Thiation of Nucleosides. II. Synthesis of 5-Methyl-2'-deoxycytidine and Related Pyrimidine Nucleosides<sup>1</sup>

Fox, Jack J.; Praag, Dina Van; Wempen, Iris; Doerr, Iris L.; Cheong, Loretta; Knoll, J.; Eidinoff, Maxwell L.; Bendich, Adrianne; Brown, George Bosworth

doi:10.1021/ja01510a042

Cited by 239 publications

(84 citation statements)

References 2 publications

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“…The first three nucleotides in bold are 5-methylcytidine LNA residues, designed to favor and rigidify the A-form strand conformation (26) and thereby facilitate RNA crystallization. At each end of the RNA duplex, the mCmC overhang serves as the binding site for G-G dinucleotides because the mC residues form Watson-Crick base pairs with G (23,27). The RNA cocrystallized with the GpppG ligand with hexagonal symmetry, as in our previous RNA-GMP and RNA-PZG complexes (23).…”

Section: Resultsmentioning

confidence: 81%

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex

Zhang

Tam

Walton

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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The nonenzymatic copying of RNA templates with imidazoleactivated nucleotides is a well-studied model for the emergence of RNA self-replication during the origin of life. We have recently discovered that this reaction can proceed through the formation of an imidazolium-bridged dinucleotide intermediate that reacts rapidly with the primer. To gain insight into the relationship between the structure of this intermediate and its reactivity, we cocrystallized an RNA primer-template complex with a close analog of the intermediate, the triphosphate-bridged guanosine dinucleotide GpppG, and solved a high-resolution X-ray structure of the complex. The structure shows that GpppG binds the RNA template through two Watson-Crick base pairs, with the primer 3ʹ-hydroxyl oriented to attack the 5ʹ-phosphate of the adjacent G residue. Thus, the GpppG structure suggests that the bound imidazoliumbridged dinucleotide intermediate would be preorganized to react with the primer by in-line S N 2 substitution. The structures of bound GppG and GppppG suggest that the length and flexibility of the 5ʹ-5ʹ linkage are important for optimal preorganization of the complex, whereas the position of the 5ʹ-phosphate of bound pGpG explains the slow rate of oligonucleotide ligation reactions. Our studies provide a structural interpretation for the observed reactivity of the imidazolium-bridged dinucleotide intermediate in nonenzymatic RNA primer extension.RNA self-replication | diguanosine dinucleotide | crystal structure | origin of life I n the RNA world hypothesis, the emergence of RNA-catalyzed RNA replication is thought to have been preceded by a stage in which RNA replication was driven purely through chemical processes (1, 2). The nonenzymatic RNA-templated polymerization of activated nucleotides or oligonucleotides has been extensively studied, with the intent of optimizing the rate, extent, and fidelity of nonenzymatic RNA/DNA polymerization (3, 4). Numerous phosphate-activating groups have been studied in the context of nonenzymatic RNA replication. For example, imidazoles such as 2-methylimidazole (5) and, more recently, 2-aminoimidazole (6), have been found to be useful phosphate activators. The potentially prebiotic synthesis of imidazoles under primitive Earth conditions has been investigated (7). On the other hand, Richert and coworkers reported the use of benzotriazole-activated monomers to improve the rate of primer extension (8). In an alternative approach, the in situ activation of monoribonucleotides, and subsequent template-guided polymerization, has been achieved by Richert and coworkers (9), using a carbodiimide reagent together with N-alkyl-imidazole catalysts.Many of the thermodynamic and kinetic parameters associated with nonenzymatic RNA replication have been quantitatively determined (10-14). Until recently, the general assumption has been that nonenzymatic primer extension with activated mononucleotides involves classical S N 2 nucleophilic substitution, in which the nucleophilic 3ʹ-hydroxyl group of the primer attack...

