Time-resolved structural analysis of an RNA-cleaving DNA catalyst

A conformational study of the 10–23 DNAzyme via programmed DNA self-assembly

“…At the final stage of the preparation of this manuscript, we became aware of a recent NMR study of 10–23 DNAzyme. 20 The measured interhelical angle (122°, Fig. S7, ESI†) is well consistent with our measurement.…”

“…18,19 While this manuscript was under preparation, an NMR study was reported to deduce the 10–23 DNAzyme catalytic structure. 20 Herein, we report a rapid and convenient structural study of the global conformation of the DNAzyme–substrate complex. The inter-helical angle ( θ ) between the two flanking duplex arms in the DNAzyme–substrate complex has been directly measured by atomic force microscopy (AFM).…”

“…Indeed, similar modifications (changing one 2 0 -OH to 2 0 -F or -OCH 3 ) have been used in the literature and shown little impact on the complex structure. 18,20 In principle, we could use AFM imaging to investigate the conformation of individual DNAzyme-substrate complexes. However, the conformation of the individual complex would be easily deformed during AFM sample preparation by fluidic shearing and sample-surface interactions.…”

DNA-based enzymatic systems and their applications

“…Recently, Victor et al. used 10–23 Dz as the model to study high-resolution structural characteristics of the relevant status of the Dzs during the catalytic process ( Borggräfe et al., 2022 ). The molecular conformation of Dzs has been firstly characterized with high temporal resolution at the atomic level.…”

Solution Structure of a Lanthanide‐binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints

“…However, all such metal‐binding oligonucleotide systems are currently discovered by in vitro selection from random libraries, their rational design being hampered by the lack of structural understanding of metal‐nucleic acid interactions in such systems. The solution structure of LnA_28 constitutes the first reported high‐resolution structure of a metal‐binding DNA aptamer and, together with the recently reported structures of 8–17 [30] and 10–23 [31] DNAzymes, constitutes a starting point for deeper mechanistic understanding of metal‐sensing oligonucleotide devices.…”