- A Stark Contrast to Modern Earth: Phosphate Mineral Transformation and Nucleoside Phosphorylation in an Iron- and Cyanide-Rich Early Earth Scenario
-
Organophosphates were likely an important class of prebiotic molecules. However, their presence on the early Earth is strongly debated because the low availability of phosphate, which is generally assumed to have been sequestered in insoluble calcium and iron minerals, is widely viewed as a major barrier to organophosphate generation. Herein, we demonstrate that cyanide (an essential prebiotic precursor) and urea-based solvents could promote nucleoside phosphorylation by transforming insoluble phosphate minerals in a “warm little pond” scenario into more soluble and reactive species. Our results suggest that cyanide and its derivatives (metal cyanide complexes, urea, ammonium formate, and formamide) were key reagents for the participation of phosphorus in chemical evolution. These results allow us to propose a holistic scenario in which an evaporitic environment could concentrate abiotically formed organics and transform the underlying minerals, allowing significant organic phosphorylation under plausible prebiotic conditions.
- Burcar, Bradley,Casta?eda, Alma,Lago, Jennifer,Daniel, Mischael,Pasek, Matthew A.,Hud, Nicholas V.,Orlando, Thomas M.,Menor-Salván, César
-
p. 16981 - 16987
(2019/11/11)
-
- An improved one-pot synthesis of nucleoside 5'-triphosphate analogues
-
Nucleoside 5'-triphosphate (NTP) analogues are valuable tools for biochemical and medicinal research. Therefore, a facile and efficient synthesis of NTP analogues is required. Here, we report on an improved nucleoside 5'-triphosphorylation procedure to obtain pure products after liquid chromotagrpahy (LC) separation with no need for high performance liquid chromatography (HPLC) purification. To improve the selectivity of the reaction we attempted the optimization of several parameters such as solvent, pyrophosphate nucleophilicity, time and temperature of the reaction. Eventually, the reaction was optimized by decreasing the temperature to -15°C and increasing the reaction time to 2 hours, based on monitoring time-dependent product distribution using 31P NMR. Furthermore, the NTPs were obtained as pure products after LC separation, which was impossible in the original Ludwig procedure. Good yields were obtained for all studied natural and synthetic nucleosides.
- Gillerman, Irina,Fischer, Bilha
-
p. 245 - 256
(2011/08/06)
-
- Natural occurrence of 2′,5′-linked heteronucleotides in marine sponges
-
2′,5′-oligoadenylate synthetases (OAS) as a component of mammalian interferon-induced antiviral enzymatic system catalyze the oligomerization of cellular ATP into 2′,5′-linked oligoadenylates (2-5A). Though vertebrate OASs have been characterized as 2′-nucleotidyl transferases under in vitro conditions, the natural occurrence of 2′,5′-oligonucleotides other than 2-5A has never been demonstrated. Here we have demonstrated that OASs from the marine sponges Thenea muricata and Chondrilla nucula are able to catalyze in vivo synthesis of 2-5A as well as the synthesis of a series 2′,5′-linked heteronucleotides which accompanied high levels of 2′,5′-diadenylates. In dephosphorylated perchloric acid extracts of the sponges, these heteronucleotides were identified as A2′p5′G, A2′p5′U, A2′p5′C, G2′p5′A and G2′p5′U. The natural occurrence of 2′-adenylated NAD+ was also detected. In vitro assays demonstrated that besides ATP, GTP was a good substrate for the sponge OAS, especially for OAS from C. nucula. Pyrimidine nucleotides UTP and CTP were also used as substrates for oligomerization, giving 2′,5′-linked homo-oligomers. These data refer to the substrate specificity of sponge OASs that is remarkably different from that of vertebrate OASs. Further studies of OASs from sponges may help to elucidate evolutionary and functional aspects of OASs as proteins of the nucleotidyltransferase family.
- Lopp, Annika,Reintamm, Tonu,Kuusksalu, Anne,Tammiste, Indrek,Pihlak, Arno,Kelve, Merike
-
experimental part
p. 235 - 254
(2010/10/19)
-
- Kinetic analysis of hydrolytic reaction of homo- and heterochiral adenylyl(3′-5′)adenosine isomers: Breaking homochirality reduces hydrolytic stability of RNA
-
The hydrolytic stability of the diastereomeric isomers of ApA was compared and the results show that heterochiral ApAs are more rapidly hydrolyzed than homochiral ApAs at low temperatures, suggesting that hydrolytic selection in cold environments in conjunction with selective polymerization may have been effective in enriching the homochirality of RNA. The Royal Society of Chemistry 2005.
- Urata, Hidehito,Sasaki, Rie,Morita, Hiroyo,Kusumoto, Marina,Ogawa, Yoko,Mitsuda, Kozue,Akagi, Masao
-
p. 2578 - 2580
(2007/10/03)
-
- Dinuclear Zn2+ complexes in the hydrolysis of the phosphodiester linkage in a diribonucleoside monophosphate diester.
