DNA and RNA induced enantioselectivity in chemical synthesis

Controllable stereoinversion in DNA-catalyzed olefin cyclopropanation via cofactor modification

The assembly of DNA with metal-complex cofactors can form promising biocatalysts for asymmetric reactions, although catalytic performance is typically limited by low enantioselectivities and stereo-control remains a challenge. Here, we engineer G-quadruplex-based DNA biocatalysts for an asymmetric cyclopropanation reaction, achieving enantiomeric excess (eetrans) values of up to +91% with controllable stereoinversion, where the enantioselectivity switches to -72% eetrans through modification of the Fe-porphyrin cofactor. Complementary circular dichroism, nuclear magnetic resonance, and fluorescence titration experiments show that the porphyrin ligand of the cofactor participates in the regulation of the catalytic enantioselectivity via a synergetic effect with DNA residues at the active site. These findings underline the important role of cofactor modification in DNA catalysis and thus pave the way for the rational engineering of DNA-based biocatalysts.

Artificial Enzymes for Diels-Alder Reactions

The Diels-Alder (DA) reaction is a cycloaddition of a conjugated diene and an alkene (dienophile) leading to the formation of a cyclohexene derivative through a concerted mechanism. As DA reactions generally proceed with a high degree of regio- and stereoselectivity, they are widely used in synthetic organic chemistry. Considering eco-conscious public and governmental movements, efforts are now directed towards the development of synthetic processes that meet environmental concerns. Artificial enzymes, which can be developed to catalyze abiotic reactions, appear to be important synthetic tools in the synthetic biology field. This review describes the different strategies used to develop protein-based artificial enzymes for DA reactions, including for in cellulo approaches.

DNA as a chiral scaffold for asymmetric synthesis

The application of DNA-based hybrid catalysts for enantioselective synthesis has recently emerged. These catalysts, self-assembled from DNA and a metal complex with a specific ligand through supramolecular or covalent anchoring strategies, have demonstrated high enantioselectivity in a variety of carbon-carbon or carbon-heteroatom bond-forming reactions and have expanded their role in asymmetric catalysis. In this review, we summarize the advent and significant progress of DNA-based asymmetric catalysis and discuss remaining challenges in using DNA as a chiral scaffold. We hope that this review will inspire many of today’s active scientists in asymmetric catalysis.

Click reactions in protein chemistry: from the preparation of semisynthetic enzymes to new click enzymes

Click-chemistry is an approach based on cycloaddition reactions which has been successfully used as a chemical approach for complex organic molecules and which has recently starred in a boom in the world of protein chemistry. The advantage of the use of this technique in protein chemistry is based on a very high and efficient chemoselectivity, which usually requires simple or no purification and is extremely rate-accelerated in aqueous media. The perspective discusses some of the most recent advances in the application of this reaction in selective enzyme surface modification for the creation of new semisynthetic enzymes (fluorescence labeled enzymes, peptide-enzyme conjugates, glycosylated enzymes), and interestingly, the recent design and creation of "click" enzymes.

Impact of histidine residue on chelating ability of 2'-deoxyriboadenosine

Copper(II) complexes with a new chelator-type nucleoside-histidine modified 2'-deoxyriboadenosine (N-[(9-β-D-2'-deoxyribofuranosylpurin-6-yl)-carbamoyl]histidine) were studied by potentiometric and spectroscopic (UV-visible, CD, EPR) techniques, in conjunction with computer modeling optimization. The ligand can act as bidentate or tridentate depending on pH range. In acidic pH a very stable dimeric complex Cu(2)L(2) predominates with coordination spheres of both metal ions composed of oxygen atoms from carboxylic groups, one oxygen atom from ureido group and two nitrogen atoms derived from purine base and histidine ring. Above pH 5, deprotonation of carbamoyl nitrogens leads to the formation of CuL(2), Cu(2)L(2)H(-1) and Cu(2)L(2)H(-2) species. The CuL(2)H(-1) and CuL(2)H(-2) complexes with three or four nitrogens in Cu(II) coordination sphere have been detected in alkaline medium. Our findings suggest that N-[(9-beta-D-2'-deoxyribofuranosylpurin-6-yl)-carbamoyl]histidine chelates copper(II) ions very efficiently. The resulting complex might be used as an alternative base-pairing mode in which hydrogen-bonded base pairs present in natural DNA are replaced by metal-mediated ones.

DNA as a versatile chemical component for catalysis, encoding, and stereocontrol

DNA (deoxyribonucleic acid) is the genetic material common to all of Earth's organisms. Our biological understanding of DNA is extensive and well-exploited. In recent years, chemists have begun to develop DNA for nonbiological applications in catalysis, encoding, and stereochemical control. This Review summarizes key advances in these three exciting research areas, each of which takes advantage of a different subset of DNA's useful chemical properties.

