131-83-9Relevant academic research and scientific papers
Hydrolysis of 2'- and 3'-C-Methyluridine 2',3'-Cyclic Monophosphates and Interconversion and Dephosphorylation of the Resulting 2'- and 3'-Monophosphates: Comparision with the Reactions of Uridine Monophosphates
Mikhailov, Sergey N.,Oivanen, Mikko,Oksman, Pentti,Loennberg, Harri
, p. 4122 - 4126 (1992)
2',3'-Cyclic monophosphates of 2'- and 3'-C-methyluridines have been prepared and shown to hydrolyze to a mixture of the corresponding 2'- and 3'-monophosphates.The predominant product isomer is the one having the tertiary hydroxyl group phosphorylated, but on longer treatment a phosphate migration from the tertiary to secondary hydroxyl function takes place.Hydrolytic dephosphorylation competes with the phosphate migration, the tertiary hydroxyl group being dephosphorylated 1 order of magnitude faster than the secondary one.Kinetics of the partial reactions have been described and compared to the data obtained with uridine 2',3'-cyclic monophosphate.The tertiary monophosphate has been shown to be exceptionally susceptible to nucleophilic attack of the neighboring hydroxyl group.
Ribonuclease Mimic: Zn2+ Promoted Cleavage of C8-Histamino-r(UpA) proceeds through 2',3'-cUMP as Intermediate
Prakash, Thazha P.,Ganesh, Krishna N.
, p. 1357 - 1358 (1994)
The designed ribodinucleotide 1 containing a proximal imidazole, in the presence of ZnCl2, undergoes self hydrolysis faster than unmodified r(UpA); like its enzymatic counterpart, this reaction goes through the same steps of initial transesterification to 2',3'-cUMP followed by hydrolysis to 2'- or 3'-UMP.
Cleavage and isomerization of UpU promoted by dinuclear metal ion complexes
Linjalahti, Heidi,Feng, Guoqiang,Mareque-Rivas, Juan C.,Mikkola, Satu,Williams, Nicholas H.
, p. 4232 - 4233 (2008)
The catalysis of phosphoryl transfer by metal ions has been intensively studied in both biological and artificial systems, but the status of the transient pentacoordinate phosphoryl species (as transition state or intermediate) is the subject of considerable debate. We report that dinuclear metal ion complexes that incorporate second sphere hydrogen bond donors not only promote the cleavage of RNA fragments just as efficiently as the activated analogue HPNPP but also provide the first examples of metal ion catalyzed phosphate diester isomerization close to neutral pH. This observation implies that the reaction catalyzed by these complexes involves the formation of a phosphorane intermediate that is sufficiently long-lived to pseudorotate. Copyright
Reactivity of a 2'-thio nucleotide analog
Dantzman, Cathy L.,Kiessling, Laura L.
, p. 11715 - 11719 (1996)
The chemical reactivity of ribonucleotide analog 2'-deoxy-2'-thiouridine 3'-(p-nitrophenyl phosphate) (1), in which the 2' hydroxyl is replaced with a 2'-thiol group, has been characterized. The major reaction pathway for 1, as monitored by 31P NMR spectroscopy, is transphosphorylation to afford 2',3'-cyclic phosphorothioate 3, followed by hydrolysis of 3 to produce 2'-deoxy-2'-thiouridine 2'-phosphorothioate (4). Thus, the reaction pathway of 1 is similar to that of the hydrolysis of ribonucleotides, yet there are significant differences. The pH-rate profile for transphosphorylation of 1 was determined by monitoring the formation of p-nitrophenol or p-nitrophenolate by UV-visible spectroscopy. Analysis of the profile reveals the attacking nucleophile to be thiolate, and the pK(a) of the 2'-thiol was determined to be 8.3 ± 0.1. At pH 7.4, the thiol-containing ribonucleotide analog 1 is hydrolyzed at an observed rate 27-fold slower than its 2'-hydroxyl counterpart. These results indicate that the rate of thiolate attack on the adjacent phosphodiester bond is 107-fold slower than that of the corresponding alkoxide. Thiolate nucleophiles, therefore, are remarkably reticent toward attack at electrophilic phosphate centers. In addition to providing new information about the reactivity of phosphodiester bonds, our studies highlight the potential of 2'-thiol-containing nucleotides for the study of an array of RNA processes, especially those in which the 2'-substituent plays a critical role.
Substrate specificity of an active dinuclear Zn(II) catalyst for cleavage of RNA analogues and a dinucleoside
O'Donoghue, Annmarie,Pyun, Sang Yong,Yang, Meng-Yin,Morrow, Janet R.,Richard, John P.
, p. 1615 - 1621 (2006)
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.
Buffer catalyzed cleavage of uridylyl-3′,5′-uridine in aqueous DMSO: Comparison to its activated analog, 2-hydroxypropyl 4-nitrophenyl phosphate
Lain,L?nnberg,L?nnberg
, p. 3484 - 3492 (2015)
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.
Hydrolytic dethiophosphorylation and desulfurization of the monothioate analogues of uridine monophosphates under acidic conditions
Ora, Mikko,Oivanen, Mikko,Loennberg, Harri
, p. 771 - 774 (1996)
The hydrolytic reactions of uridine 2′-, 3′- and 5′-phosphoromonothioates (2′-, 3′- and 5′-UMPS) under acidic and neutral conditions have been followed by HPLC. Under slightly acidic conditions (pH 2-5), only pH-independent dethiophosphorylation to uridine takes place. This reaction is 200- to 300-fold as fast as dephosphorylation of the corresponding uridine monophosphates (UMP), presumably due to higher stability of the thiometaphosphate monoanion compared to metaphosphate anion. At pH > 5, i.e. at pH > pKa2 of the thiophosphate moiety, the dethiophosphorylation is retarded with increasing basicity of the solution. At pH 1, acid-catalysed desulfurization of 2′- and 3′-UMPS to an isomeric mixture of 2′/3′-UMP competes with their dethiophosphorylation. This reaction is suggested to proceed by a nucleophilic attack of the neighbouring hydroxy group on phosphorus. No such reaction occurs with 5′-UMPS. In contrast to 2′- and 3′-UMP, no sign of interconversion of 2′- and 3′-UMPS is detected.
Tethered dinuclear europium(III) macrocyclic catalysts for the cleavage of RNA
Nwe, Kido,Andolina, Christopher M.,Morrow, Janet R.
body text, p. 14861 - 14871 (2009/02/08)
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.
Dinuclear Zn2+ complexes in the hydrolysis of the phosphodiester linkage in a diribonucleoside monophosphate diester.
Yashiro, Morio,Kaneiwa, Hideki,Onaka, Kenichi,Komiyama, Makoto
, p. 605 - 610 (2007/10/03)
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.
The pKa of the internucleotidic 2′-hydroxyl group in diribonucleoside (3′→5′) monophosphates
Acharya,Foeldesi,Chattopadhyaya
, p. 1906 - 1910 (2007/10/03)
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.