-
Dizinc complexes that were formed from 2:1 mixtures of Zn(NO3)2 and dinucleating ligands TPHP (1), TPmX (2) or TPpX (3) in aqueous solutions efficiently hydrolyzed diribonucleoside monophosphate diesters (NpN) under mild conditions. The dinucleating ligand affected the structure of the aquo-hydroxo-dizinc core, resulting in different characteristics in the catalytic activities towards NpN cleavage. The pH-rate profile of ApA cleavage in the presence of (Zn2+)(2)-1 was sigmoidal, whereas those of (Zn2+)(2)-2 and (Zn2+)(2)-3 were bell-shaped. The pH titration study indicated that (Zn2+)(2)-1 dissociates only one aquo proton (up to pH 12), whereas (Zn2+)(2)-2 dissociates three aquo protons (up to pH 10.7). The observed differences in the pH-rate profile are attributable to the various distributions of the monohydroxo-dizinc species, which are responsible for NpN cleavage. As compared to that using (Zn2+)(2)-1, the NpN cleavage using (Zn2+)(2)-2 showed a greater rate constant, with a higher product ratio of 3'-NMP/2'-NMP. The saturation behaviors of the rate, with regard to the concentration of NpN, were analyzed by Michaelis-Menten type kinetics. Although the binding of (Zn2+)(2)-2 to ApA was weaker than that of (Zn2+)(2)-1, (Zn2+)(2)-2 showed a greater kcat value than (Zn2+)(2)-1, resulting in higher ApA cleavage activity of the former.
- Yashiro, Morio,Kaneiwa, Hideki,Onaka, Kenichi,Komiyama, Makoto
-
p. 605 - 610
(2007/10/03)
-
- The pKa of the internucleotidic 2′-hydroxyl group in diribonucleoside (3′→5′) monophosphates
-
Ionization of the internucleotidic 2′-hydroxyl group in RNA facilitates transesterification reactions in Group I and II introns (splicing), hammerhead and hairpin ribozymes, self-cleavage in lariatRNA, and leadzymes and tRNA processing by RNase P RNA, as well as in some RNA cleavage reactions promoted by ribonucleases. Earlier, the pKa of 2′-OH in mono- and diribonucleoside (3′-5′) monophosphates had been measured under various nonuniform conditions, which make their comparison difficult. This work overcomes this limitation by measuring the pKa values for internucleotidic 2′-OH of eight different diribonucleoside (3′-5′) monophosphates under a set of uniform noninvasive conditions by 1H NMR. Thus the pKa is 12.31 (±0.02) for ApG and 12.41 (±0.04) for ApA, 12.73 (±0.04) for GpG and 12.71 (±0.08) for GpA, 12.77 (±0.03) for CpG and 12.88 (±0.02) for CpA, and 12.76 (±0.03) for UpG and 12.70 (±0.03) for UpA. By comparing the pKas of the respective 2′-OH of monomeric nucleoside 3′-ethyl phosphates with that of internucleotidic 2′-OH in corresponding diribonucleoside (3′→5′) monophosphates, it has been confirmed that the aglycons have no significant effect on the pKa values of their 2′-OH under our measurement condition, except for the internucleotidic 2′-OH of 9-adeninyl nucleotide at the 5′-end (ApA and ApG), which is more acidic by 0.3-0.4 pKα units.
- Acharya,Foeldesi,Chattopadhyaya
-
p. 1906 - 1910
(2007/10/03)
-
- Phosphodiester Cleavage of Ribonucleoside Monophosphates and Polyribonucleotides by Homo- and Heterodinuclear Metal Complexes of a Cyclohexane-Based Polyamino-Polyol Ligand
-
The ability of the dinuclear complexes of tdci [1,3,5-trideoxy-1,3,5-tris(dimethylamino)-cis-inositol] to promote the cleavage of the phosphodiester bonds of nucleoside 2′,3′-cyclic monophosphates, dinucleoside monophosphates and polyribonucleotides has been studied. The homodinuclear copper(II) and zinc(II) complexes efficiently promote the hydrolysis of cyclic nucleotides. The second-order rate constant (k2≈0.44M-1S-1) estimated for the cleavage of 2′,3′-cAMP induced by dinuclear copper(II) complexes is about 107 times greater than that for the hydroxide-ion-catalysed reaction. The complex selectively cleaves the 2′O-P bond of 2′,3′-cUMP and forms the 3′-product in 91% yield. An equimolar mixture of copper(II), zinc(II) and tdci proved to be more efficient than either of the binary systems: a 7-20-fold rate enhancement was observed for the cleavage of 2′,3′-cNMP substrates. The half-life for the hydrolysis of 2′,3′-cAMP decreased from 300 days to five minutes at 25°C when the concentration of each of the three components was 2.5mM. In contrast to the copper(II) or zinc(II) complexes of tdci, the heterodinuclear species promoted the hydrolysis of several dinucleoside monophosphates. For two ApA isomers, cleavage of the 3′,5′-bond was about 6.5 times faster than cleavage of the 2′,5′-bond. On the basis of the kinetic data, a trifunctional mechanism is suggested for the heterodinuclear-complex-promoted cleavage of the phosphodiester bond. Double Lewis acid activation occurs when the metal ions bind to the phosphate oxygen atoms. In particular, a metal-bound hydroxide ion serves as a general base or a nucleophilic catalyst, and, presumably, a zinc(II)-bound aqua ligand behaves as a general acid and facilitates the departure of the leaving alkoxide group. The effect of the complexes on the hydrolysis of poly(U), poly(A) and type III native RNA was also investigated, and, for the first time, kinetic data on the cleavage of the phosphodiester bonds of polyribonucleotides by a dinuclear complex was obtained.
