Synthesis and properties of 2'-deoxy-2'-thiocytidine

Patel, Anjali; Schrier, Wayne H.; Nagyvary, Joseph

doi:10.1021/jo01312a005

Cited by 31 publications

(6 citation statements)

References 9 publications

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“…The pK a for protonation of the amine is expected to be approximately 6 (38,39), while the pK a for deprotonation of the sulfhydryl is approximately 7 (40,41). Selective binding of either inhibitor as a function of pH (the NH 3 + forms at low pH or the Sforms at high pH) would provide evidence that the ribosome stabilizes an ionized form of the A76 2′-OH group.…”

Section: Resultsmentioning

confidence: 99%

Transition State Chirality and Role of the Vicinal Hydroxyl in the Ribosomal Peptidyl Transferase Reaction

et al. 2008

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The ribosomal peptidyl transferase is a biologically essential catalyst responsible for protein synthesis. The reaction is expected to proceed through a transition state approaching tetrahedral geometry with a specific chirality. To establish that stereospecificity, we synthesized two diastereomers of a transition state inhibitor with mimics for each of the four ligands around the reactive chiral center. Preferential binding of the inhibitor that mimics a transition state with S chirality establishes the spatial position of the nascent peptide, the oxyanion and places the amine near the critical A76 2′-OH on the P-site tRNA. Another inhibitor series with 2′-NH 2 and 2′-SH substitutions at the critical 2′-OH group was used to test the neutrality of the 2′-OH as predicted if the hydroxyl functions as a proton shuttle in the transition state. Lack of significant pH dependent binding by these inhibitors argues that the 2′-OH remains neutral in the transition state. Both of these observations are consistent with a proton shuttle mechanism for the peptidyl transferase reaction.

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Section: Resultsmentioning

confidence: 99%

Transition State Chirality and Role of the Vicinal Hydroxyl in the Ribosomal Peptidyl Transferase Reaction

et al. 2008

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“…Although 2‘-mercaptonucleosides have been known for almost two decades, they rarely have been exploited as biochemical probes, possibly because there has been no convenient method for incorporating them into oligonucleotides. Additionally, early reports that the glycosidic linkage of 2‘-mercaptonucleosides is highly labile under physiological conditions may have discouraged biological chemists from using them.…”

Section: Introductionmentioning

confidence: 99%

Unconventional Origin of Metal Ion Rescue in the Hammerhead Ribozyme Reaction: Mn²⁺-Assisted Redox Conversion of 2‘-Mercaptocytidine to Cytidine

et al. 2000

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A specific oxygen atom in RNA is identified as a ligand for a metal ion when sulfur substitution of that atom shifts the metal ion specificity of the RNA-mediated process to a more thiophilic metal. Extensive discussion and debate have centered around whether a metal ion activates the 2′-oxygen nucleophile during the phosphotransesterification reaction catalyzed by the hammerhead ribozyme (HH). To test this possibility, we probed the metal ion specificity of HH reactions using a substrate that contained 2′-mercaptocytidine at the cleavage site. This substrate is generated in situ from a disulfide-protected precursor by treatment with tris(carboxyethyl)phosphine (TCEP). In HH reactions with this substrate, phosphotransesterification does not occur when Mg 2+ is present as the only divalent cation but does occur in the presence of Mn 2+ . These results are consistent with a direct interaction between the metal ion and the nucleophile. However, further analysis reveals that this switch in metal ion specificity does not arise because Mn 2+ coordinates sulfur more readily than Mg 2+ does, but because under the assay conditions, the 2′-mercaptocytidine residue is converted to a mixture of cytidyl-1-β-D-arabinofuranoside and cytidyl-1-β-D-ribofuranoside, the natural substrate for the ribozyme. This conversion occurs in the absence of HH ribozyme, requires Mn 2+ (or Co 2+ ), O 2 , and TCEP, and is inhibited by a free radical scavenger. The mechanism presumably involves a multistep free radical process, in which the key step is homolytic fission of the C2′-sulfur bond induced by TCEP. The putative 2′-carbon radical then reacts with an oxygen species to produce the cytidyl-1-β-D-arabinofuranoside and ribocytidine products. To our knowledge, this chemical transformation is unprecedented in the literature and represents a new reaction for nucleic acids. If O 2 is excluded from the HH reactions, the 2′-sulfur is not modified in the presence of Mn 2+ but is still blocked in the phosphotransesterification reaction, both in the forward direction as the mercapto (-SH) group or in the reverse direction as part of a cyclic phosphorothiolate. Although we are unable to provide evidence for metal ion activation of the nucleophile in the HH ribozyme reaction, this work establishes the groundwork for further use of 2′-mercaptonucleotides in biochemical analyses.

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“…2 H -Thiocytidine derivatives can be prepared not only by transamination of uridine, 93,97 but also by opening of the O 2 ,2 Hanhydrocytidine ring. 98 An intramolecular attack of the 3 H -Odithiophosphate group at the C(2 H ) atom of substituted O 2 ,2 Hanhydrocytidine 52 has been described. 98 This yields a mixture of 2 H ,3 H -cyclodithiophosphate 53 and 2 H ,3 H -cyclothiophosphate 54 which can be prepared from compound 53 by treatment with iodine.…”

Section: Synthesis Of Nucleosides Containing a Thiol Groupmentioning

confidence: 99%

Nucleosides and oligonucleotides containing 2'-reactive groups: synthesis and applications

Zatsepin¹,

Романова²,

Oretskaya³

2004

Russ. Chem. Rev.

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The known methods for the synthesis of 2 The known methods for the synthesis of 2 H -functional--functionalised nucleosides, oligonucleotides and their conjugates are sys-ised nucleosides, oligonucleotides and their conjugates are systematised. The applications of 2 tematised. The applications of 2 H -modified nucleosides and -modified nucleosides and oligonucleotides are discussed. The bibliography includes 451 oligonucleotides are discussed. The bibliography includes 451 references references. .

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Synthesis and properties of 2'-deoxy-2'-thiocytidine

Cited by 31 publications

References 9 publications

Transition State Chirality and Role of the Vicinal Hydroxyl in the Ribosomal Peptidyl Transferase Reaction

Transition State Chirality and Role of the Vicinal Hydroxyl in the Ribosomal Peptidyl Transferase Reaction

Unconventional Origin of Metal Ion Rescue in the Hammerhead Ribozyme Reaction: Mn²⁺-Assisted Redox Conversion of 2‘-Mercaptocytidine to Cytidine

Nucleosides and oligonucleotides containing 2'-reactive groups: synthesis and applications

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Synthesis and properties of 2'-deoxy-2'-thiocytidine

Cited by 31 publications

References 9 publications

Transition State Chirality and Role of the Vicinal Hydroxyl in the Ribosomal Peptidyl Transferase Reaction

Transition State Chirality and Role of the Vicinal Hydroxyl in the Ribosomal Peptidyl Transferase Reaction

Unconventional Origin of Metal Ion Rescue in the Hammerhead Ribozyme Reaction: Mn2+-Assisted Redox Conversion of 2‘-Mercaptocytidine to Cytidine

Nucleosides and oligonucleotides containing 2'-reactive groups: synthesis and applications

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Unconventional Origin of Metal Ion Rescue in the Hammerhead Ribozyme Reaction: Mn²⁺-Assisted Redox Conversion of 2‘-Mercaptocytidine to Cytidine