scholarly journals Regulation of 2D DNA Nanostructures by the Coupling of Intrinsic Tile Curvature and Arm Twist

2021 ◽  
Author(s):  
Chuan Jiang ◽  
Biao Lu ◽  
Wei Zhang ◽  
Yoel P. Ohayon ◽  
Feiyang Feng ◽  
...  
Keyword(s):  
High Resolution ◽  
Theoretical Approach ◽  
Transverse Section ◽  
Regular Polygon ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Intrinsic Curvature ◽  
Left Handed ◽  
Sticky End ◽  
Structural Descriptions

The overwinding and underwinding of duplex segments between junctions have been used in designing both left-handed and right-handed DNA origami nanostructures. For a variety of DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the DNA tile (specified as the intrinsic tile curvature) has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile curvature and its evolution in DNA tubes by the coupling of the twist of the inter-tile arm (specified as the arm twist) have never been addressed. In this work, we designed three types of tile cores built around a circular 128 nucleotide scaffold by using longitudinal weaving (LW), bridged longitudinal weaving (bLW) and transverse weaving (TW). Joining the tiles with inter-tile arms having the length of an odd number of DNA half-turns (termed O-tiling) almost resulted into planar 2D lattices, whereas joining the tiles with the arms having the length of an even number of DNA half-turns (termed E-tiling) nearly generated tubes. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the E-tiling tubes and thereby the conformations of their component tiles with addressable concave and convex curvatures. When the arms have the normal winding at the relaxed B-form of DNA, the intrinsic tile curvature deter-mines the chirality of the E-tiling tubes. By regulating the arm length and the sticky end length of the bLW-Ep/q (E-tiling of the bLW cores with the arm length of p-bp and the sticky end length of q-nt) assemblies, the arm can be overwound, resulting in a left-handed twist, and can also be underwound, resulting in a right-handed twist. Chiral bLW-Ep/q tubes with either a right-handed curvature or a left-handed curvature can also be formed by the coupling of the intrinsic tile curvature and the arm twist. We were able to assign the chiral indices (n,m) to each tube using high-resolution AFM images, and therefore were able to estimate the tile curvature using a regular polygon model that approximated the transverse section of the tube. A deeper understanding of the integrated actions of dif-ferent types of twisting forces on the DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future.

scholarly journals Regulation of 2D DNA Nanostructures by the Coupling of Tile Curvatures and Arm Twists

2021 ◽  
Author(s):  
Chuan Jiang ◽  
Biao Lu ◽  
Wei Zhang ◽  
Yoel P. Ohayon ◽  
Caihong Ni ◽  
...  
Keyword(s):  
Transverse Section ◽  
Regular Polygon ◽  
Holliday Junctions ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Base Pairs ◽  
Left Handed ◽  
Different Types ◽  
Sticky End ◽  
Structural Descriptions

DNA overwinding and underwinding between adjacent Holliday junctions have been applied in DNA origami constructs to design both left-handed and right-handed nanostructures. For a variety of DNA tubes assembled from small tiles, only a theoretical approach of the intrinsic tile curvature was previously used to explain their formation. Details regarding the quantitative and structural descriptions of the intrinsic tile curvature and its evolution in DNA tubes by coupling with arm twists were missing. In this work, we designed three types of tile cores from a circular 128 nucleotide scaffold by longitudinal weaving (LW), bridging longitudinal weaving (bLW), and transverse weaving (TW) and assembled their 2D planar or tubular nanostructures via inter-tile arms with a distance of an odd or even number of DNA half-turns. The biotin/streptavidin (SA) labeling technique was applied to define the tube configuration with addressable inside and outside surfaces and thus their component tile conformation with addressable concave and convex curvatures. Both chiral tubes possessing left-handed and right-handed curvatures could be generated by finely tuning p and q in bLW-E<sub>p/q</sub> designs (bLW tile cores joined together by inter-tile arms of an even number of half-turns with the arm length of p base pairs (bp) and the sticky end length of q nucleotides (nt)). We were able to assign the chiral indices (n,m) to each specific tube from the high-resolution AFM images, and thus estimated the tile curvature angle with a regular polygon model that approximates each tube’s transverse section. We attribute the curvature evolution of bLW-E<sub>p/q</sub> tubes composed of the same tile core to the coupling of the intrinsic tile curvature and different arm twists. A better understanding of the integrated actions of different types of twisting forces on DNA tubes will be much more helpful in engineering DNA nanostructures in the future.