- Jancso, Attila,Mikkola, Satu,Loennberg, Harri,Hegetschweiler, Kaspar,Gajda, Tamas
-
p. 5404 - 5415
(2007/10/03)
-
- Modeling of prebiotic catalysis with adenylated polymeric templates: Crystal structure studies and kinetic characterization of template-assisted phosphate ester hydrolysis
-
We have synthesized and characterized novel, copper-metalated, polymeric templates that contain adenine nucleobases. These promote hydrolysis of nonnatural and natural phosphate ester substrates in a highly efficient and catalytic fashion. The crystal structure of the copper-containing adenylated monomer reveals the formation of a polymeric array, through coordination to both N1 and N7 atoms. Possible implications of these studies for prebiotic catalysis, involving synergism between adenine and copper ions, are also discussed.
- Srivatsan,Parvez, Masood,Verma, Sandeep
-
p. 5184 - 5191
(2007/10/03)
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- Effect of alkaline earth metal ions on the phosphodiester hydrolysis of RNA
-
Hydrolyses of di- and triribonucleotides assisted by alkaline earth metal ions were investigated at pH 7.3 and 50 °C. Mg2+ was the most effective for the phosphodiester hydrolysis, and the rate exhibited first-order dependence on the concentration of Mg2+ in a range of 0.1-1.0 mol dm-3.
- Yashiro, Morio,Higuchi, Maiko,Washizu, Yusuke,Komiyama, Makoto
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p. 1843 - 1844
(2007/10/03)
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- Rapid and highly base selective RNA cleavage by a dinuclear Cu(II) complex
-
A bis-Cu(II) complex based on a covalently linked terpyridine and bipyridine ligand system is shown to rapidly cleave bis-ribonucleotides with remarkable selectivity for adenine bases.
- Liu, Shanghao,Hamilton, Andrew D.
-
p. 587 - 588
(2007/10/03)
-
- Photo-regulation of RNA hydrolysis by the zinc(II) complex carrying azobenzene
-
The first photo-regulation of non-enzymatic RNA hydrolysis has been achieved. A positively-charged and bulky regulator has been linked to a catalytically active Zn(II) complex, via a photo-responsive linker involving an azobenzene. The rate of RNA hydrolysis has been reversibly modulated by photoirradiation.
- Sumaoka, Jun,Kawata, Kentaro,Komiyama, Makoto
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p. 439 - 440
(2007/10/03)
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- Efficient RNA hydrolysis by lanthanide(III)-hydrogen peroxide combinations. Novel aggregates as the catalytic species
-
Combinations of lanthanum(III) ion and hydrogen peroxide efficiently hydrolyze RNA under physiological conditions, because of a synergetic cooperation. The rate constant for the hydrolysis of adenylyl(3′-5′)adenosine at pH 7.2 and 30°C is 7.7 x 10-2 min-1, when [LaIII]0 = 10 and [H2O2]0 = 100 mM. This value is 460 times as great as that for the ApA hydrolysis by La alone (1.7 x 10-4 min-1). Hydrogen peroxide is inactive when used separately. A similar synergism operates between NdIII and H2O2. According to the kinetic analysis and the potentiometric titration, a trimeric aggregate of [La(O-O)3La] complex is responsible for the RNA hydrolysis. This result is in contrast with the previous proposal on the hydrolysis of bis(4-nitrophenyl)phosphate that monomeric species of [La(O-O)2La]2+ is the active species (B. K. Takasaki and J. Chin, J. Am. Chem. Soc., 1995, 117, 8582). The discrepancy is ascribed to the difference in the basicities of the leaving groups in the substrates.
- Kamitani, Jun,Sumaoka, Jun,Asanuma, Hiroyuki,Komiyama, Makoto
-
p. 523 - 527
(2007/10/03)
-
- Hetero-dinuclear metal complexes for RNA hydrolysis
-
In the presence of a ligand having two metal-binding sites, Fe(III)/Zn(II) and Fe(III)/Cd(II) combinations hydrolyze adenylyl(3′-5′)adenosine. The notable activities are ascribed to the synergetic cooperation between the two kinds of metal ions in the hetero-dinuclear complexes.
- Kamitani, Jun,Kawahara, Ryuto,Yashiro, Morio,Komiyama, Makoto
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p. 1047 - 1048
(2007/10/03)
-
- RNA hydrolysis by cobalt(III) complexes
-
Adenylyl(3′-5′)adenosine (ApA) and uridylyl(3′-5′)uridine (UpU) are hydrolyzed at pH 7.0 and 50°C by [Co(N)4(OH2)2]3+ complexes (N: coordinated nitrogen atom). The pseudo-first-order rate constants for ApA hydrolysis by the triethylenetetramine and the tris(2-aminoethyl)amine complexes (0.1 mol dm-3) are 1.5 x 10-2 h-1, corresponding to 105-fold acceleration. The CoIII complexes are also active for the hydrolysis of 2′,3′-cyclic monophosphates of ribonucleotides. The pH-rate constant profile for ApA hydrolysis is bell-shaped with a maximum around pH 7, and a notable D2O solvent isotope effect (2.0) is observed. It is proposed that the coordination water molecules on the CoIII ions promote (as general acid catalysts) the departure of the alkoxide ion of 5′-OH from the phosphorus atom.
