Masayuki Endo

A novel strategy for regulation of an enzymatic DNA modification reaction has been developed by employing a designed nanoscale DNA scaffold. DNA modification using enzymes often requires bending of specific DNA strands to facilitate the reaction. The DNA methylation enzyme EcoRI methyltransferase (M.EcoRI) bends double helix DNA by 55 degrees-59 degrees during the reaction with flipping out of the second adenine in the GAATTC sequence as the methyl transfer reaction proceeds. In this study, two

Due to its self-assembling nature, DNA is undoubtedly an excellent molecule for the creation of various multidimensional nanostructures and the placement of functional molecules and materials. DNA molecules behave according to the programs of their sequences. Mixtures of numbers of DNA molecules can be placed precisely and organized into single structures to form nanoarchitectures. Once the appropriate sequences for the target nanostructure are established, the predesigned structure can be built

CONSPECTUS: Direct imaging of molecular motions is one of the most fundamental issues for elucidating the physical properties of individual molecules and their reaction mechanisms. Atomic force microscopy (AFM) enables direct molecular imaging, especially for biomolecules in the physiological environment. Because AFM can visualize the molecules at nanometer-scale spatial resolution, a versatile observation scaffold is needed for the precise imaging of molecule interactions in the reactions. The

Novel multiarm DNA structures were designed using two-dimensional DNA origami scaffolds, and these structures were folded into hollow three-dimensional (3D) structures by introducing connection strands into the arms. The opening of the prism structures was examined by high-speed AFM imaging, which showed the dissociation of the connecting arms in the 3D structures.

Repair kit: The single DNA-repair enzymes 8-oxoguanine glycosylase and T4 pyrimidine dimer glycosylase were analyzed by a nanoscale DNA chip containing two double-stranded DNA molecules (see picture). Dynamic movement of the enzymes and the single DNA-repair reaction on the DNA nanochip was visualized by fast-scanning atomic force microscopy. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or type

We have demonstrated the construction of multiple porphyrin arrays in the tobacco mosaic virus (TMV) supramolecular structures by self-assembly of recombinant TMV coat protein (TMVCP) monomers, in which Zn-coordinated porphyrin (ZnP) and free-base porphyrin (FbP) were site-selectively incorporated. The photophysical properties of porphyrin moieties incorporated in the TMV assemblies were also characterized. TMV-porphyrin conjugates employed as building blocks self-assembled into unique disk and

Reparaturset: Einzelne Moleküle der DNA-Reparaturenzyme 8-Oxoguanin-Glycosylase und T4-Pyrimidindimer-Glycosylase wurden auf einem nanoskaligen DNA-Chip mit zwei doppelsträngigen DNA-Molekülen analysiert (siehe Bild). Dynamische Bewegungen der Enzyme und die DNA-Reparaturreaktion auf dem DNA-Nanochip wurden durch schnelle Rasterkraftmikroskopie visualisiert.

Tiles go down the tube: A novel method for the preparation of DNA tubes by using the DNA tile system with the assistance of a four-way-branched DNA–porphyrin connector is described (see schematic representation). The detailed DNA tube structures were characterized by atomic force microscopy. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z501034_s.pdf or from the author. Please note: The publisher is not responsible for the con

A novel method for assembling multiple DNA origami structures has been developed by using designed 2D DNA origami rectangles, so-called "DNA jigsaw pieces" that have sequence-programmed connectors. Shape and sequence complementarity were introduced to the concavity and convex connectors in the DNA rectangles for selective connection with the help of nonselective pi-stacking interactions between the side edges of the DNA jigsaw piece structures. Single DNA jigsaw piece units were assembled into u

DNA origami is an emerging technology for designing and constructing defined multidimensional nanostructures. This technology is now expanding to materials science. This article introduces the basics of DNA origami, the design of various two-dimensional and three-dimensional DNA origami structures, and the programmed assembly of origami structures. DNA origami has unique properties, such as an addressable surface, which enables selective functionalization with biomolecules and nanomaterials. The

DNA can assemble various molecules and nanomaterials in a programmed fashion and is a powerful tool in the nanotechnology and biology research fields. DNA also allows the construction of desired nanoscale structures via the design of DNA sequences. Structural nanotechnology, especially DNA origami, is widely used to design and create functionalized nanostructures and devices. In addition, DNA molecular machines have been created and are operated by specific DNA strands and external stimuli to pe

Two-dimensional self-assembly of DNA origami structures was carried out using a connector that has connection sites at all four edges. By utilizing this four-way connector, five and eight origami monomers were assembled to form a cruciate and a hollow square structure, respectively.

A framed photo of DNA: A pair of photoresponsive oligonucleotides containing azobenzene moieties was introduced into double-stranded DNA within the cavity of a DNA nanostructure (see scheme). The two dsDNAs, in contact at the center, were dissociated using UV irradiation and hybridized with visible light; this was directly observed using high-speed atomic force microscopy.

We demonstrate direct observation of the dynamic opening and closing behavior of photocontrollable DNA origami nanoscissors using high-speed atomic force microscopy (HS-AFM). First the conformational change between the open and closed state controlled by adjustment of surrounding salt concentration could be directly observed during AFM scanning. Then light-responsive moieties were incorporated into the nanoscissors to control these structural changes by photoirradiation. Using photoswitchable DN

A photofunctionalized square bipyramidal DNA nanocapsule (NC) was designed and prepared for the creation of a nanomaterial carrier. Photocontrollable open/close system and toehold system were introduced into the NC for the inclusion and release of a gold nanoparticle (AuNP) by photoirradiation and strand displacement. The reversible open and closed states were examined by gel electrophoresis and atomic force microscopy (AFM), and the open behavior was directly observed by high-speed AFM. The enc