- Prebiotically Plausible RNA Activation Compatible with Ribozyme-Catalyzed Ligation
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RNA-catalyzed RNA ligation is widely believed to be a key reaction for primordial biology. However, since typical chemical routes towards activating RNA substrates are incompatible with ribozyme catalysis, it remains unclear how prebiotic systems generated and sustained pools of activated building blocks needed to form increasingly larger and complex RNA. Herein, we demonstrate in situ activation of RNA substrates under reaction conditions amenable to catalysis by the hairpin ribozyme. We found that diamidophosphate (DAP) and imidazole drive the formation of 2′,3′-cyclic phosphate RNA mono- and oligonucleotides from monophosphorylated precursors in frozen water-ice. This long-lived activation enables iterative enzymatic assembly of long RNAs. Our results provide a plausible scenario for the generation of higher-energy substrates required to fuel ribozyme-catalyzed RNA synthesis in the absence of a highly evolved metabolism.
- Song, Emilie Yeonwha,Jiménez, Eddy Ivanhoe,Lin, Huacan,Le Vay, Kristian,Krishnamurthy, Ramanarayanan,Mutschler, Hannes
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supporting information
p. 2952 - 2957
(2020/12/13)
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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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- 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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- Phosphodiester cleavage of guanylyl-(3′,3′)-(2′-amino- 2′-deoxyuridine): Rate acceleration by the 2′-amino function
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Hydrolytic reactions of the structural analogue of guanylyl-(3′, 3′)-uridine, guanylyl-(3′,3′)-(2′-amino-2′- deoxyuridine), having one of the 2′-hydroxyl groups replaced with an amino function, have been followed by RP HPLC in the pH range 0-13 at 90°C. The results are compared to those obtained earlier with guanylyl-(3′,3′) -uridine, guanylyl-(3′,3′)-(2′,5′-di-O-methyluridine), and uridylyl-(3′,5′)-uridine. Under basic conditions (pH > 8), the hydroxide ion-catalyzed cleavage of the P-O3′ bond (first-order in [OH-]) yields a mixture of 2′-amino-2′-deoxyuridine and guanosine 2′,3′-cyclic phosphate which is hydrolyzed to guanosine 2′- and 3′-phosphates. Under these conditions, guanylyl-(3′, 3′)-(2′-amino-2′-deoxyuridine) is 10 times less reactive than guanylyl-(3′,3′)-uridine. Under acidic and neutral conditions (pH 3-8), where the pH-rate profile for the cleavage consists of two pH-independent regions (from pH 3 to pH 4 and from 6 to 8), guanylyl-(3′,3′)- (2′-amino-2′-deoxyuridine) is considerably reactive. For example, in the latter pH range, guanylyl-(3′,3′)-(2′-amino-2′- deoxyuridine) is more than 2 orders of magnitude more labile than guanylyl(3′,3′)-(2′,5′-di-O-methyluridine), while in the former pH range the reactivity difference is 1 order of magnitude. Under very acidic conditions (pH +]) compete with the cleavage. The Zn2+-promoted cleavage ([Zn2+] = 5 mmol L-1) is 15 times faster than the uncatalyzed reaction at pH 5.6. The mechanisms of the reactions of guanylyl-(3′,3′)-(2′-amino-2′-deoxyuridine) are discussed, particularly focusing on the possible stabilization of phosphorane intermediate and/or transition state via an intramolecular hydrogen bonding by the 2′-amino group.
- Ora, Mikko,Linjalahti, Heidi,Loennberg, Harri
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p. 1826 - 1832
(2007/10/03)
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- Hydrolytic reactions of guanosyl-(3′,3′)-uridine and guanosyl-(3′,3′)-(2′,5′-di-O-methyluridine)
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Hydrolytic reactions of guanosyl-(3′,3′)-uridine and guanosyl-(3′,3′)-(2′,5′-di-O-methyluridine) have been followed by RP HPLC over a wide pH range at 363.2 K in order to elucidate the role of the 2′-hydroxyl group as a hydrogen-bond donor upon departure of the 3′-uridine moiety. Under neutral and basic conditions, guanosyl-(3′,3′)-uridine undergoes hydroxide ion-catalyzed cleavage (first order in [OH-]) of the P-O3′ bonds, giving uridine and guanosine 2′,3′-cyclic monophosphates, which are subsequently hydrolyzed to a mixture of 2′- and 3′-monophosphates. This bond rupture is 23 times as fast as the corresponding cleavage of the P-O3′ bond of guanosyl-(3′,3′)-(2,5′-di-O-methyluridine) to yield 2′,5′-O-dimethyluridine and guanosine 2′,3′-cyclic phosphate. Under acidic conditions, where the reactivity differences are smaller, depurination and isomerization compete with the cleavage. The effect of Zn2+ on the cleavage of the P-O3′ bonds of guanosyl-(3′,3′)-uridine is modest: about 6-fold acceleration was observed at [Zn2+] = 5 mmol L-1 and pH 5.6. With guanosyl-(3′,3′)-(2′,5′-di-O-methyluridine) the rate-acceleration effect is greater: a 37-fold acceleration was observed. The mechanisms of the partial reactions, in particular the effects of the 2′-hydroxyl group on the departure of the 3′-linked nucleoside, are discussed.
- Kiviniemi, Anu,Loennberg, Tuomas,Ora, Mikko
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p. 11040 - 11045
(2007/10/03)
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- Hydrolysis of diribonucleoside monophosphate diesters assisted by a manganese(II) complex
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An Mn2+ complex with 2,2′:6′,2″-terpyridine (terpy) was found to promote the hydrolysis of NpN (NpN = diribonucleoside monophosphate diester) efficiently at pH 7.0 and 50 °C under ambient conditions. The structure of the Mn2+ complex involving a phosphodiester molecule, [(terpy)(dpp)MnII(μ-dpp) 2MnII(dpp)(terpy)], dpp = diphenyl phosphate anion, was established by X-ray crystallography, and the coordination mode of Mn 2+ to a phosphodiester molecule was considered.
- Yashiro, Morio,Higuchi, Maiko,Komiyama, Makoto,Ishii, Youichi
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p. 1813 - 1817
(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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