- Komiyama, Makoto,Matsumoto, Yoichi,Takahashi, Hideyuki,Shiiba, Tetsuro,Tsuzuki, Hidetoshi,Yajima, Hideaki,Yashiro, Morio,Sumaoka, Jun
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p. 691 - 695
(2007/10/03)
-
- Use of lanthanide metal complexes for the hydrolysis of 3′, 5′- and 2′, 3′- cyclic nucleotides
-
Lutetium(III) and lanthanum(III) complexes of 2-carboxyethylgermanium sesquioxide (Ge-132) can hydrolyze the phosphodiester linkage of 3′, 5′-cyclic adenosine monophosphate (cAMP), 3′, 5′-cyclic deoxyadenosine monophosphate (dcAMP) and 2′, 3′-cyclic adenosine monophosphate (2′ 3′cAMP). Both cAMP and dcAMP are hydrolyzed with high selectivity, yielding predominantly 3′- monophosphates. 2′, 3′cAMP is converted to 3′-AMP and 2′-AMP, the ratio of 3′AMP to 2′-AMP produced being 1.4.
- Zhu, Bing,Zhao, Da-Qing,Ni, Jia-Zuan
-
p. 755 - 758
(2007/10/03)
-
- Kinetic Analysis of Diamine-Catalyzed RNA Hydrolysis
-
The catalysis of various amines for the hydrolysis of RNA has been kinetically investigated, and the catalytic rate constants for each of the ionic states of these amines are determined. Ethylenediamine and 1,3-propanediamine are highly active under the physiological conditions, mainly because they preferentially take the catalytically active monocationic forms. The catalysis of these diamines is further promoted by the intramolecular acid-base cooperation of the neutral amine and the ammonium ion. In contrast, monoamines overwhelmingly exist at pH 7 as the inactive cations. Potential application of the catalysis by the diamines and the related oligoamines is discussed.
- Komiyama, Makoto,Yoshinari, Koichi
-
p. 2155 - 2160
(2007/10/03)
-
- Rapid and highly selective cleavage of ribonucleoside 2',3'-cyclic monophosphates by dinuclear Cu(II) complexes
-
Two characteristics that never before appeared together are combined in complexes 1 and 2, which show high activity and high selectivity in the hydrolysis of cyclic nucleoside 2',3'-monophosphates as model compounds for RNA. In the case of 1 the regioselectivity is exceptional, and, in the case of 2, the base selectivity.
- Liu,Luo,Hamilton
-
p. 2678 - 2680
(2007/10/03)
-
- Structure-reactivity relationship for the cobalt(III) complex-catalysed hydrolysis of adenosine 3′,5′-cyclic monophosphate
-
Hydrolysis of adenosine 3′,5′-cyclic monophosphate (cAMP) by cobalt(III) complexes [Co(N4XH2O)2]3+ (N4: two diamines or one tetraamine) has been systematically studied at pH 7 and 50°C. Both the catalytic activity and the product distribution are highly dependent on the nature of the amine ligand. The relative catalytic activities are cyclen (4000) > trien (500) > (tme)2 (57) > tren (37) > (tn)2 (22) > 2,3,2-tet (7) > (en)2 (1) ? cyclam, cth, dien. The pseudo-first-order rate constant for the cyclen complex (0.05 M) is 1.2 h-1 (half-life 35 min), corresponding to a 1010-fold acceleration with respect to the uncatalysed reaction. Of the two P-O linkages in cAMP, the cyclen, the trien and the 2,3,2-tet complexes preferentially cleave the P-O(5′) linkage, whereas the (tme)2 and the (tn)2 complexes promote P-O(3′) scission. Adenosine is the main product for hydrolysis by the (tme)2 complex, whereas adenosine monophosphates as the hydrolysis intermediates are accumulated in the catalysis by the trien complex.
- Komiyama, Makoto,Sumaoka, Jun,Yonezawa, Koji,Matsumoto, Yoichi,Yashiro, Morio
-
-
- RNA hydrolysis by the combination of the lanthanum(III) ion and hydrogen peroxide
-
Diribonucleotides are efficiently hydrolyzed by the combination of the lanthanum(III) ion and hydrogen peroxide at pH 7.2 and 30 °C. The rate constant for the hydrolysis of adenylyl(3′-5′)adenosine by the mixture of La(ClO4)3 (10 mmol dm-3) and H2O2 (100 mmol dm-3) is 7.7 x 10-2 min-1 (half-life 9 min), corresponding to a 460 fold cooperative promotion of the catalysis.
- Komiyama, Makoto,Kamitani, Jun,Sumaoka, Jim,Asanuma, Hiroyuki
-
p. 869 - 870
(2007/10/03)
-
- Efficient cleavage of ribonucleoside 3′,5′-cyclic phosphates and deoxyribonucleoside 3′,5′-cyclic phosphate by lanthanides
-
The cleavage of 3′,5′-cAMP, 3′,5′-cGMP and 3′,5′-dcAMP by lanthanides has been investigated by HPLC and 1H NMR. Rapid cleavage of cAMP, cGMP and dcAMP by Ce(III) under air at pH 8 and 37°C has been observed. Regioselective cleavage of P.O(5′) bond in cAMP, cGMP and dcAMP to give the corresponding 3′-AMP, 3′-GMP and 3′-dAMP by lanthanide chlorides has been achieved, and 3′-AMP and 3′-GMP are cleaved to adenosine(A) and guanosine(G) more slowly, respectively. The notable difference in reactivity between Ce(III) and the other lanthanide ions under air has also been studied. The cleavage is enhanced with the increase in the molar fraction of Ce(IV). The fast cleavage of cAMP by Ce(III) under air at pH 8 is ascribed to the resultant Ce(IV) in the reaction mixture.
