Exploring copper(I) as a catalyst for nucleic acid alkylation

Chemical manipulations of nucleic acids have been crucial in the development of methodologies to study and understand epigenetics and transcriptomes. However, a complete understanding of these complex and dynamic systems is still missing and therefore we believe new synthetic tools for selective nucleic acid engineering are required. We report here the discovery that copper(I) carbenes derived from α-diazocarbonyl compounds selectively alkylate the O6-position of guanine (O6-G) in mono- and oligonucleotides. This new methodology allows the targeting of only purine-type lactam oxygen, whereas other types of amides or lactams are poorly reactive under the smooth guanine alkylation conditions. Mechanistic studies point to a substrate-directed alkylation reaction with the N7G as the key functionality of the purine-nucleobase that controls the high chemoselectivity. We used copper(I)-catalyzed O6-G alkylation to readily engineer O6-G derivatives to study two open questions in the biochemistry of O6-G adducts: the repair by alkylguanine transferases and their incorporation efficiency during DNA replication. Furthermore, with a reactivity and stability screen of functionalized water soluble N-heterocyclic carbene ligands we could identify tight-binding variants that permanently stabilized copper(I) in water. This system allowed alkylation of oligonucleotides in a reducing agent free environment maintaining the selectivity for the O6-G position. Most importantly, the tight-binding ligands that stabilize copper(I) provide access to further functionalization such as bio-conjugation. Given the importance of O6-G lesion in biology and the need for simple methods to engineer nucleic acids, we believe that copper(I)-catalyzed O6-G alkylation will find broad applicability

Copper carbenes alkylate guanine chemoselectively through a substrate directed reaction

Cu(I) carbenes derived from α-diazocarbonyl compounds lead to selective alkylation of the O6 position in guanine (O6-G) in mono- and oligonucleotides. Only purine-type lactam oxygens are targeted – other types of amides or lactams are poorly reactive under conditions that give smooth alkylation of guanine. Mechanistic studies point to N7G as a directing group that controls selectivity. Given the importance of O6-G adducts in biology and biotechnology we expect that Cu(I)-catalyzed O6-G alkylation will be a broadly used synthetic tool. While the propensity for transition metals to increase redox damage is well-appreciated, our results suggest that transition metals might also increase the vulnerability of nucleic acids to alkylation damage

A new water soluble copper N-heterocyclic carbene complex delivers mild O6G-selective RNA alkylation

We show here that copper carbenes generated from diazo acetamides alkylate single RNAs, mRNAs, or pools of total transcriptome RNA, delivering exclusively alkylation at the O 6 position in guanine (O 6 G). Although the reaction is effective with free copper some RNA fragmentation occurs, a problem we resolve by developing a novel water-stable copper N-heterocyclic carbene complex. Carboxymethyl adducts at O 6 G are known mutagenic lesions in DNA but their relevance in RNA biochemistry is unknown. As a case-in-point we re-examine an old controversy regarding whether O 6 G damage in RNA is susceptible to direct RNA repair

Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics

Developments in epigenomics, toxicology, and therapeutic nucleic acids all rely on a precise understanding of nucleic acid properties and chemical reactivity. In this review we discuss the properties and chemical reactivity of each nucleobase and attempt to provide some general principles for nucleic acid targeting or engineering. For adenine-thymine and guanine-cytosine base pairs, we review recent quantum chemical estimates of their Watson-Crick interaction energy, pi-pi stacking energies, as well as the nuclear quantum effects on tautomerism. Reactions that target nucleobases have been crucial in the development of new sequencing technologies and we believe further developments in nucleic acid chemistry will be required to deconstruct the enormously complex transcriptome

Modular ligands for dirhodium complexes facilitate catalyst customization

Although stereoselectivity is often the focus of ligand optimizations in catalysis, ligand modularity can be used to control many other properties of catalysts. For example, solubility, amenability to purification, and steric shielding of sensitive catalytic intermediates are all important, but seldom appreciated, functions of ligands. We describe a brief and modular approach to various homo- and heteroleptic lantern-type rhodium(II) complexes and perform benchmarking studies with the new catalysts in common rhodium(II)-catalyzed reactions. We demonstrate the power of ligand modularity by creating catalysts customized for aqueous catalysis or for applications in chemical biology

Copper carbenes alkylate guanine chemoselectively through a substrate directed reaction

Cu(I) carbenes derived from α-diazocarbonyl compounds lead to selective alkylation of the O6 position in guanine (O6-G) in mono- and oligonucleotides. Only purine-type lactam oxygens are targeted – other types of amides or lactams are poorly reactive under conditions that give smooth alkylation of guanine. Mechanistic studies point to N7G as a directing group that controls selectivity. Given the importance of O6-G adducts in biology and biotechnology we expect that Cu(I)-catalyzed O6-G alkylation will be a broadly used synthetic tool. While the propensity for transition metals to increase redox damage is well-appreciated, our results suggest that transition metals might also increase the vulnerability of nucleic acids to alkylation damage.ISSN:2041-6520ISSN:2041-653