Merging DNA Repair with Bioorthogonal Conjugation Enables Accessible and Versatile Asymmetric DNA Catalysis.

Optimizing catalysts through high-throughput screening for asymmetric catalysis is challenging due to the difficulty associated with assembling a library of catalyst analogues in a timely fashion. Here, we repurpose DNA excision repair and integrate it with bioorthogonal conjugation to construct a diverse array of DNA hybrid catalysts for highly accessible and high-throughput asymmetric DNA catalysis, enabling a dramatically expedited catalyst optimization process, superior reactivity and selectivity, as well as the first atroposelective DNA catalysis. The bioorthogonality of this conjugation strategy ensures exceptional tolerance toward diverse functional groups, thereby facilitating the facile construction of 44 DNA hybrid catalysts bearing various unprotected functional groups. This unique feature holds the potential to enable catalytic modalities in asymmetric DNA catalysis that were previously deemed unattainable.

Multifaceted nucleic acid probing with a rationally upgraded molecular rotor.

Probing the sequence alterations, structures, interactions, and other important aspects of nucleic acids serves as the cornerstone of understanding nucleic acid-mediated biology and etiology, as well as the development of nucleic acid-based therapeutics. New strategies capable of accommodating these imperatives without necessitating specialized instrument or skills and potentially complementing existing methods are highly desired. Herein, we describe a rationally designed molecular rotor CCVJ-H ((9-(2-carboxy-2-cyanovinyl)julolidine-hydrazide)) and its superior performances compared to the universal base excision reporter probe CCVJ-1 in applications such as nucleic acid detection and DNA glycosylase assays. Furthermore, we showcase that the CCVJ-H probe accurately profiles the interactions between nucleic acids and small molecules, providing binding affinity and binding site information in a single reaction. We subsequently demonstrate the feasibility of applying the CCVJ-H system in high-throughput screening to identify nucleic acid-binding small molecules such as DNA CTG repeat expansion binders, potentially providing therapeutic interventions for myotonic dystrophy type 1. Finally, we profile the recognition difference between DNA/DNA and DNA/RNA against a library of small molecules, uncovering two drug-like molecules that preferentially bind DNA/RNA. We anticipate the versatile CCVJ-H probe will be a useful tool for both fundamental and translational nucleic acid research and application.

RNA Control via Redox-Responsive Acylation.

Incorporating stimuli-responsive components into RNA constructs provides precise spatiotemporal control over RNA structures and functions. Despite considerable advancements, the utilization of redox-responsive stimuli for the activation of caged RNAs remains scarce. In this context, we present a novel strategy that leverages post-synthetic acylation coupled with redox-responsive chemistry to exert control over RNA. To achieve this, we design and synthesize a series of acylating reagents specifically tailored for introducing disulfide-containing acyl adducts into the 2'-OH groups of RNA ("cloaking"). Our data reveal that these acyl moieties can be readily appended, effectively blocking RNA catalytic activity and folding. We also demonstrate the traceless release and reactivation of caged RNAs ("uncloaking") through reducing stimuli. By employing this strategy, RNA exhibits rapid cellular uptake, effective distribution and activation in the cytosol without lysosomal entrapment. We anticipate that our methodology will be accessible to laboratories engaged in RNA biology and holds promise as a versatile platform for RNA-based applications.

Designer Fluorescent Adenines Enable Real-Time Monitoring of MUTYH Activity.

The human DNA base excision repair enzyme MUTYH (MutY homolog DNA glycosylase) excises undamaged adenine that has been misincorporated opposite the oxidatively damaged 8-oxoG, preventing transversion mutations and serving as an important defense against the deleterious effects of this damage. Mutations in the MUTYH gene predispose patients to MUTYH-associated polyposis and colorectal cancer, and MUTYH expression has been documented as a biomarker for pancreatic cancer. Measuring MUTYH activity is therefore critical for evaluating and diagnosing disease states as well as for testing this enzyme as a potential therapeutic target. However, current methods for measuring MUTYH activity rely on indirect electrophoresis and radioactivity assays, which are difficult to implement in biological and clinical settings. Herein, we synthesize and identify novel fluorescent adenine derivatives that can act as direct substrates for excision by MUTYH as well as bacterial MutY. When incorporated into synthetic DNAs, the resulting fluorescently modified adenine-release turn-on (FMART) probes report on enzymatic base excision activity in real time, both in vitro and in mammalian cells and human blood. We also employ the probes to identify several promising small-molecule modulators of MUTYH by employing FMART probes for in vitro screening.

Distal γ-C(sp3 )-H Olefination of Ketone Derivatives and Free Carboxylic Acids.