- Li, Xinmin,Zhu, Bing,Zhao, Daqing,Ni, Jiazuan
-
p. 1144 - 1147
(2007/10/03)
-
- One- and two-metal ion catalysis of the hydrolysis of adenosine 3'-alkyl phosphate esters. Models for one- and two-metal ion catalysis of RNA hydrolysis
-
Adenosine 3'-O(PO2-)OCH2R phosphate esters have been synthesized with R = 8-hydroxyquinol-2-yl (1a) and 8-(hydroxyquinolyl)-2-methylene (1b). The adenosine 3'-O(PO2-)OCH2R structure has the essential features of an RNA dinucleotide. Equilibrium binding studies with metal ions Mg2+, Zn2+, Cu2+, and La3+ have been carried out with 1a, 1b, HOCH2R (7a and 7b), and 8-hydroxyquinoline (8), and equilibrium constants (K(as)) have been determined for the formation of 1:1 (L)M(n+) complexes. The hydrolysis of 1a and 1b as well as (1a)M(n+) and (1b)M(n+) species are first order in HO-. The rate enhancement for hydrolysis of 1a by complexation with metal ions is as follows: ~105 with Zn2+, ~103 with Mg2+, ~105 with Cu2+, and ~109 with La3+. Molecular modeling indicates that metal ions ligated to the 8-hydroxyquinoline moiety in the complexes (1a)M(n+) and (1b)M(n+) catalyze 1a and 1b hydrolysis by interacting as Lewis acid catalysts with the negatively charged oxygen atom of the phosphate group. In the instance of La3+ complexes, the ligated metal ion is within an interactive distance with both the negative phosphate oxygen and the leaving oxygen. This bimodal assistance by La3+ to the displacement reaction at phosphorus by the 2'-hydroxyl anion results in remarkable rate accelerations for the hydrolysis of (1a)La3+ and (1b)La3+ complexes. The complexes (1a)M(n+) and (1b)M(n+) are themselves hydrolyzed by metal ion catalysis in a reaction that is first order in HO-, an observation consistent with a transition state composition of [(1a,b)M(n+)][M(n+)][HO-]. We assume the kinetic equivalent [(1a,b)M(n+)][M(n+)OH] to represent the reacting species. In this catalysis the M(n+)OH is proposed to play the role of general base to deprotonate the 2'-OH while the metal in the complexes (1a,b)M(n+) is coordinated to a negative oxygen of the -(PO2-)- moiety. This double metal ion catalysis mimics a mechanism proposed for the ribozyme self-cleavage of RNA.
- Bruice,Tsubouchi,Dempcy,Olson
-
p. 9867 - 9875
(2007/10/03)
-
- Synergetic Catalysis by Two Non-lanthanide Metal Ions for Hydrolysis of Diribonucleotides
-
Adenylyl(3'-5')adenosine and uridylyl(3'-5')uridine are efficiently hydrolysed at pH 7 by bimetallic cooperation of zinc(ii) with tin(iv), indium(iii), iron(iii) or aluminium(iii).
- Irisawa, Makoto,Takeda, Naoya,Komiyama, Makoto
-
p. 1221 - 1222
(2007/10/02)
-
- Preparation and Study of Dinuclear Zinc(II) Complex for the Efficient Hydrolysis of the Phosphodiester Linkage in a Diribonucleotide
-
A dinuclear zinc(II) complex with N,N,N',N'-tetrakis-2-hydroxy-1,3-diaminopropane efficiently hydrolyses ApA at pH 7 and 50 deg C; the complex can thus be regarded as a good artificial ribonuclease which effectively mimics enzyme active sites.
- Yashiro, Morio,Ishikubo, Akira,Komiyama, Makoto
-
p. 1793 - 1794
(2007/10/02)
-
- Lanthanide Complexes with High Stability and Efficiency for the Hydrolysis of a Ribonucleotide Dimer
-
Lanthanide complexes with N,N,N'N'-tetrakisethylenediamine (TPEN) efficiently hydrolyze a ribonucleotide dimer, ApA, at 35 deg C, pH = 7.2.The activity of La3+-TPEN is greater than of free La3+ ion.The Ln3+-TPEN complexes are sufficiently stable in neutral aqueous solutions (the formation constants are in the range log K/mol-1dm3 = 3.9 - 6.2).These complexes are promising for the active site of artificial ribonucleases.
