Spectral broadening in convex-concave multipass cells.

Since its first demonstration in 2016, the multi-pass spectral broadening technique has covered impressive ranges of pulse energy (3 µJ - 100 mJ) and peak power (4 MW - 100 GW). Energy scaling of this technique into the joule-level is currently limited by phenomena such as optical damage, gas ionization and spatio-spectral beam inhomogeneity. These limitations can be overcome by the novel multi-pass convex-concave arrangement, which exhibits crucial properties such as large mode size and compactness. In a proof-of-principle experiment, 260 fs, 15 µJ and 200 µJ pulses are broadened and subsequently compressed to approximately 50 fs with 90% efficiency and excellent spatio-spectral homogeneity across the beam profile. We simulate the proposed concept for spectral broadening of 40 mJ and 1.3 ps input pulses and discuss the possibility of further scaling.

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. Using Evolink, we evolved a tethered ribosome with a 58% increased activity in orthogonal protein translation and a 97% improvement in doubling times in SQ171 cells compared to a previously developed tethered ribosome, and reveal new permissible sequences in a pair of ribosomal helices with previously explored biological function. The Evolink approach may enable enhanced engineering of macromolecular machines for new and improved functions for synthetic biology.

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.

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. We then demonstrate site-specific incorporation of these non-canonical, backbone-extended monomers at the N- and C- terminus of peptides using wild-type and engineered ribosomes. This work expands the scope of ribosome-mediated polymerization, setting the stage for new medicines and materials.

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. Furthermore, this system is applied to enhance reaction rates in conventional ring-closing metathesis reactions.

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. Here we report the systematic synthesis of 37 substrates based on 4 chemically diverse scaffolds (phenylalanine, benzoic acid, heteroaromatic, and aliphatic monomers) with different electronic and steric factors. Of these substrates, 32 were acylated onto tRNA and incorporated into peptides by in vitro translation. Based on the design rules derived from this expanded alphabet, we successfully predicted the acylation of 6 additional monomers that could uniquely be incorporated into peptides and direct N-terminal incorporation of an aldehyde group for orthogonal bioconjugation reactions.

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. Alkylated products were obtained with very high levels of enantioselectivity, and this method has been applied toward the synthesis of the thrombin inhibitor DX-9065a.

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.