Reported herein is the distal γ-C(sp3 )-H olefination of ketone derivatives and free carboxylic acids. Fine tuning of a previously reported imino-acid directing group and using the ligand combination of a mono-N-protected amino acid (MPAA) and an electron-deficient 2-pyridone were critical for the γ-C(sp3 )-H olefination of ketone substrates. In addition, MPAAs enabled the γ-C(sp3 )-H olefination of free carboxylic acids to form diverse six-membered lactones. Besides alkyl carboxylic acids, benzylic C(sp3 )-H bonds also could be functionalized to form 3,4-dihydroisocoumarin structures in a single step from 2-methyl benzoic acid derivatives. The utility of these protocols was demonstrated in large scale reactions and diversification of the γ-C(sp3 )-H olefinated products.

Enantioselective C(sp3)‒H bond activation by chiral transition metal catalysts.

Organic molecules are rich in carbon-hydrogen bonds; consequently, the transformation of C-H bonds to new functionalities (such as C-C, C-N, and C-O bonds) has garnered much attention by the synthetic chemistry community. The utility of C-H activation in organic synthesis, however, cannot be fully realized until chemists achieve stereocontrol in the modification of C-H bonds. This Review highlights recent efforts to enantioselectively functionalize C(sp3)-H bonds via transition metal catalysis, with an emphasis on key principles for both the development of chiral ligand scaffolds that can accelerate metalation of C(sp3)-H bonds and stereomodels for asymmetric metalation of prochiral C-H bonds by these catalysts.

Ligand-Enabled γ-C(sp3)-H Activation of Ketones.

We report the first example of Pd(II)-catalyzed γ-C(sp3)-H activation of ketones directed by a practical 2,2-dimethyl aminooxyacetic acid auxiliary. 2-Pyridone ligands are identified to enable C(sp3)-H activation for the first time. A rare six-membered palladacycle intermediate is isolated and characterized to elucidate the reaction mechanism. Both (hetero)arylation and vinylation of γ-C(sp3)-H bonds are demonstrated. Sequential ß- and γ-C(sp3)-H (hetero)arylation of muscone showcases the utility of this method for late-stage diversification. A convenient Mn(II)-catalyzed auxiliary removal is also developed to further underscore the practicality of this transformation.

Versatile Alkylation of (Hetero)Aryl Iodides with Ketones via ß-C(sp3)-H Activation.

We report Pd(II)-catalyzed ß-C(sp3)-H (hetero)arylation of a variety of ketones using a commercially available 2,2-dimethyl aminooxyacetic acid auxiliary. Facile installation and removal of the auxiliary as well as its superior scope for both ketones and (hetero)aryl iodides overcome the significant limitations of the previously reported ß-C(sp3)-H arylation of ketones. The ready availability of ketones renders this reaction a broadly useful method for alkyl-(hetero)aryl coupling involving both primary and secondary alkyls.

An Epoxide-Mediated Deprotection Method for Acidic Amide Auxiliary.

A practical method for the removal of a versatile acidic amide auxiliary has been developed. Facile alcoholysis of the amide in the presence of KOAc is enabled by an epoxide, which mechanistically resembles the removal of the Myers' auxiliary. The protocol has been applied to the removal of a variety of amide substrates and their C-H functionalization products with high efficiency and low cost, representing a step forward toward the development of a versatile directing group for C-H activation.

Highly Versatile ß-C(sp3)-H Iodination of Ketones Using a Practical Auxiliary.

The first example of palladium(II)-catalyzed ß-C(sp3)-H iodination of a wide range of ketones using a commercially available aminooxyacetic acid auxiliary has been achieved. This L, X-type directing group overcomes the limitations of the transient directing group approach for C(sp3)-H functionalization of ketones. Practical advantages of this method include simple installation of the auxiliary without chromatography, exceptional tolerance of α-functional groups, as well as alkenes and alkynes, and rapid access to diverse sterically hindered quaternary centers.

Ligand-Enabled Pd(II)-Catalyzed Bromination and Iodination of C(sp3)-H Bonds.

We herein report the palladium(II)-catalyzed bromination and iodination of a variety of α-hydrogen-containing carboxylic acid and amino acid-derived amides. These reactions are exclusively enabled by quinoline-type ligands. The halogenated products obtained in this reaction are highly versatile and rapidly undergo further diversification. Further, we report the first example of a free carboxylic acid-directed Pd(II)-catalyzed C(sp3)-H bromination, enabled by quinoline ligands.

Formation of α-chiral centers by asymmetric ß-C(sp3)-H arylation, alkenylation, and alkynylation.

The enzymatic ß-C-H hydroxylation of the feedstock chemical isobutyric acid has enabled the asymmetric synthesis of a wide variety of polyketides. The analogous transition metal-catalyzed enantioselective ß-C-H functionalization of isobutyric acid-derived substrates should provide a versatile method for constructing useful building blocks with enantioenriched α-chiral centers from this abundant C-4 skeleton. However, the desymmetrization of ubiquitous isopropyl moieties by organometallic catalysts has remained an unanswered challenge. Herein, we report the design of chiral mono-protected aminomethyl oxazoline ligands that enable desymmetrization of isopropyl groups via palladium insertion into the C(sp3)-H bonds of one of the prochiral methyl groups. We detail the enantioselective ß-arylation, -alkenylation, and -alkynylation of isobutyric acid/2-aminoisobutyric acid derivatives, which may serve as a platform for the construction of α-chiral centers.