- Yashiro, Morio,Ishikubo, Akira,Takarada, Tohru,Komiyama, Makoto
-
p. 665 - 666
(2007/10/02)
-
- Additional Evidence for the Exceptional Mechanism of the Acid-catalysed Hydrolysis of 4-Oxopyrimidine Nucleosides: Hydrolysis of 1-(1-Alkoxyalkyl)uracils, Seconucleosides, 3'-C-Alkyl Nucleosides and Nucleoside 3',5'-Cyclic Monophosphates
-
The rate constants for the acid-catalysed hydrolysis of 1-(1-alkoxyethyl)uracils and 1-alkoxymethyluracils have been determined.With both series of compounds, the hydrolysis rate is rather insensitive to the polar nature of the alkoxy group, in striking contrast with the hydrolysis of the corresponding analogues of adenine and cytosine nucleosides, which react via rate-limiting formation of an oxocarbenium ion intermediate.Furthermore, it has been shown that 3',5'-cyclic monophosphates of thymidine and uridine undergo hydrolysis of the N-glycosidic bond 760 and 260 times as fast as their parent nucleosides, while the cyclic monophosphates of 2'-deoxyadenosine and adenosine are depurinated much more slowly than the corresponding nucleosides.On this basis it is suggested that 4-oxopyrimidine nucleosides are hydrolysed by opening of the sugar ring.To obtain further evidence for this exceptional mechanism, comparative kinetic measurements with some seco- and 3'-C-alkyl nucleosides of uracil and adenine have been carried out.
- Oivanen, Mikko,Rajamaeki, Markku,Varila, Jaana,Hovinen, Jari,Mikhailov, Sergey,Loennberg, Harri
-
p. 309 - 314
(2007/10/02)
-
- Enormous Acceleration by Cerium(IV) for the Hydrolysis of Nucleoside 3',5'-Cyclic Monophosphates at pH 7
-
At pH 7 and 30 deg C, 3',5'-cyclic monophosphates of adenosine and guanosine are promptly hydrolysed by Ce(NH4)2(NO3)6 (10-2 mol dm-3), with half-lives of 7 and 16 s, respectively.
- Sumaoka, Jun,Miyama, Sachiko,Komiyama, Makoto
-
p. 1755 - 1756
(2007/10/02)
-
- Catalytic Hydrolysis of 2',3'-Cyclic Adenosine Monophosphate by Aqua(2,2':6',2''-terpyridine)copper(II): Breakdown of the Analogy Between Activated Phosphodiesters and RNA
-
Aqua(2,2':6',2''-terpyridine)copper(II) catalyses the hydrolysis of 2',3'-cyclic adenosine monophosphate, but does not hydrolyse the 'activated' substrate bis(p-nitrophenyl) phosphate indicating that the latter is not a reliable model for biological phosphoric ester hydrolysis.
- Bashkin, James K.,Jenkins, Lisa A.
-
p. 3631 - 3632
(2007/10/02)
-
- Unprecedentedly Fast Hydrolysis of the RNA Dinucleoside Monophosphates ApA and UpU by Rare Earth Metal Ions
-
Rare earth metal(III) ions rapidly hydrolyse adenylyl(3'-5')adenosine and uridyl(3'-5')uridine at pH 8, 30 deg C; the half-life of the former is 10 min with 0.01 mol dm-3 TmIII.
- Komiyama, Makoto,Matsumura, Kazunari,Matsumoto, Yoichi
-
p. 640 - 641
(2007/10/02)
-
- Cooperation of cyclodextrin and alkali-metal halide for regioselective cleavage of ribonucleoside 2′,3′-cyclic phosphates
-
Regioselective catalysis of β- and γ-cyclodextrins (β- and γ-CyDs) for the P-O(3′) cleavage of adenosine 2′,3′-cyclic phosphate (A>p) to adenosine 2′-phosphate is significantly promoted, with respect to both selectivity and reaction rate, by cooperation with NaCl, KCl, RbCl, CsCl, KBr, and KF. A selectivity of 94% is achieved at pH 9.5 and 30 °C by the combination of β-CyD and KCl (3.0 M); the values with β-CyD alone and with KCl alone are 79% and 41%, respectively. By contrast, LiCl and KI reduce the regioselectivity. The logarithm of the 2′-phosphate/3′-phosphate ratio decreases linearly with an increase in the logarithm of the mean ionic activity coefficient of the medium. The α-CyD-induced regioselective P-O(2′) cleavage of A>p and U>p to the 3′-phosphates is also enhanced by KCl. The difference in chemical environment of the P-O(2′) and P-O(3′) bonds provided by CyDs on complex formation with the cyclic phosphates is amplified by the metal salts, resulting in the increase in regioselectivity.
- Komiyama, Makoto,Sawata, Shinya,Takeshige, Yuichi
-
p. 1070 - 1074
(2007/10/02)
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- Remarkably Fast Hydrolysis of 3',5'-Cyclic Adenosine Monophosphate by Cerium(III) Hydroxide Cluster
-
Cerium(III) hydroxide cluster hydrolyses 3',5'-cyclic adenosine monophosphate at an unprecedentedly large rate (half-life 35 s at pH 8.0; 30 deg C).
- Sumaoka, Jun,Yashiro, Morio,Komiyama, Makoto
-
p. 1707 - 1708
(2007/10/02)
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- Interconversion and Hydrolysis of Monomethyl and Monoisopropyl Esters of Adenosine 2'- and 3'-Monophosphates: Kinetics and Mechanisms
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First-order rate constants for mutual isomerization and hydrolytic cleavage of the monomethyl and monoisopropyl esters of adenosine 2'- and 3'-monophosphates (2'- and 3'-AMP) have been determined by HPLC over a wide pH range.Both reactions preceed at comparable rates under acidic conditions, exhibiting a second-order dependence of rate on hydronium ion concentration at 1 -> -3.No sign of mutual isomerization was detected under these conditions.With the isopropyl esters alkaline degradation of the adenine moiety is considerably faster than the phosphodiester hydrolysis.Mechanisms of phosphate migration and phosphodiester hydrolysis under various conditions have been discussed.
