- Characterization of the transition-state structures and mechanisms for the isomerization and cleavage reactions of uridine 3′-m-nitrobenzyl phosphate
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The transition-state structures and mechanisms of the isomerization to the 2′-isomer and cleavage reactions of uridine 3′-m-nitrobenzyl phosphate to m-nitrobenzyl alcohol and a 2′,3′-cyclic UMP at 86 °C and at pH 2.5, 5.5, and 10.5 have been characterized through kinetic isotope effects. The 18O primary isotope effect of 1.0019 ± 0.0007 and the secondary isotope effect of 0.9904 observed for the cleavage reaction at pH 2.5 are consistent with a neutral phosphorane-like transition-state structure. The cleavage and isomerization reactions at pH 2.5 proceed through a neutral phosphorane intermediate. The 18kbridge and 18knonbridge of unity measured for the pH-independent isomerization reaction at neutral pH support a stepwise mechanism with a monoanionic phosphorane intermediate. The primary and secondary isotope effects of 1.009 ± 0.001 and of 0.9986 ± 0.0004 observed for the pH-independent cleavage reaction are consistent with either a stepwise mechanism through a monoanionic phosphorane intermediate or with an ANDN reaction with a transition state resembling a monoanionic phosphorane intermediate. The absolute requirement of a water-mediated proton transfer for the formation of a phosphorane intermediate is proven by the absence of the isomerization reaction in anhydrous tert-butyl alcohol. The primary isotope effect of 1.0272 ± 0.0001 for the cleavage reaction at pH 10.5 is consistent with a concerted reaction through a transition state in which the leaving group departs with almost a full negative charge.
- Gerratana,Sowa,Cleland
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- Cleavage of short oligoribonucleotides by a Zn2+binding multi-nucleating azacrown conjugate
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A multi-nucleating azacrown conjugate (5a) consisting of two 3,5-bis(1,5,9-triazacyclododecan-3-yloxymethyl)benzyl groups attached to 1 and 7 sites of cyclen was prepared and tested as an artificial ribonuclease. The conjugate in the presence of five equivalents of zinc nitrate expectedly showed uridine selectivity comparable to that 1,3,5-tris(1,5,9-triazacyclododecan-3-yl)benzene (2), a compound known to bind to two adjacent uridine residues and cleave the intervening phosphodiester bond. 5a was, however, unable to discriminate between two and three adjacent uridine residues, but cleaved oligonucleotides containing a UpU and UpUpU site at a comparable rate, even when present at sub-saturating concentrations.
- Laine, Maarit,L?nnberg, Tuomas,Helkearo, Mia,L?nnberg, Harri
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p. 111 - 117
(2016/10/04)
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- Buffer catalyzed cleavage of uridylyl-3′,5′-uridine in aqueous DMSO: Comparison to its activated analog, 2-hydroxypropyl 4-nitrophenyl phosphate
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Buffer catalysis of the cleavage and isomerization of uridylyl-3′,5′-uridine (UpU) has been studied over a wide pH range in 80% aq. DMSO. The diminished hydroxide ion concentration in this solvent system made catalysis by amine buffers (morpholine, 4-hydroxypiperidine and piperidine) visible even at relatively low buffer concentrations (10-200 mmol L-1). The observed catalysis was, however, much weaker than what has been previously reported for the activated RNA model 2-hydroxypropyl 4-nitrophenyl phosphate (HPNP) in the same solvent system. In the case of morpholine, contribution of both the acidic and the basic buffer constituent was significant, whereas with 4-hydroxypiperidine and piperidine participation of the acidic constituent could not be established unambiguously. The results underline the importance of using realistic model compounds, along with activated ones, in the study of the general acid/base catalysis of RNA cleavage.
- Lain,L?nnberg,L?nnberg
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p. 3484 - 3492
(2015/03/18)
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- Guanidine based self-assembled monolayers on Au nanoparticles as artificial phosphodiesterases
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Gold nanoparticles passivated with a long chain alkanethiol decorated with a phenoxyguanidine moiety were prepared and investigated as catalysts in the cleavage of the RNA model compound HPNP and diribonucleoside monophosphates. The catalytic efficiency and the high effective molarity value of the Au monolayer protected colloids points to a high level of cooperation between the catalytic groups.