A Simple and Versatile Amide Directing Group for C-H Functionalizations.

Achieving selective C-H activation at a single and strategic site in the presence of multiple C-H bonds can provide a powerful and generally useful retrosynthetic disconnection. In this context, a directing group serves as a compass to guide the transition metal to C-H bonds by using distance and geometry as powerful recognition parameters to distinguish between proximal and distal C-H bonds. However, the installation and removal of directing groups is a practical drawback. To improve the utility of this approach, one can seek solutions in three directions: 1) Simplifying the directing group, 2) using common functional groups or protecting groups as directing groups, and 3) attaching the directing group to substrates via a transient covalent bond to render the directing group catalytic. This Review describes the rational development of an extremely simple and yet broadly applicable directing group for Pd(II) , Rh(III) , and Ru(II) catalysts, namely the N-methoxy amide (CONHOMe) moiety. Through collective efforts in the community, a wide range of C-H activation transformations using this type of simple directing group have been developed.

Ligand-Enabled Arylation of γ-C-H Bonds.

Pd(II) -catalyzed arylation of γ-C(sp(3) )-H bonds of aliphatic acid-derived amides was developed by using quinoline-based ligands. Various γ-aryl-α-amino acids were prepared from natural amino acids using this method. The influence of ligand structure on reactivity was also systematically investigated.

Ligand-Promoted Borylation of C(sp(3))-H Bonds with Palladium(II) Catalysts.

A quinoline-based ligand effectively promotes the palladium-catalyzed borylation of C(sp(3))-H bonds. Primary ß-C(sp(3))-H bonds in carboxylic acid derivatives as well as secondary C(sp(3))-H bonds in a variety of carbocyclic rings, including cyclopropanes, cyclobutanes, cyclopentanes, cyclohexanes, and cycloheptanes, can thus be borylated. This directed borylation method complements existing iridium(I)- and rhodium(I)-catalyzed C-H borylation reactions in terms of scope and operational conditions.

Ligand-Enabled Meta-C-H Alkylation and Arylation Using a Modified Norbornene.

2-Carbomethoxynorbornene is identified as a more effective transient mediator to promote a Pd(II)-catalyzed meta-C(sp(2))-H alkylation of amides with various alkyl iodides as well as arylation with previously incompatible aryl iodides. The use of a tailor-made quinoline ligand is also crucial for this reaction to proceed.

Ligand-Enabled Stereoselective ß-C(sp(3))-H Fluorination: Synthesis of Unnatural Enantiopure anti-ß-Fluoro-α-amino Acids.

A quinoline-based ligand was shown to promote palladium-catalyzed ß-C(sp(3))-H fluorination for the first time. A range of unnatural enantiopure fluorinated α-amino acids were obtained through sequential ß-C(sp(3))-H arylation and subsequent stereoselective fluorination from readily available L-alanine.

Ligand-enabled meta-C-H activation using a transient mediator.

Achieving site selectivity in C-H functionalization reactions is a significant challenge, especially when the target C-H bond is distant from existing functional groups. Coordination of a functional group to a metal is often a key driving force and control element in many important reactions including asymmetric hydrogenation, epoxidation and lithiation. Exploitation of this effect has led to the development of a broad range of directed C-H activation reactions. However, these C-H activation methods are limited to proximal C-H bonds, which are spatially and geometrically accessible from the directing functional group. The development of meta-selective C-H functionalizations remains a significant challenge. We recently developed a U-shaped template that can be used to overcome this constraint and have shown that it can be used to selectively activate remote meta-C-H bonds. Although this approach has proved to be applicable to various substrates and catalytic transformations, the need for a covalently attached, complex template is a substantial drawback for synthetic applications. Here we report an alternative approach employing norbornene as a transient mediator to achieve meta-selective C-H activation with a simple and common ortho-directing group. The use of a newly developed pyridine-based ligand is crucial for relaying the palladium catalyst to the meta position by norbornene after initial ortho-C-H activation. This catalytic reaction demonstrates the feasibility of switching ortho-selectivity to meta-selectivity in C-H activation of the same substrate by catalyst control.

Direct cross-coupling of benzyl alcohols to construct diarylmethanes via palladium catalysis.

A direct arylation to furnish diarylmethanes from benzyl alcohols was realized through Pd(PPh3)4-catalyzed Suzuki-Miyaura coupling via benzylic C-O activation in the absence of any additives. The arylation is compatible with various functional groups. This development provides an atom- and step-economic way to approach a diarylmethane scaffold under mild and environmentally benign conditions.

Ligand-promoted alkylation of C(sp3)-H and C(sp2)-H bonds.

9-Methylacridine was identified as a generally effective ligand to promote a Pd(II)-catalyzed C(sp(3))-H and C(sp(2))-H alkylation of simple amides with various alkyl iodides. This alkylation reaction was applied to the preparation of unnatural amino acids and geometrically controlled tri- and tetrasubstituted acrylic acids.