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Section: Resultsmentioning

confidence: 81%

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex

Zhang

Tam

Walton

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…1-Cyclohexylcytosine [(chx)ICI was prepared from 1-cyclohexyl-4-thiouracil as described by Fox et al (14). Guanosine (Guo), 1-methylguanosine (ml Guo), deoxyguanosine (dGuo), and inosine (Ino) were obtained from Sigma.…”

Section: Methodsmentioning

confidence: 99%

Selective recognition of nucleic acids by proteins: the specificity of guanine interaction with carboxylate ions.

Lancelot¹,

Hélène²

1977

Proc. Natl. Acad. Sci. U.S.A.

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The interaction of carboxylate ions (acetate, butyrate) with nucleic acid bases and nucleosides has been investigated by proton magnetic resonance in dimethyl sulfoxide (d6)/H20 mixtures. Carboxylate ions interacted only .with guanine derivatives and led to a large downfield shift of the NH2 resonance. A 1:1 stoichiometry was deduced from a study of the concentration de endence of chemical shifts. A study of substituted guanine showed that hydrogen bonding involved N(1)H and NH(An association constant of 110 M-' was determined. This value is about 30 times higher than the association constant for guaninecytosine base pair formation under the same experimental conflitions. As a matter of fact, carboxylate ions induced a dissociation of guaninecytosine base pairs. This guanine-carl)6 late association is experimental evidence for a highly specific interaction that could play an important role in protein/nucleic acid recognition.

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“…3), some previous workers are of the opinion that (A) represents CH+. On the contrary, potentiometric, spectrophotometric, and ultrasonic studies (14,18) and similarity of pK, values of CH+ and protonated aniline (PhNH:) (19) Since ultrasonic absorption studies of proton transfer reactions in alkaline range shows no absorption maximum, Zana et al conclude that C molecule does not contain lactam group. Therefore, as per Scheme 2, the lactim form of C is predominantly involved in yielding the extractable proton in alkaline range.…”

Section: R -H Uracil R --C H3thyminementioning

confidence: 99%

Protonation/deprotonation energetics of uracil, thymine, and cytosine in water from e.m.f./spectrophotometric measurements

Ganguly¹,

Kundu²

1994

Can. J. Chem.

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The protonatioddeprotonation constants for uracil (U) (pK, and pK2), thymine (T) (pK1) and cytosine (C) (pK1 and pK2) in water have been determined from emf measurements of Harned-Ehler type cells comprising HZ and Ag-AgI electrodes at five equidistant temperatures ranging from 15-35°C. The pKa values were fitted in the temperature equation pK, = AT-' + B + CT by the method of least squares and the standard free energies (AGO), entropies (AS0), and enthalpies (AH0) of protonatioddeprotonation processes in water were evaluated using the values of the coefficients A, B, and C of the respective acids. The second step deprotonation constant for T was determined using precise spectrophotometric method. The results have been duly compared with the existing literature data and are also shown to derive important reflections on the sites of protonatioddeprotonation in the light of pK values of some acids and bases of comparable~functional groups and especially the entropies of protonatioddeprotonation of the key DNA-RNA base molecules.

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Thiation of Nucleosides. II. Synthesis of 5-Methyl-2'-deoxycytidine and Related Pyrimidine Nucleosides¹

Cited by 239 publications

References 2 publications

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex

Selective recognition of nucleic acids by proteins: the specificity of guanine interaction with carboxylate ions.

Protonation/deprotonation energetics of uracil, thymine, and cytosine in water from e.m.f./spectrophotometric measurements

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Thiation of Nucleosides. II. Synthesis of 5-Methyl-2'-deoxycytidine and Related Pyrimidine Nucleosides1

Cited by 239 publications

References 2 publications

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex

Selective recognition of nucleic acids by proteins: the specificity of guanine interaction with carboxylate ions.

Protonation/deprotonation energetics of uracil, thymine, and cytosine in water from e.m.f./spectrophotometric measurements

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Thiation of Nucleosides. II. Synthesis of 5-Methyl-2'-deoxycytidine and Related Pyrimidine Nucleosides¹