- Salvio, Riccardo,Cincotti, Antonio
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p. 28678 - 28682
(2014/07/22)
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- Fully automated continuous meso-flow synthesis of 5′-nucleotides and deoxynucleotides
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The first continuous meso-flow synthesis of natural and non-natural 5′-nucleotides and deoxynucleotides is described, representing a significant advance over the corresponding in-flask method. By means of this meso-flow technique, a synthesis with time consumption and high-energy consumption becomes facile to generate products with great efficiency. An abbreviated duration, satisfactory output, and mild reaction conditions are expected to be realized under the present procedure.
- Zhu, Chenjie,Tang, Chenglun,Cao, Zhi,He, Wei,Chen, Yong,Chen, Xiaochun,Guo, Kai,Ying, Hanjie
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p. 1575 - 1581
(2015/02/19)
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- An RNA modification with remarkable resistance to RNase A
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A 3′-deoxy-3′-C-methylenephosphonate modified diribonucleotide is highly resistant to degradation by spleen phosphodiesterase and not cleaved at all by snake venom phosphodiesterase. The most remarkable finding is that, despite the fact that both the vicinal 2-hydroxy nucleophile and the 5′-oxyanion leaving group are intact, the 3′-methylenephosponate RNA modification is also highly resistant towards the action of RNase A.
- Ghidini, Alice,Ander, Charlotte,Winqvist, Anna,Stroemberg, Roger
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supporting information
p. 9036 - 9038
(2013/09/24)
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- Tethered dinuclear europium(III) macrocyclic catalysts for the cleavage of RNA
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Dinuclear europium(III) complexes of the macrocycles 1,3-bis[1-(4,7,10- tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane]-m-xylene (1), 1,4-bis[1-(4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane] -p-xylene (2), and mononuclear europium(III) complexes of macrocycles 1-methyl-,4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane (3), 1-[3′-(N,N-diethylaminomethyl)benzyl]-4,7,10-tris(carbamoylmethyl)-1,4,7, 10-tetraazacyclododecane (4), and 1,4,7-tris(carbamoylmethyl)-1,4,7,10- tetraazacyclododecane (5) were prepared. Studies using direct excitation ( 7F0 → 5D0) europium(III) luminescence spectroscopy show that each Eu(III) center in the mononuclear and dinuclear complexes has two water ligands at pH 7.0, I = 0.10 M (NaNO 3) and that there are no water ligand ionizations over the pH range of 7-9. All complexes promote cleavage of the RNA analogue 2-hydroxypropyl-4- nitrophenyl phosphate (HpPNP) at 25°C (I = 0.10 M (NaNO3), 20 mM buffer). Second-order rate constants for the cleavage of HpPNP by the catalysts increase linearly with pH in the pH range of 7-9. The second-order rate constant for HpPNP cleavage by the dinuclear Eu(III) complex (Eu2(1)) at pH 7 is 200 and 23-fold higher than that of Eu(5) and Eu(3), respectively, but only 7-fold higher than the mononuclear complex with an aryl pendent group, Eu(4). This shows that the macrocycle substituent modulates the efficiency of the Eu(III) catalysts. Eu2(1) promotes cleavage of a dinucleoside, uridylyl-3′,5′-uridine (UpU) with a second-order rate constant at pH 7.6 (0.021 M-1 s-1) that is 46-fold higher than that of the mononuclear Eu(5) complex. Methyl phosphate binding to the Eu(III) complexes is energetically most favorable for the best catalysts, and this supports an important role for the catalyst in stabilization of the developing negative charge on the phosphorane transition state. Despite the formation of a bridging phosphate ester between the two Eu(III) centers in Eu2(1) as shown by luminescence spectroscopy, the two metal ion centers are only weakly cooperative in cleavage of RNA and RNA analogues.
- Nwe, Kido,Andolina, Christopher M.,Morrow, Janet R.
