Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner

Abstract

Dynamic control of DNA assembly by external stimuli has received increasing attention in recent years. Dynamic ligand exchange in metal complexes can be a central element in the structural and...

Ligase-mediated synthesis of CuII-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases

“…Aiming to switch DNA functions efficiently by metal complexation, we have recently established a new concept of metal-mediated base pair switching of bifacial 5-modied pyrimidine nucleobases. [4][5][6][7] Bifacial bases such as 5-hydroxyuracil (U OH ) 4,5 and 5-carboxyuracil (caU) 6 are designed to form metal-mediated self-base pairs (e.g., U OH -Gd III -U OH ) in the presence of certain metal ions and to form Watson-Crick-like base pairs with a natural nucleobase in DNA duplexes (e.g., U OH -A). Based on the switching between U OH -A and U OH -Gd III -U OH base pairs, Gd III -triggered DNA strand displacement reactions were demonstrated and Gd III -mediated control of DNA tweezer structures and DNAzyme functions was successfully achieved.…”

“…Aiming to switch DNA functions efficiently by metal complexation, we have recently established a new concept of metal-mediated base pair switching of bifacial 5-modified pyrimidine nucleobases. 4–7 Bifacial bases such as 5-hydroxyuracil ( U OH ) 4,5 and 5-carboxyuracil ( caU ) 6 are designed to form metal-mediated self-base pairs ( e.g. , U OH –Gd III – U OH ) in the presence of certain metal ions and to form Watson–Crick-like base pairs with a natural nucleobase in DNA duplexes ( e.g.…”

Selective Formation of Pd‐DNA Hybrids Using Tailored Palladium‐Mediated Base Pairs: Towards Heteroleptic Pd‐DNA Systems

“…Notably, significant attention is focused on advancing metal‐DNA systems, wherein the metal entities are precisely arranged along specific sequences. This precision aims to construct dynamic metal‐DNA hybrids, gathering significant thought for their potential to stimulate diverse applications [5–9] . In this context, the possibility of scheduling specific sequences for rational self‐assembly through base pairs recognition has made DNA an ideal candidate for building highly organized functional systems at the nanoscale.…”

Contiguous Silver(I)-Mediated Base Pairs of Imidazophenanthroline and Canonical Nucleobases in DNA Duplexes: Formation of Classical Duplexes versus Homodimer Formation

“…The use of these artificial nucleosides enables a fine-tuning of the metal-binding abilities of the nucleic acids, thereby enabling the development of different applications. A more recently reported use of nucleic acids with metal-mediated base pairs involves improved strand displacement reactions, metal-responsive DNAzymes, , responsive nucleic acids in general, hybridization probes, − modulation of aptamer function, and the generation of DNA-templated silver nanoclusters . In addition, contiguous metal-mediated base pairs are currently under investigation in the context of generating one-dimensional arrays of metal ions − with potential applicability as conducting DNA nanowires. , …”