'A2'p5' A (2-5A) is required for activation of the 2-5A-dependent endonuclease

To investigate the relative importance of each of the ribose 3'-hydroxyl groups of 2-5A (ppp5' A2'p5'A2'-p5' A) in determining binding to and activation of the 2-5A-dependent endonuclease (RNase L), the 3'-hydroxyl functionality of each adenosine moiety of 2-5A trimer triphosphate was sequentially replaced by hydrogen. The analog in which the 5'-terminal adenosine was replaced by 3'-deoxyadenosine (viz. ppp5'(3'dA)-2'p5' A2'p5' A) was bound to RNase L as well as 2-5A itself and was only 3 times less potent than 2-5A as an activator of RNase L. On the other hand, when the second adenosine unit was replaced by 3'-deoxyadenosine (viz. ppp5' A2'p5'(3'dA)2'p5' A), binding to RNase L was decreased by a factor of eight relative to 2-5A trimer and, even more dramatically, there was a 500-1000-fold drop in ability to activate the 2-5A-dependent endonuclease. Finally, when the 3'-hydroxyl substituent was converted to hydrogen in the 2'-terminal residue of 2-5A, a significant increase in both binding and activation ability occurred. We conclude that only the 3'-hydroxyl group of the second (from the terminus) nucleotide residue of 2-5A is needed for effective activation of RNase L.     

Rat liver contains a novel nucleotide, Ypp5'A2'p, related to adenosine 2',5'-bisphosphate

A novel nucleotide, Ypp5'A2'p, has been purified through perchloric acid extraction of rat liver followed by DEAE-cellulose and ion pair high pressure liquid chromatographies. Y stands for an unknown compound, probably a nucleoside, whose sugar moiety is different to beta-D (deoxy) ribose. Treatment of Ypp5'A2'p with snake venom phosphodiesterase renders Yp and adenosine 2',5'-bisphosphate (pAp). After elimination of the terminal phosphate with alkaline phosphatase, the resulting nucleotide (Ypp5'A) yielded Yp and 5'-AMP when hydrolyzed by the phosphodiesterase. The following ultraviolet absorption spectral characteristics were determined at pH 7: Ypp5'A2'p (lambda max = 265 nm; A250/A260 = 0.76; A280/A260 = 0.79); Yp (lambda max = 279 nm; A250/A260 = 0.70; A280/A260 = 1.70). The molar extinction coefficient found for Yp at 280 nm was 20.6 x 10(3) M-1 cm-1.     

2'5'-linked polynucleotides do form a double-stranded helical structure: a result from the energy minimization study of A2'p5'A

Experimental results on 2′5′-linked subunit systems of nucleic acids are interpreted to substantiate the view that the 2′5′-linked polynucleotides cannot form double-stranded helical structures. In order to look into this aspect of the 2′5′-linked units, as well as to make a detailed comparison between the conformational characteristics of 3′5′- and 2′5′-linked systems, we carried out an exhaustive theoretical study on A2′p5′A. The method was to compute the various terms of energy contributions to a conformational state and then to minimize the total energy, permitting all the relevant dihedral angles to adjust themselves. Four hundred thirty two probable starting conformations were considered for this treatment, but we found only 10 of them to come under low-energy states, i.e., within 5 kcal/mol energy difference with reference to the global minimum energy state. The characteristic properties of these 10 conformations were compared in detail with those previously obtained on the corresponding 3′5′-linked subunit, as well as such units with other base sequences. As a further step, a model-building study was undertaken. Using the backbone-course, base-stacking, and hydrogen-bonding possibilities of the 10 low-energy conformations of the dimer A2′p5′A, double-stranded helical structures were scrutinized for the 2′5′-linked polynucleotide. Of a few reasonable forms, a right-handed duplex structure satisfied our requirements. We describe this new duplex, making comparisons with the standard A- and B-form states of DNA. The available experimental and theoretical results on 2′5′-linked systems are also analyzed.     