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body text
p. 14861 - 14871
(2009/02/08)
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- Simultaneous interaction with base and phosphate moieties modulates the phosphodiester cleavage of dinucleoside 3′,5′-monophosphates by dinuclear Zn2+complexes of Di(azacrown) ligands
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Five dinucleating ligands (1-5) and one trinucleating ligand (6) incorporating 1,5,9-triazacyclododecan-3-yloxy groups attached to an aromatic scaffold have been synthesized. The ability of the Zn2+ complexes of these ligands to promote the transesterification of dinucleoside 3′,5′-monophosphates to a 2′,3′-cyclic phosphate derived from the 3′-linked nucleoside by release of the 5′-linked nucleoside has been studied over a narrow pH range, from pH 5.8 to 7.2, at 90 °C. The dinuclear complexes show marked base moiety selectivity. Among the four dinucleotide 3′,5′-phosphates studied, viz. adenylyl-3′,5′-adenosine (ApA), adenylyl-3′,5′-uridine (ApU), uridylyl-3′,5′-adenosine (UpA), and uridylyl-3′, 5′-uridine (UpU), the dimers containing one uracil base (ApU and UpA) are cleaved up to 2 orders of magnitude more readily than those containing either two uracil bases (UpU) or two adenine bases (ApA). The trinuclear complex (6), however, cleaves UpU as readily as ApU and UpA, while the cleavage of ApA remains slow. UV spectrophotometric and 1H NMR spectroscopic studies with one of the dinucleating ligands (3) verify binding to the bases of UpU and ApU at less than millimolar concentrations, while no interaction with the base moieties of ApA is observed. With ApU and UpA, one of the Zn2+- azacrown moieties in all likelihood anchors the cleaving agent to the uracil base of the substrate, while the other azacrown moiety serves as a catalyst for the phosphodiester transesterification. With UpU, two azacrown moieties are engaged in the base moiety binding. The catalytic activity is, hence, lost, but it can be restored by addition of a third azacrown group on the cleaving agent.
- Wang, Qi,Loennberg, Harri
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p. 10716 - 10728
(2007/10/03)
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- Catalysis of diribonucleoside monophosphate cleavage by water soluble copper(II) complexes of calix[4]arene based nitrogen ligands
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Calix[4]arenes functionalized at the 1,2-, 1,3-, and 1,2,3-positions of the upper rim with [12]ane-N3 ligating units were synthesized, and their bi- and trimetallic zinc(II) and copper(II) complexes were investigated as catalysts in the cleavage of phosphodiesters as RNA models. The results of comparative kinetic studies using monometallic controls indicate that the subunits of all of the zinc(II) complexes and of the 1,3-distal bimetallic copper(II) complex 7-Cu2 act as essentially independent monometallic catalysts. The lack of cooperation between metal ions in the above complexes is in marked contrast with the behavior of the 1,2-vicinal bimetallic copper(II) complex 6-Cu2, which exhibits high catalytic efficiency and high levels of cooperation between metal ions in the cleavage of HPNP and of diribonucleoside monophosphates NpN′. A third ligated metal ion at the upper rim does not enhance the catalytic efficiency, which excludes the simultaneous cooperation in the catalysis of the three metal ions in 8-Cu 3. Rate accelerations relative to the background brought about by 6-Cu2 and 8-Cu3 (1.0 mM catalyst, water solution, pH 7.0, 50 °C) are on the order of 104-fold, largely independent of the nucleobase structure, with the exception of the cleavage of diribonucleoside monophosphates in which the nucleobase N is uracil, namely UpU and UpG, for which rate enhancements rise to 105-fold. The rationale for the observed selectivity is discussed in terms of deprotonation of the uracil moiety under the reaction conditions and complexation of the resulting anion with one of the copper(II) centers.
