Three-dimensional structure-guided evolution of a ribosome with tethered subunits.

RNA-based macromolecular machines, such as the ribosome, have functional parts reliant on structural interactions spanning sequence-distant regions. These features limit evolutionary exploration of mutant libraries and confound three-dimensional structure-guided design. To address these challenges, we describe Evolink (evolution and linkage), a method that enables high-throughput evolution of sequence-distant regions in large macromolecular machines, and library design guided by computational RNA modeling to enable exploration of structurally stable designs.

Ribosome-mediated incorporation of fluorescent amino acids into peptides in vitro.

We report the design, chemical synthesis, and flexizyme-catalyzed transfer RNA (tRNA) acylation of a variety of fluorescent amino acids (FAAs). The fluorescent groups include pyrene, coumarin, nitrobenzoxadiazole, and fluorescein variants. We further demonstrate site-specific incorporation of the FAAs into peptides by the ribosome in vitro through genetic code reprogramming.

Photoexcitation of Grubbs' Second-Generation Catalyst Initiates Frontal Ring-Opening Metathesis Polymerization.

In this work, a simple method is reported for control over initiation in frontal ring-opening metathesis polymerization (FROMP). This noncontact approach uses 375 nm light to excite Grubbs' second-generation catalyst in the presence of a phosphite inhibitor. Photoinitiated FROMP of dicylcopentadiene (DCPD) displays a similar cure profile to that of its thermally initiated counterpart, yielding a robust polymer with high glass transition temperature.

Ribosome-mediated polymerization of long chain carbon and cyclic amino acids into peptides in vitro.

Ribosome-mediated polymerization of backbone-extended monomers into polypeptides is challenging due to their poor compatibility with the translation apparatus, which evolved to use α-L-amino acids. Moreover, mechanisms to acylate (or charge) these monomers to transfer RNAs (tRNAs) to make aminoacyl-tRNA substrates is a bottleneck. Here, we rationally design non-canonical amino acid analogs with extended carbon chains (γ-, δ-, ε-, and ζ-) or cyclic structures (cyclobutane, cyclopentane, and cyclohexane) to improve tRNA charging.

Expanding the limits of the second genetic code with ribozymes.

The site-specific incorporation of noncanonical monomers into polypeptides through genetic code reprogramming permits synthesis of bio-based products that extend beyond natural limits. To better enable such efforts, flexizymes (transfer RNA (tRNA) synthetase-like ribozymes that recognize synthetic leaving groups) have been used to expand the scope of chemical substrates for ribosome-directed polymerization. The development of design rules for flexizyme-catalyzed acylation should allow scalable and rational expansion of genetic code reprogramming.

Enantioselective α-Benzylation of Acyclic Esters Using π-Extended Electrophiles.

The first asymmetric cooperative Lewis base/palladium catalyzed benzylic alkylation of acyclic esters is reported. This reaction proceeds via stereodefined C1-ammonium enolate nucleophiles. Critical to its success was the identification of benzylic phosphate electrophiles, which were uniquely reactive.

Traversing Steric Limitations by Cooperative Lewis Base/Palladium Catalysis: An Enantioselective Synthesis of α-Branched Esters Using 2-Substituted Allyl Electrophiles.

Cooperative catalysis enables the direct enantioselective α-allylation of linear prochiral esters with 2-substituted allyl electrophiles. Critical to the successful development of the method was the recognition that metal-centered reactivity and the source of enantiocontrol are independent. This feature is unique to simultaneous catalysis events and permits logical tuning of the supporting ligands without compromising enantioselectivity.

Uniting C1-Ammonium Enolates and Transition Metal Electrophiles via Cooperative Catalysis: The Direct Asymmetric α-Allylation of Aryl Acetic Acid Esters.

The direct, catalytic, asymmetric α-functionalization of acyclic esters constitutes a significant challenge in the area of asymmetric catalysis, particularly where the configurational integrity of the products is problematic. Through the unprecedented merger of two independent, yet complementary, catalysis events it has been possible to facilitate the direct asymmetric α-allylation of readily available aryl acetic acid esters. Since enantioselection is determined by the nucleophile, this conceptual approach to cooperative catalysis constitutes a potentially general solution to the direct catalytic asymmetric α-functionalization of acyclic esters.