Mechanism of interferon action: inhibition of pppA(2'p5'A)n-dependent ribonucleases activity in micrococcal nuclease-treated mouse L cell-free extracts

The ability of nonpreincubated as compared to micrococcal nuclease-treated mouse L cell-free extracts supplemented with 2′-deoxythymidine-3′, 5′-diphosphate (pTp) and ethyleneglycol-bis (β-aminoethyl ether)-N,N′-tetraacetic acid (EGTA) to catalyze the 2′,5′-oligoadenylate-dependent degradation of reovirus [³H]mRNA was investigated. 2′,5′-Oligo A tetramer enhanced degradation in nonpreincubated but not micrococcal nuclease-treated extracts. Neither pTp nor EGTA significantly affected the 2′,5′-oligo A-dependent degradation in nonpreincubated extracts. The presence of both micrococcal nuclease and calcium was required to establish the subsequent reduction in both 2′,5′-oligo A-dependent and -independent degradation observed in micrococcal nuclease-treated extracts containing pTp and EGTA.     

Conformational analysis of the trinucleoside diphosphate 3'd(A2'-5'A2'-5'A). An NMR and CD study.

A 500 MHz and 300 MHz NMR study of the trinucleoside diphosphate 3'd(A2'-5'A2'-5'A) is presented. In addition, circular dichroism is used to study base stacking in the title compound. The complete 1H-NMR spectral assignment of the sugar ring proton signals is given. Information about the sugar ring (N- or S-type conformation) and about the backbone geometry along C4'-C5' and C5'-O5' bonds is obtained from the NMR coupling constants. It is shown that the trimer mainly occurs in the N-N-N stacked state at low temperatures; the presence of a minor amount of N-N-S conformational sequence is indicated.     

Inorganic models of photosystem II of plant photosynthesis. Catalytic and photocatalytic oxidation of water with participation of manganese compounds

Manganese dioxide is shown to be the catalyst of oxygen evolution at the oxidation of water by the one-electron oxidant Ru(bpy)₃³⁺ in neutral and slightly acidic media. Catalytic activity of MnO₂ depends on the method of preparation, the most active samples being those consisting of the smallest particles, i.e., having the largest surface-to-volume ratio. Ru(bpy)₃³⁺ was found to be formed at the irradiation of Ru(bpy)₃²⁺ solutions by visible light (λ = 436 nm) in the presence of such acceptors as Ce(IV), Hg(II), and Mn(IV) pyrophosphate. Continuous O₂ evolution from water is observed when the system Mn(IV) pyrophosphate plus Ru(bpy)₃²⁺ plus MnO₂ is irradiated by visible light. The system is discussed in connection with the active center of photosystem II of plant photosynthesis.     

Structure and conformation of the branch core triribonucleotide containing 2'-5' and 3'-5' phosphodiester linkages (A 2'p5'G 3'p5'C) i solution, essential for yeast mRNA splicing, deduced from 1H-NMR

The non-exchangeable 1H-NMR signals of the branch core trinucleotide of the lariat branch site (A2'p5'G3'p5'C, 1) and its derivatives 2 and 3 are completely assigned using one- and two-dimensional NMR techniques including NOE, COSY, NOESY, 1H-1H INADEQUATE and 2D-J-resolved spectroscopy. From the vicinal coupling constants in the individual ribose rings, NOE data and T1 measurements, the following properties of the trimers are deduced. (i) The unique stacking behavior of the trimers is S2'N3'N, and the sugar rings exist predominantly in the N-conformation (3'-endo-2'-exo). (ii) The sugar-base orientations appear to be anti. (iii) The branched trimers exist in solution as single-stranded right-handed conformations resembling A-RNA with stacking between the adenine and guanine residues in aqueous solution at 21 degrees C and pH 7.2. (iv) The calculated values for the torsion angles epsilon t and gamma+ for the trimers are 201-203 degrees and 71-86%, respectively, while the percent beta t values are higher for the guanine (87-92%) than the cytosine residues (73-77%). The computer generated depiction of the triribonucleotide 1 is also shown. These subtle structural features may act as recognition signals for this critical lariat branch site which is essential for the second step in yeast mRNA splicing.