DNA-based asymmetric catalysis

The unique chiral structure of DNA has been a source of inspiration for the development of a new class of bio-inspired catalysts. The novel concept of DNA-based asymmetric catalysis, which was introduced only five years ago, has been applied successfully in a variety of catalytic enantioselective reactions. In this tutorial review, the ideas behind this novel concept will be introduced, an overview of the catalytic chemistry available to date will be given and the role of DNA in catalysis will be discussed. Finally, an overview of new developments of potential interest for DNA-based asymmetric catalysis will be provided.

A kinetic and structural investigation of DNA-based asymmetric catalysis using first-generation ligands

The recently developed concept of DNA-based asymmetric catalysis involves the transfer of chirality from the DNA double helix in reactions using a noncovalently bound catalyst. To date, two generations of DNA-based catalysts have been reported that differ in the design of the ligand for the metal. Herein we present a study of the first generation of DNA-based catalysts, which contain ligands comprising a metal-binding domain linked through a spacer to a 9-aminoacridine moiety. Particular emphasis has been placed on determining the effect of DNA on the structure of the Cu(II) complex and the catalyzed Diels-Alder reaction. The most important findings are that the role of DNA is limited to being a chiral scaffold; no rate acceleration was observed in the presence of DNA. Furthermore, the optimal DNA sequence for obtaining high enantioselectivities proved to contain alternating GC nucleotides. Finally, DNA has been shown to interact with the Cu(II) complex to give a chiral structure. Comparison with the second generation of DNA-based catalysts, which bear bipyridine-type ligands, revealed marked differences, which are believed to be related to the DNA microenvironment in which the catalyst resides and where the reaction takes place.

Enantioselective phytoeffects of chiral pesticides

Chirality exists extensively in nature. Synthetic chiral plant growth regulators and other pesticides usually behave enantioselectively in phyto-biochemical processes. Chiral plant growth regulators regulate the physiological processes of plants enantioselectively, and chiral pesticides cause enantioselective toxicities or ecotoxicities to plants. On the other hand, these chiral agrochemicals can be absorbed and enantioselectively metabolized by plants. This review summarizes the enantioselective effects of chiral plant growth regulators on plants and the phytotoxic and biotransformation effects of chiral herbicides and several persistent organic pollutants (POPs) on plants. Together, this information on the interactions between chiral agrochemicals and plants might shed light on studies on the chemical and biological behaviors of chiral chemicals, and direct research into the selection of plants, which can potentially decontaminate the environment.

DNA-based asymmetric catalysis: sequence-dependent rate acceleration and enantioselectivity

This study shows that the role of DNA in the DNA-based enantioselective Diels-Alder reaction of azachalcone with cyclopentadiene is not limited to that of a chiral scaffold. DNA in combination with the copper complex of 4,4'-dimethyl-2,2'-bipyridine (Cu-L1) gives rise to a rate acceleration of up to 2 orders of magnitude compared to Cu-L1 catalysis alone. Furthermore, both the enantioselectivity and the rate enhancement prove to be dependent on the DNA-sequence. These features are the main reasons for the efficient and enantioselective catalysis observed with salmon testes DNA/Cu-L1 in the Diels-Alder reaction. The fact that absolute levels of stereocontrol can be achieved with a simple and weak DNA-binding complex like Cu-L1 is a clear demonstration of the power of the supramolecular approach to hybrid catalysis.

Investigation of DNA as a catalyst for Henry reaction in water

Double-stranded DNA of natural origin can be used to facilitate nitro-aldol (or Henry) reaction in aqueous solution.

Conformational change induced by metal-ion-binding to DNA containing the artificial 1,2,4-triazole nucleoside

A conformational switch can be induced upon the addition of transition-metal ions to oligonucleotides that contain a row of successive artificial nucleobases flanked by complementary sequences of natural nucleobases, provided that the artificial bases cannot undergo self-pairing via hydrogen bonding but only via the formation of metal-ion-mediated base pairs. Such oligonucleotides adopt a hairpin structure in the absence of transition-metal ions, yet they show a preference for the formation of a regular double helix if the appropriate metal ions are present. We report here our experimental data on the structure of the oligonucleotide d(A7X3T7) (A=adenine, T=thymine, X=1,2,4-triazole) in the absence and presence of silver(I). This study comprising temperature-dependent UV spectroscopy, CD spectroscopy, MALDI-TOF measurements, fluorescence spectroscopy, and dynamic light scattering opens up a new approach to the generation of a large variety of metal-ion sensors with the possibility of fine-tuning their sensing capabilities, depending on the artificial nucleoside that is used.

α,β-Unsaturated 2-Acyl Imidazoles as a Practical Class of Dienophiles for the DNA-Based Catalytic Asymmetric Diels−Alder Reaction in Water

Alpha,beta-unsaturated 2-acyl imidazoles are a novel and practical class of dienophiles for the DNA-based catalytic asymmetric Diels-Alder reaction in water. The Diels-Alder products are obtained with very high diastereoselectivities and enantioselectivities in the range of 83-98%. The catalytic reaction was performed on a 1.0 mmol scale, and the imidazole auxiliary was removed readily.