scholarly journals Regulation of 2D DNA Nanostructures by the Coupling of Tile Cur-Vatures and Arm Twists

2021 ◽  
Author(s):  
Chuan Jiang ◽  
Biao Lu ◽  
Wei Zhang ◽  
Yoel P. Ohayon ◽  
Caihong Ni ◽  
...  
Keyword(s):  
Transverse Section ◽  
Regular Polygon ◽  
Holliday Junctions ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Base Pairs ◽  
Left Handed ◽  
Different Types ◽  
Sticky End ◽  
Structural Descriptions

DNA overwinding and underwinding between adjacent Holliday junctions have been applied in DNA origami constructs to design both left-handed and right-handed nanostructures. For a variety of DNA tubes assembled from small tiles, only an abstract concept of the intrinsic tile curvature was previously used to explain their formation. Details regarding the quantitative and structural descriptions of the intrinsic tile curvature and its evolution in DNA tubes by coupling with arm twists have been lacking. In this work, we designed three types of tile cores from a circular 128 nucleotide scaffold by longitudinal weaving (LW), bridging longitudinal weaving (bLW), and transverse weaving (TW) and assembled their 2D planar or tubular nanostructures via inter-tile arms with a distance of an odd or even number of DNA half-turns. The biotin/streptavidin (SA) labeling technique was applied to define the tube configuration with addressable inside and outside surfaces and thus their component tile conformation with addressable concave and convex curvatures. Both chiral tubes possessing left-handed and right-handed curvatures could be generated by finely tuning p and q in bLW-E<sub>p/q</sub> designs (bLW tile cores joined together by inter-tile arms of even number of half-turns with the arm length of p base pairs (bp) and the sticky end length of q nucleotides (nt)). We were able to assign the chiral indices (n,m) to each specific tube from the high-resolution AFM images, and thus estimated the tile curvature angle with a regular polygon model that approximates each tube’s transverse section. We attribute the curvature evolution of bLW-E<sub>p/q</sub> tubes composed of the same tile core to the coupling of the intrinsic tile curvature and different arm twists. A better understanding of integrated actions of different types of twisting forces on DNA tubes will be much more helpful in engineering DNA nanostructures in the future.

scholarly journals Regulation of 2D DNA Nanostructures by the Coupling of Tile Cur-Vatures and Arm Twists

2021 ◽  
Author(s):  
Chuan Jiang ◽  
Biao Lu ◽  
Wei Zhang ◽  
Yoel P. Ohayon ◽  
Caihong Ni ◽  
...  
Keyword(s):  
Transverse Section ◽  
Regular Polygon ◽  
Holliday Junctions ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Base Pairs ◽  
Left Handed ◽  
Different Types ◽  
Sticky End ◽  
Structural Descriptions

DNA overwinding and underwinding between adjacent Holliday junctions have been applied in DNA origami constructs to design both left-handed and right-handed nanostructures. For a variety of DNA tubes assembled from small tiles, only an abstract concept of the intrinsic tile curvature was previously used to explain their formation. Details regarding the quantitative and structural descriptions of the intrinsic tile curvature and its evolution in DNA tubes by coupling with arm twists have been lacking. In this work, we designed three types of tile cores from a circular 128 nucleotide scaffold by longitudinal weaving (LW), bridging longitudinal weaving (bLW), and transverse weaving (TW) and assembled their 2D planar or tubular nanostructures via inter-tile arms with a distance of an odd or even number of DNA half-turns. The biotin/streptavidin (SA) labeling technique was applied to define the tube configuration with addressable inside and outside surfaces and thus their component tile conformation with addressable concave and convex curvatures. Both chiral tubes possessing left-handed and right-handed curvatures could be generated by finely tuning p and q in bLW-E<sub>p/q</sub> designs (bLW tile cores joined together by inter-tile arms of even number of half-turns with the arm length of p base pairs (bp) and the sticky end length of q nucleotides (nt)). We were able to assign the chiral indices (n,m) to each specific tube from the high-resolution AFM images, and thus estimated the tile curvature angle with a regular polygon model that approximates each tube’s transverse section. We attribute the curvature evolution of bLW-E<sub>p/q</sub> tubes composed of the same tile core to the coupling of the intrinsic tile curvature and different arm twists. A better understanding of integrated actions of different types of twisting forces on DNA tubes will be much more helpful in engineering DNA nanostructures in the future.