- Cacciapaglia, Roberta,Casnati, Alessandro,Mandolini, Luigi,Reinhoudt, David N.,Salvio, Riccardo,Sartori, Andrea,Ungaro, Rocco
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p. 12322 - 12330
(2007/10/03)
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- Substrate specificity of an active dinuclear Zn(II) catalyst for cleavage of RNA analogues and a dinucleoside
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The cleavage of the diribonucleoside UpU (uridylyl-3′-5′- uridine) to form uridine and uridine (2′,3′)-cyclic phosphate catalyzed by the dinuclear Zn(II) complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)- 2-hydroxypropane (Zn2(1)(H2O)) has been studied at pH 7-10 and 25 °C. The kinetic data are consistent with the accumulation of a complex between catalyst and substrate and were analyzed to give values of kc (S-1), Kd (M), and kc/K d (M-1 s-1) for the Zn2(1)(H 2O)-catalyzed reaction. The pH rate profile of values for log k C/Kd for Zn2(1)(H2O)-catalyzed cleavage of UpU shows the same downward break centered at pH 7.8 as was observed in studies of catalysis of cleavage of 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) and uridine-3′-4-nitrophenyl phosphate (UpPNP). At low pH, where the rate acceleration for the catalyzed reaction is largest, the stabilizing interaction between Zn2(1)(H2O) and the bound transition states is 9.3, 7.2, and 9.6 kcal/mol for the catalyzed reactions of UpU, UpPNP, and HpPNP, respectively. The larger transition-state stabilization for Zn 2(1)(H2O)-catalyzed cleavage of UpU (9.3 kcal/mol) compared with UpPNP (7.2 kcal/mol) provides evidence that the transition state for the former reaction is stabilized by interactions between the catalyst and the C-5′-oxyanion of the basic alkoxy leaving group.
- O'Donoghue, Annmarie,Pyun, Sang Yong,Yang, Meng-Yin,Morrow, Janet R.,Richard, John P.
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p. 1615 - 1621
(2007/10/03)
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- The pKa of the internucleotidic 2′-hydroxyl group in diribonucleoside (3′→5′) monophosphates
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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
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p. 1906 - 1910
(2007/10/03)
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- Lanthanide catalyzed cyclization of uridine 3′-p-nitrophenyl phosphate
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Steady state kinetics and 15N isotope effects have been used to study the cyclization reaction of uridine 3′-p-nitrophenyl phosphate. The cyclization reaction is catalyzed by transition metal ions and lanthanides, as are substitution reactions of many phosphate esters. Kinetic analysis reveals that the erbium-catalyzed cyclization reaction involves the concerted deprotonation of the 2′-OH group and departure of the leaving group. The transition state is very late, with a very large degree of bond cleavage to the leaving group, which could be due to a large degree of polarization of the P-O bonds by erbium.
- Rishavy, Mark A.,Hengge, Alvan C.,Cleland
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p. 283 - 292
(2007/10/03)
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- Preparation and cleavage reactions of 3′-thiouridylyl-(3′→5′)-uridine
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3′-Thiouridylyl-(3′→5′)-uridine [(Us)pU] 3 is prepared by coupling together the disulfide 14 and the 5′-H-phosphonate 18, and then removing the protecting groups. (Us)pU 3 readily undergoes cleavage in 0.05 mol dm-3 sodium glycinate buffer (pH 10.06) at 50 °C to give, in the first instance, uridine 4 and 3′-thiouridine 2′,3′-cyclic phosphorothioate 21; in glacial acetic acid at 30 °C, it rapidly undergoes cleavage in essentially the same way. The behaviour of (Us)pU 3 is compared with that of uridylyl-(3′→5′)-uridine (UPU) 1a under the same basic and acidic reaction conditions. (Us)pU 3 and 3′-thiouridine 2′,3′-cyclic phosphorothioate 21 are both substrates for ribonuclease A; (Us)pU 3 is a substrate for Crotalus adamanteus snake venom phosphodiesterase but not for calf spleen phosphodiesterase.
- Liu, Xiaohai,Reese, Colin B.
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p. 2227 - 2236
(2007/10/03)
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- Catalysts, anticatalysts, and receptors for unactivated phosphate diesters in water
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A set of substituted bisguanidines have been prepared and examined for their ability to bind and catalyze the hydrolysis of uridylyl-3',5'-uridine (UpU), an unactivated RNA substrate in water. The unexpected result is that this set includes both catalysts (binding the transition state better than the ground state) and anticatalysts (binding the ground state better than the transition state), each with respectable rate enhancements and/or affinities, despite the fact that these molecules all have very similar structures. These results therefore show the level of sophistication that must be achieved in the conformational theory of small molecules if we hope to truly 'design' supramolecular structures that bind preferentially to a transition state over the ground state.