- Oivanen, Mikko,Schnell, Ralf,Pfleiderer, Wolfgang,Loennberg, Harri
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p. 3623 - 3628
(2007/10/02)
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- Hydrolysis of Adenosine 2',3'-Cyclic Phosphate and Adenylyl(3'-5')adenosine Catalyzed By Alkylenediamines
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Alkylenediamines exhibit remarkable catalysis for the hydrolysis of adenosine 2',3'-cyclic phosphate and adenylyl(3'-5')adenosine.The significant catalysis is ascribed to the intramolecular cooperation between the neutral amine and the protonated amine in the alkylenediamines.
- Yoshinari, Koichi,Komiyama, Makoto
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p. 519 - 522
(2007/10/02)
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- SYNTHESIS OF 2'-END LIPOPHILIZED DERIVATIVES OF 2',5'-TRIADENYLATES
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Synthesis of protected derivatives of 2 - 5 A3 core starting from 2',3'-O-ethoxymethylene-N6-benzoyladenosine (I) by triazolidate and/or modified triester method are described.Preparation of adenylyl-(2'-5')-adenylyl-(2'-5')-2',3'-O-(1-methoxyhexadecylidene)adenosine (X), adenylyl-(2'-5')-adenylyl-(2'-5')-2'(3')-O-palmitoyladenosine (XIII) and 5'-phosphoryladenyl-(2'-5')-adenylyl-(2'-5')-2',3'-O-(1-methoxyhexadecylidene)adenosine (XVI) are described.
- Pressova, Martina,Smrt, Jiri
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p. 487 - 497
(2007/10/02)
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- Cooperation of Alkali Metal Ions and β-Cyclodextrin for the Regioselective Cleavage of Adenosine 2',3'-Cyclic Phosphate
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Sodium(I), potassium(I), rubidium(I), and cesium(I) ions significantly increase both the selectivity and the rate constant for the β-cyclodextrin-induced regioselective cleavage of adenosine 2',3'-cyclic phosphate.The ratio of the 2'-phosphate to the 3'-phosphate in the product is 11.2 with sodium chloride and β-cyclodextrin (3.0 and 0.015 mol*dm-3) at pH 11, 30 deg C.
- Komiyama, Makoto,Takeshige, Yuichi,Sawada, Shinya
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p. 1785 - 1788
(2007/10/02)
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- Stereospecific Cleavage of Adenosine 2',3'-Cyclic Monophosphate Catalyzed by Cyclodextrins
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Stereospecific cleavage of adenosine 2',3'-cyclic monophosphate to the 2'-monophosphate is achieved at pH 11.08, 20 deg C by use of β- and γ-cyclodexrins as catalysts.The 2'/3' ratio for the product is 7.7 at the concentration 1.5x10-2 mol dm-3 of β-cyclodextrin.In contrast, α-cyclodextrin promotes the formation of the 3'-monophosphate, giving the product 2'/3' ratio 0.49 at the concentration 1.0x10-2 mol dm-3.
- Komiyama, Makoto
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p. 689 - 692
(2007/10/02)
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- Chemical synthesis of a pentaribonucleoside tetraphosphate constituting the 3'-acceptor stem sequence of E. coli tRNAIle using 2'-O-(3-methoxy-1,5-dicarbomethoxypentan-3-yl)-ribonucleoside building blocks. Application of a new achiral and acid-labile 2'-hydroxyl protecting group in tRNA synthesis.
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A synthesis of a pentaribonucleotide fragment constituting the residues 59-63 of 3'-terminus of E. coli tRNAIle, 5'-ApGpUpCpC-3', has been carried out using a new, easily accessible and achiral 2'-ketal protecting group. The new 2'-ketal group has an additional advantage in that it is easily functionalized to the diamide with aqueous ammonia in the penultimate step of deblocking of fully protected oligoribonucleotides. Such a functionalization of the 2'-ketal group at the penultimate step of deblocking of the fully protected tRNA molecule enhances its relative rate of removal under an acidic condition with a minimum of damage of the target tRNA molecule.
- Sandstr?m,Kwiatkowski,Chattopadhyaya
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p. 273 - 290
(2007/10/02)
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- Synthesis of adenylyl-(3'----5')-guanosine and some analogues as probes to explore the molecular mechanism of stimulation of influenza virus RNA polymerase.
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Influenza virus mRNA synthesis is primed by a capped oligonucleotide which is cleaved off from a cellular mRNA by a viral protein. The dinucleotide A3'p5'G can be used as a primer for the viral RNA polymerase mediated RNA synthesis in a cell-free system. Analogues of A3'p5'G have therefore been synthesized using the phosphotriester approach, and their priming ability for the influenza virus mRNA synthesis has been determined. An absence of the 2'-hydroxyl function in the guanosine residue in the dinucleotide, as in A3'p5'dG, drastically decreased its priming ability. Similarly, an alteration of the 3'----5' phosphate linkage to a 2'----5' phosphodiester linkage affected the priming ability quite severely. However a dinucleotide, with the 2'-hydroxyl function omitted in the adenosine moiety, as in dA3'p5'G, could still stimulate the mRNA synthesis. None of the modified dinucleotides inhibited A3'p5'G or globin mRNA primed influenza mRNA synthesis.
