An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction.

The ribosome has an active site comprised of RNA that catalyzes peptide bond formation. To understand how RNA promotes this reaction requires a detailed understanding of the chemical transition state. Here, we report the Brønsted coefficient of the alpha-amino nucleophile with a series of puromycin derivatives. Both 50S subunit- and 70S ribosome-catalyzed reactions displayed linear free-energy relationships with slopes close to zero under conditions where chemistry is rate limiting. These results indicate that, at the transition state, the nucleophile is neutral in the ribosome-catalyzed reaction, in contrast to the substantial positive charge reported for typical uncatalyzed aminolysis reactions. This suggests that the ribosomal transition state involves deprotonation to a degree commensurate with nitrogen-carbon bond formation. Such a transition state is significantly different from that of uncatalyzed aminolysis reactions in solution.

RNA oligonucleotide synthesis via 5'-silyl-2'-orthoester chemistry.

Rapid, reliable, and cost-efficient methods of ribonucleic acid (RNA) oligonucleotide synthesis are in demand owing to an increasing awareness of critical structural, functional, and regulatory roles of RNA throughout biology. The most promising area of growth and development is in RNA interference as an emerging technology for facilitating research in drug discovery and therapeutic intervention. Traditional methods of RNA synthesis, which are based on 2'-silyl protection strategies derived from deoxyribonucleic acid (DNA) synthesis strategies, are limited in their ability to produce oligos of sufficient purity and length for high-throughput applications. The more recently developed 5'-silyl-2'-acetoxy ethyl orthoester chemistry (2'-ACE trade mark ), circumvents several limitations of the 2'-silyl approaches. A clear improvement in RNA synthesis technology, 2'-ACE results in faster coupling rates, higher yields, greater purity, and superior ease of handling. Another advantage of the 2'-ACE protecting group strategy is that the molecules can be produced in an intermediately protected form that is soluble in aqueous solutions but resistant to nuclease attack. The chemistry can be scaled up or down and is flexible enough to allow for the incorporation of modifying groups if desired. A detailed description of the 2'-ACE protocol and procedures for end product analysis are presented.

Chromophoric 5'-O-Silyl protection of N-protected 2'-ACE ribonucleosides for solid-phase RNA synthesis.

Recent advances in the understanding of the pivotal roles played by endogenous small RNAs in gene regulation have resulted in a substantial and rapidly growing market for synthetic RNA. 5'-Silyl-2'-ACE chemistry has proven to be a robust and reliable technology for the synthesis of oligoribonucleotides. This unit describes an important improvement to this chemistry, by adding a cycle-to-cycle traceability analogous to that inherent in 5'-dimethoxytrityl-based approaches. This is achieved by first regioselectively introducing a 5'-alkynylsilyl protecting group onto the 2'-ACE-protected nucleosides. The 5'-alkynylsilyl group is then reacted with an azide derivative of the chromophore Disperse Red 1, which enables spectrophotometric interrogation of each coupling step following 5'-deprotection. Finally, the protected nucleosides are elaborated into their 3'-phosphoramidite derivatives for use in solid-phase RNA synthesis.

Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction.

Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of the large ribosomal subunit. Crystal structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with several analogs that represent either the substrates or the transition state intermediate of the peptidyl transferase reaction show that this reaction proceeds through a tetrahedral intermediate with S chirality. The oxyanion of the tetrahedral intermediate interacts with a water molecule that is positioned by nucleotides A2637 (E. coli numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions observed in the PTC that could directly promote catalysis. The A76 2' hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and could facilitate peptide bond formation by substrate positioning and by acting as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the peptidyl-tRNA.