- Zepik, Helmut H.,Benner, Steven A.
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p. 8080 - 8083
(2007/10/03)
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- Metal-Ion-Promoted Cleavage, Isomerization, and Desulfurization of the Diastereomeric Phosphoromonothioate Analogues of Uridylyl(3′,5′)uridine
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Metal-ion-promoted hydrolytic reactions of the SP and RP diastereomers of the phosphoromonothioate analogues of uridylyl(3′,5′)uridine [3′,5′-Up(s)U] and their cleavage products, diastereomeric uridine 2′,3′-cyclic phosphates [2′,3′-cUMPS], were followed by HPLC as a function of pH (4.7-5.6) and metal ion concentration (1-10 mmol L-1). With 3′,5′-Up(s)U, three reactions compete: (i) cleavage to 2′,3′-cUMPS, (ii) isomerization to 2′,5′-Up(s)U, and (iii) desulfurization to an equilibrium mixture of 2′,5′- and 3′,5′-UpU. Of these, the cleavage to 2′,3′-cUMPS is markedly accelerated by Zn2+, Cd2+, and Gd3+, the rate enhancements observed with the Sp isomer at [Mz+] = 5 mmol L-1 and pH 5.6 (T = 363.2 K) being 410-, 3600-, and 2000-fold, respectively. The effect of Mn2+ and Mg2+ on the cleavage rate is, in turn, modest (6- and 1.7-fold acceleration, respectively). The rate-accelerations are almost equal with the SP and RP diastereomers. The metal-ion-promoted reaction is first-order in both the hydroxide and metal ion concentration, and it proceeds by inversion of configuration at phosphorus, consistent with an in-line displacement mechanism. The isomerization and desulfurization are much less susceptible to metal ion catalysis: 6.4- and 7.7-fold accelerations were observed with Zn2+, respectively. Gd3+ does not promote these reactions at all. The isomerization proceeds by retention of configuration at phosphorus, consistent with formation of a pentacoordinated thiophosphorane intermediate having the entering 2′-hydroxy group apical and the leaving 3′-hydroxy equatorial, and subsequent pseudorotation posing the leaving group apical. The hydrolysis of 2′,3′-cUMPS is accelerated by metal ions slightly more efficiently than the cleavage of 3′,5′-Up(s)U to 2′,3′-cUMPS. In striking contrast to the reactions of 3′,5′-Up(s)U, the hydrolytic desulfurization to 2′,3′-cUMP is accelerated as efficiently as its endocyclic hydrolysis to uridine 2′and 3′-phosphoromonothioates [2′- and 3′-UMPS]. Somewhat unexpectedly, the latter compounds were observed to undergo metal-ion-promoted cyclization/desulfurization to 2′,3′-cUMP. The hydrolysis of 2′- or 3′-UMPS to uridine was, in turn, observed to be retarded by metal ions. The mechanisms of the partial reactions are discussed.