- Heikkil?,Stridh,Oberg,Chattopadhyaya
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p. 657 - 669
(2007/10/02)
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- Synthesis of a Dodecaribonucleotide, GUAUCAAUAAUG, by Use of "Fully" Protected Ribonucleotide Building Blocks
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The fully protected ribonucleotide monomer units (17, 19, 26, and 32) have been synthesized in excellent overall yields from unprotected ribonucleosides.Several carbamoyl groups were tested for protection of the guanosine base moiety.Finally, the diphenylcarbamoyl group was chosen and O6-(diphenylcarbamoyl)-N2-propionylguanosine was readily prepared in high yield and converted to the guanosine units 12 and 17.The uridine unit 19 was prepared by the acylation of the previous unit 18 with anisoyl chloride in the presence of i-Pr2EtN.In the case of the adenosine and cytidine units (26 and 32) , the regioselective 2'-O-tetrahydropyranylation was involved in their syntheses.These "perfectly" protected monomer units have succesfully been utilized in the synthesis of GUAUCAAUAAUG, a modified 5'-terminal structure, of brome mosic virus (BMV) mRNA no. 4 filament.The dodecamer chain was elongated by fragment condensation from the 3'-5' direction.The yields of the oligomer blocks have proved to be dramatically high because no side reactions occurred during the condensation reactions.Indeed, the final coupling to give the target 12-mer was achieved in 91percent yield.The deprotection of the fully protected in the usual manner gave GUAUCAAUAAUG in ca. 30percent yield.
- Kamimura, Takashi,Tsuchiya, Masahiko,Urakami, Ken-ichi,Koura, Koji,Sekine, Mitsuo,et al.
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p. 4552 - 4557
(2007/10/02)
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- A NEW SOLID PHASE APPROACH FOR RAPID SYNTHESES OF OLIGONUCLEOTIDES BEARING A 3'-TERMINAL PHOSPHATE GROUP
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Synthesis of pentanucleotide ApTpCpTpTp containing a 3'-terminal phosphomonoester group was accomplished with the help of the new phosphate-solid phase link 2-(4-carboxyphenylmercapto)ethanol; a similar molecule, 2-benzylsulfonylethanol, revealed interesting features as a temporary 3'-phosphate protecting group.
- Felder, Eduard,Schwyzer, Robert,Charubala, Ramamurthy,Pfleiderer, Wolfgang,Schulz, Bernd
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p. 3967 - 3970
(2007/10/02)
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- DECYCLIZING PHOSPHODIESTERASES ASSOCIATED WITH PLASMA MEMBRANES OF THE CHICK CHORIOALANTOIS
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Two different enzymatic activities hydrolyzing 2',3'-cyclic phosphates of purine and pyrimidine ribonucleosides to give 2'- or 3'-ribonucleotides have been detected in plasma membranes of the chick chorioalantois.The enzymes differ in their temperature optima: At lower temperatures, cleavage to the 2'-isomers predominates.
- Pristasova, Svetlana,Rosenbergova, Marta,Holy, Antonin
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p. 520 - 524
(2007/10/02)
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- SYNTHESIS OF 2'(3')-PHOSPHATES AND 2'(3')-PHOSPHOROTHIOATES OF 5'-O-CARBOXYMETHYLINOSINE AND RELATED COMPOUNDS
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5'-O-Carboxymethylinosine (IX) was prepared from disodium salt of 2',3'-O-isopropylideneinosine (VIII) by treatment with sodium chloroacetate, followed by acid hydrolysis. 5'-O-(2-Aminoethylamidocarbonylmethyl)inosine (XIII) was obtained by reaction of IX with p-nitrophenol and subsequent treatment with ethylenediamine.Action of triethyl phosphite on the compounds IX and XIII afforded the corresponding 5'-O-substituted 2'(3')-phosphites X and XIV which on reaction with trimethylsilyl chloride and sulfur gave the 2'(3')-phosphorothioates XI and XV.The compound IX was transformed by phosphorus oxychloride in 5'-O-carboxymethylinosine 2'(3')-phosphate (XII).Uridine, adenosine and inosine 2'(3')-phosphorothioates (Ia-Ic) were obtained from 2',3'-O-di-n-butylstannylene derivatives of the nucleosides IV by treatment with thiophosphoryl chloride followed by alkaline hydrolysis; inosine and guanosine 2'(3')-phosphorothioates (Ic, Id) were prepared by reaction of the corresponding 2'(3')-phosphites VIc, VId with trimethylsilyl chloride and sulfur.Cyclisation of Ic and Id with ethyl chloroformate in the presence of tri-n-butylamine afforded inosine 2',3'-O,O-cyclophosphorothioate (VIIc) and the corresponding guanosine derivative VIId.Compounds VIIc and VIId are not cleaved by Streptomyces aureofaciens ribonuclease.
- Holy, Antonin,Kois, Pavol
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p. 2817 - 2829
(2007/10/02)
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