scholarly journals Biophysical characterization of DNA origami nanostructures reveals inaccessibility to intercalation binding sites

2019 ◽  
Author(s):  
Helen L. Miller ◽  
Sonia Contera ◽  
Adam J.M. Wollman ◽  
Adam Hirst ◽  
Katherine E. Dunn ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Single Molecule ◽  
Targeted Drug Delivery ◽  
Binding Sites ◽  
Dna Origami ◽  
Target Cells ◽  
Dna Nanostructures ◽  
Synthetic Dna ◽  
Drug Molecules ◽  
Targeted Drug

AbstractIntercalation of drug molecules into synthetic DNA nanostructures formed through self-assembled origami has been postulated as a valuable future method for targeted drug delivery. This is due to the excellent biocompatibility of synthetic DNA nanostructures, and high potential for flexible programmability including facile drug release into or near to target cells. Such favourable properties may enable high initial loading and efficient release for a predictable number of drug molecules per nanostructure carrier, important for efficient delivery of safe and effective drug doses to minimise non-specific release away from target cells. However, basic questions remain as to how intercalation-mediated loading depends on the DNA carrier structure. Here we use the interaction of dyes YOYO-1 and acridine orange with a tightly-packed 2D DNA origami tile as a simple model system to investigate intercalation-mediated loading. We employed multiple biophysical techniques including single-molecule fluorescence microscopy, atomic force microscopy, gel electrophoresis and controllable damage using low temperature plasma on synthetic DNA origami samples. Our results indicate that not all potential DNA binding sites are accessible for dye intercalation, which has implications for future DNA nanostructures designed for targeted drug delivery.

scholarly journals Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States

2019 ◽  
Author(s):  
Jie Deng ◽  
Andreas Walther
Keyword(s):  
Molecular Recognition ◽  
Enzymatic Reaction ◽  
Reaction Network ◽  
Steady States ◽  
Hierarchical Level ◽  
Dna Nanostructures ◽  
Structural Dynamic ◽  
Systems Chemistry ◽  
Sticky End ◽  
Autonomous Evolution

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization system. The systems are based on a monomeric species pool that is fueled by ATP and orchestrated by an enzymatic reaction network (ERN) of ATP-powered ligation and concurrent cleavage. Such systems display autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomer of dimers to ultimately randomized polymer structure before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition with respect to the structure-forming step (ATP-powered ligation) by encoding different sticky-end overhangs into the ligation area. However, all formed structures are equally degraded, and the orthogonal molecular recognition of the different starting species are harmonized during the constantly occurring restriction process, leading in consequence to a reconfiguration of the driven dynamic nanostructures on a higher hierarchical level. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.

scholarly journals DNA Origami Nanomachines

Molecules ◽  
2018 ◽  
Vol 23 (7) ◽  
pp. 1766 ◽  
Author(s):  
Masayuki Endo ◽  
Hiroshi Sugiyama
Keyword(s):  
Dna Sequences ◽  
Molecular Motors ◽  
Molecular Machines ◽  
Dna Origami ◽  
Dna Nanostructures ◽  
Molecular Systems ◽  
Nanoscale Structures ◽  
Research Fields ◽  
Dna Strands ◽  
External Stimuli