- Ora, Mikko,Peltomaeki, Markku,Oivanen, Mikko,Loennberg, Harri
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p. 2939 - 2947
(2007/10/03)
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- Synthesis and properties of diuridine phosphate analogues containing thio and amino modifications
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Several analogues of diuridine phosphate (UpU) were synthesized in order to investigate why replacing the 2'-hydroxyl with a 2'-amino group prevents hydrolysis. These analogues were designed to investigate what influence the 2'-substituent and 5'-leaving group have upon the rate of hydrolysis. All the analogues were considerably more labile than UpU toward acid-base-catalyzed hydrolysis. In the pH region from 6 to 9, the rate of hydrolysis of uridylyl (3'-5') 5'-thio-5'deoxyuridine (UpsU) hydrolysis rose, in a log linear fashion, from a value of 5 x 10-6 s-1 at pH 6 to 3200 x 10-6 s-1 at pH 9, indicating that attack on the phosphorus by the 2'-oxo anion is rate-limiting in the hydrolysis mechanism. In contrast, the rate of uridylyl (3'-5') 5'-amino-5'deoxyuridine (UpnU) hydrolysis fell from a value of 1802 x 10-6 s-1 at pH 5 to 140 x 10-6 s-1 at pH 7.5, where it remained constant up to pH 11.5, thus indicating an acid-catalyzed reaction. The analogue 2'-amino-2'-deoxyuridylyl (3'-5') 5'-thio-5'-deoxyuridine (amUpsU) was readily hydrolyzed above pH 7, in contrast to the hydrolytic stability of amUpT, with rates between 85 x 10-6 s-1 and 138 x 10-6 s-1. The hydrolysis of 2'-amino-2'-deoxyuridylyl (3'-5') 5'-amino-5'-deoxythymidine (amUpnT) rose from 17 x 10-6 s-1 at pH 11.5 to 11 685 x 10-6 s-1 at pH 7.0, indicating an acid-catalyzed reaction, where protonation of the 5'-amine is rate limiting. The cleavage rates of UpsU, UpnU, and amUpsU were accelerated in the presence of Mg2+,Zn2+, and Cd2+ ions, but a correlation with interaction between metal ion and leaving group could only be demonstrated for amUpsU. UpsU and UpnU are also substrates for RNase A with UpsU having similar Michaelis-Menten parameters to UpU. In contrast, UpnU is more rapidly degraded with an approximate 35-fold increase in catalytic efficiency, which is reflected purely in an increase in the value of κ(cat).
- Thomson, James B.,Patel, Bhisma K.,Jimenez, Victor,Eckart, Klaus,Eckstein, Fritz
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p. 6273 - 6281
(2007/10/03)
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- Further studies on the buffer-catalyzed cleavage and isomerization of uridyluridine. Medium and ionic strength effects on catalysis by morpholine, imidazole, and acetate buffers help clarify the mechanisms involved and their relationship to the mechanism used by the enzyme ribonuclease and by a ribonuclease mimic
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The cleavage and isomerization of 3',5'-uridyluridine catalyzed by morpholine buffers and by imidazole buffers has been reinvestigated. The key evidence for a previously proposed partitioning mechanism - in which the buffer acid BH+ converts the substrate to a phosphorane monoanion intermediate which then partitions either to the 2',5' isomer of the substrate or (with buffer base catalysis) to the cleavage product - is confirmed. The negative catalytic effect of the buffer base on the isomerization reaction is not due to a medium effect. Indeed the medium effect on this reaction is in the opposite direction, strengthening the catalytic evidence. However, this branching mechanism with sequential bifunctional catalysis of the cleavage reaction is accompanied by an additional cleavage path using the buffer base only. This additional path, for which several alternative mechanisms are possible, is required by the results of improved studies on the imidazole catalysis. These show that the previously reported decrease in rate at a low BH+/B ratio is due to ionic strength effects. The relative importance of these two pathways - one with kinetic dependence on the buffer acid and one without such dependence - depends on the buffer basicity/acidity. With the acidic buffer acetate/acetic acid, a buffer-acid-catalyzed mechanism for the cleavage and the isomerization is dominant. A bifunctional mechanism, in which one step involves simultaneous acid-base catalysis, seems most likely. The medium effects of added dioxane on all these reactions are sensible in terms of the detailed mechanisms proposed. The relationship of these results to the mechanisms of catalysis by ribonuclease and by an enzyme mimic is discussed.
- Breslow, Ronald,Dong, Steven D.,Webb, Yael,Xu, Ruo
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p. 6588 - 6600
(2007/10/03)
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- Zn2+ -promoted hydrolysis of 3',5'-dinucleoside monophosphates and polyribonucleotides. The effect of nearest neighbours on the cleavage of phosphodiester bonds
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Pseudo first-order rate constants for the Zn2+ -promoted cleavage of 15 different dinucleoside monophosphates, 4 different ribo homopolymers and RNA III from baker's yeast have been determined. Furthermore, the distribution of various nucleosides at the 3'- and 5'-terminus of the oligomeric hydrolysis products of RNA has been quantified. On these bases, the effect of nearest neighbours on the metal-ion-promoted hydrolysis of the internucleosidic phosphodiester bonds of RNA is discussed.
