Regulation of B–Z Conformational Transition and Complex Formation with a Z‐Form Binding Protein by Introduction of Constraint to Double‐Stranded DNA by using a DNA Nanoscaffold

Abstract

B–Z transition: A constrained and rotatable double‐stranded DNA, in which the rotational freedom was controlled by its placement into a DNA nanoscaffold, was designed (see scheme). The Z α β protein bound preferentially to the rotatable strand rather than the constrained strand, even using the same CG sequence.

Triple Helix Formation in a Topologically Controlled DNA Nanosystem

“…In these experiments, the individual DNA nanostructures were assembled in the DNA origami frame, and the reactions of the nanostructures were elucidated by analyzing the DNA frames. This method can be used for the single‐molecule visualization of enzymatic processes in the DNA nanostructures . G‐multiplex and i‐motif structures, and their reconfiguration, B‐Z transitions, and the imaging of the DNAzyme reaction in the DNA nanostructures has also been demonstrated.…”

“…This method can be used for the single-molecule visualization of enzymatic processes in the DNA nanostructures. [19][20][21][22] G-multiplex and i-motif structures, and their reconfiguration, [23][24][25][26] B-Z transitions, [27] and the imaging of the DNAzyme reaction [28] in the DNA nanostructures has also been demonstrated.In the present study,w ea pplied high-speed AFM to follow triple helix formation at the single-molecule level. First, we examined the triplet Py-(Pu-Py)f or triplex formation (Figure 1a).…”

Single‐Molecule Visualization of the Activity of a Zn2+‐Dependent DNAzyme

“…[6,7] One specific class of DNAzymes is metal-ion-dependent DNAzymes.D ifferent DNAs equences dependent on metal-ion cofactors,s uch as Mg 2+ ,C a 2+ ,Z n 2+ ,U O 2 2+ ,H g 2+ , and others,h ave been reported. [13] In these experiments,t he individual unique DNAn anostructures were assembled on the DNAo rigami frames,a nd the reactions of the nanostructures were elucidated by analyzing acollection of frames.For example,DNA structural changes,i ncluding G-quadruplex reconfiguration, [14] B-Z configurational transitions, [15] and the switchable association and dissociation of photoresponsive DNA, [16] were demonstrated, and enzymatic processes on DNAn anostructures were visualized. [4c, 12] High-speed atomic force microscopy (AFM) measurements were recently implemented to probe DNAn anostructures and their reactivity at the single-molecule level.…”

“…[8,9] These metal-ion-dependent DNAzymes have been applied as amplifying labels for sensing, [10] as functional components for the construction of logic gates [11] and computing circuits,a nd as stimuli-responsive DNAs witches. [13] In these experiments,t he individual unique DNAn anostructures were assembled on the DNAo rigami frames,a nd the reactions of the nanostructures were elucidated by analyzing acollection of frames.For example,DNA structural changes,i ncluding G-quadruplex reconfiguration, [14] B-Z configurational transitions, [15] and the switchable association and dissociation of photoresponsive DNA, [16] were demonstrated, and enzymatic processes on DNAn anostructures were visualized. [13] In these experiments,t he individual unique DNAn anostructures were assembled on the DNAo rigami frames,a nd the reactions of the nanostructures were elucidated by analyzing acollection of frames.For example,DNA structural changes,i ncluding G-quadruplex reconfiguration, [14] B-Z configurational transitions, [15] and the switchable association and dissociation of photoresponsive DNA, [16] were demonstrated, and enzymatic processes on DNAn anostructures were visualized.…”

“…[4c, 12] High-speed atomic force microscopy (AFM) measurements were recently implemented to probe DNAn anostructures and their reactivity at the single-molecule level. [13] In these experiments,t he individual unique DNAn anostructures were assembled on the DNAo rigami frames,a nd the reactions of the nanostructures were elucidated by analyzing acollection of frames.For example,DNA structural changes,i ncluding G-quadruplex reconfiguration, [14] B-Z configurational transitions, [15] and the switchable association and dissociation of photoresponsive DNA, [16] were demonstrated, and enzymatic processes on DNAn anostructures were visualized. [17] Because the target DNAs trands are directly attached to the nanoscaffold, the DNAs tructural changes can be controlled in the nanospace by arranging the structures inside the DNAn anoscaffold.In the present study,w eu sed the DNAo rigami frame to follow the activity of ac atalytic nucleic acid, aZ n 2+ -dependent DNAzyme,a tt he single-molecule level.…”