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 perform linear, rotational, and reciprocating movements. Furthermore, complicated molecular systems have been created on DNA nanostructures by arranging multiple molecules and molecular machines precisely to mimic biological systems. Currently, DNA nanomachines, such as molecular motors, are operated on DNA nanostructures. Dynamic DNA nanostructures that have a mechanically controllable system have also been developed. In this review, we describe recent research on new DNA nanomachines and nanosystems that were built on designed DNA nanostructures.

scholarly journals DNA nanotechnology approaches for microRNA detection and diagnosis

2019 ◽  
Vol 47 (20) ◽  
pp. 10489-10505 ◽  
Author(s):  
Arun Richard Chandrasekaran ◽  
Jibin Abraham Punnoose ◽  
Lifeng Zhou ◽  
Paromita Dey ◽  
Bijan K Dey ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Dna Origami ◽  
Great Promise ◽  
Dna Nanostructures ◽  
New Class ◽  
Advantages And Disadvantages ◽  
Critical Comparison ◽  
Microrna Detection ◽  
Disease Diagnostics ◽  
Detection And Diagnosis

Abstract MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.

scholarly journals DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

Nanomaterials ◽  
2016 ◽  
Vol 6 (11) ◽  
pp. 196 ◽  
Author(s):  
Masudur Rahman ◽  
David Neff ◽  
Nathaniel Green ◽  
Michael Norton
Keyword(s):  
High Resolution ◽  
Dna Origami ◽  
Protein Patterning

scholarly journals Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States

2019 ◽  
Author(s):  
Jie Deng ◽  
Andreas Walther
Keyword(s):  
Molecular Recognition ◽  
Enzymatic Reaction ◽  
Reaction Network ◽  
Steady States ◽  
Hierarchical Level ◽  
Dna Nanostructures ◽  
Structural Dynamic ◽  
Systems Chemistry ◽  
Sticky End ◽  
Autonomous Evolution

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization system. The systems are based on a monomeric species pool that is fueled by ATP and orchestrated by an enzymatic reaction network (ERN) of ATP-powered ligation and concurrent cleavage. Such systems display autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomer of dimers to ultimately randomized polymer structure before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition with respect to the structure-forming step (ATP-powered ligation) by encoding different sticky-end overhangs into the ligation area. However, all formed structures are equally degraded, and the orthogonal molecular recognition of the different starting species are harmonized during the constantly occurring restriction process, leading in consequence to a reconfiguration of the driven dynamic nanostructures on a higher hierarchical level. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.

scholarly journals Dielectrophoresis of gold nanoparticles conjugated to DNA origami structures

2016 ◽  
Vol 7 ◽  
pp. 948-956 ◽  
Author(s):  
Anja Henning-Knechtel ◽  
Matthew Wiens ◽  
Mathias Lakatos ◽  
Andreas Heerwig ◽  
Frieder Ostermaier ◽  
...  
Keyword(s):  
Gold Nanoparticle ◽  
Self Assembly ◽  
Metallic Nanoparticles ◽  
Linear Chain ◽  
Construction Materials ◽  
Dna Origami ◽  
Hybrid Structures ◽  
Dna Nanostructures ◽  
Electrode Structure ◽  
Electrical Field Strength

DNA nanostructures are promising construction materials to bridge the gap between self-assembly of functional molecules and conventional top-down fabrication methods in nanotechnology. Their positioning onto specific locations of a microstructured substrate is an important task towards this aim. Here we study manipulation and positioning of pristine and of gold nanoparticle-conjugated tubular DNA origami structures using ac dielectrophoresis. The dielectrophoretic behavior was investigated employing fluorescence microscopy. For the pristine origami, a significant dielectrophoretic response was found to take place in the megahertz range, whereas, due to the higher polarizability of the metallic nanoparticles, the nanoparticle/DNA hybrid structures required a lower electrical field strength and frequency for a comparable trapping at the edges of the electrode structure. The nanoparticle conjugation additionally resulted in a remarkable alteration of the DNA structure arrangement. The growth of linear, chain-like structures in between electrodes at applied frequencies in the megahertz range was observed. The long-range chain formation is caused by a local, gold nanoparticle-induced field concentration along the DNA nanostructures, which in turn, creates dielectrophoretic forces that enable the observed self-alignment of the hybrid structures.

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