- Kuusela, Satu,Loennberg, Harri
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p. 1669 - 1678
(2007/10/03)
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- On the Mechanism of Buffer-Catalyzed Hydrolysis of RNA Models
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An alternative mechanism is proposed for the simultaneous hydrolysis and isomerization of 3',5''-uridyluridine and related dialkyl phosphates in agueous morpholine buffers, which was studied by Breslow and Xu.This alternative mechanism leads to kinetic equations that reproduce the experimental data.
- Perrin, Charles L.
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p. 1239 - 1243
(2007/10/02)
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- Oxidation of nucleic acid related compounds by the peroxodisulfate ion
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The treatment of nucleic acid bases, nucleosides, and nucleotides with peroxodisulfate ion in a phosphate buffer solution at pH 7.0 or water at 70-75°C was investigated. The reaction of thymine and 5-methylcytosine nucleosides and nucleotides resulted in the oxidation of the 5-methyl groups. The oxidation products from 1,3-dimethyluracils and the time-course of the reaction of uracils led to two plausible reaction mechanisms for the oxidation of uracils.
- Itahara,Yoshitake,Koga,Nishino
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p. 2257 - 2264
(2007/10/02)
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- Quantitative evidence for the mechanism of RNA cleavage by enzyme mimics. Cleavage and isomerization of UpU by morpholine buffers
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The cleavage of 3′,5″-UpU to form the 2′,3′-cyclic phosphate and uridine and the simultaneous isomerization of the substrate to 2′,5″-UpU have been studied in morpholine buffer. The total rate of cleavage with morpholine buffer at 90/10 base to acid ratio and constant ionic strength shows an increase with increasing buffer concentration up to 1 M, but the isomerization rate shows a decrease, followed by a constant rate below that of the uncatalyzed process. A similar increase in rate of cleavage - but decrease in rate of isomerization - is also seen with a 95/5 morpholine/ morpholinium buffer and with data that can fit the theoretical equations using those parameters that are common for the 90/10 buffer. With 80/20 morpholine/morpholinium the negative effect of buffer on the rate of isomerization is smaller and not clearly seen. These observations are consistent with the predictions from a kinetic treatment of a previously proposed mechanism: the substrate is converted to a phosphorane intermediate by buffer acid in the common first steps of both processes, but the paths then branch from that intermediate. The cleavage path shows buffer base catalysis, but the isomerization path does not. At higher buffer concentrations an additional catalytic process seems to have been detected. The dependences of the buffer-catalyzed reactions on buffer ratios are also consistent with those reported earlier for imidazole catalysis. The early imidazole data fit the theoretical predictions of our mechanistic treatment. They are also consistent with our mechanism according to a criterion suggested by a critic. The results confirm previous findings. They also furnish detailed evidence for some of the steps that were previously only suggested.
- Breslow, Ronald,Xu, Ruo
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p. 10705 - 10713
(2007/10/02)
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- Charge Description of Base-Catalyzed Alcoholysis of Aryl Phosphodiesters: A Ribonuclease Model
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The release of substituted phenol from aryl uridine-3'-phosphates is catalyzed by bases and involves cyclization to form the 2',3'-cyclic nucleotide.The rate constants for imidazole and hydroxide ion catalysis (kim and kOH, respectively) obey the Broensted equations (25 deg C and 0.25 M ionic strength) log kim = -0.59 pKArOH + 1.40 (n = 7, r = 0.955) and log kOH = -0.54 pKArOH + 6.68 (n = 9, r = 0.967).General-base-catalyzed release of 4-nitrophenol from the 4-nitrophenyl ester (kB) obeys the Broensted relationship log kB = 0.67 pKBH - 7.50 (n = 7, r = 0.989).Charge changes on base and leaving group atoms as determined from the corresponding β and βeq values do not balance.Comparison with data in the literature indicates that the difference in charge may be assigned to the attacking oxygen (2'-hydroxyl) rather than to the phosphoryl oxygens in the O...PO2... group of atoms.Both P-O bond forming and bond fission components of the reaction are considered to be only weakly advanced in a transition state that lies on a concerted pathway.
- Davis, Andrew M.,Hall, Adrian D.,Williams, Andrew
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p. 5105 - 5108
(2007/10/02)
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