Intrinsic DNA curvature of double-crossover tiles

  title={Intrinsic DNA curvature of double-crossover tiles},
  author={Seungjae Kim and Junghoon Kim and Peng Fei Qian and Jihoon Shin and Rashid Amin and Sang Jung Ahn and Thomas H. LaBean and Moon Ki Kim and Sung Ha Park},
A theoretical model which takes into account the structural distortion of double-crossover DNA tiles has been studied to investigate its effect on lattice formation sizes. It has been found that a single vector appropriately describes the curvature of the tiles, of which a higher magnitude hinders lattice growth. In conjunction with these calculations, normal mode analysis reveals that tiles with relative higher frequencies have an analogous effect. All the theoretical results are shown to be… 
10 Citations

DNA nanotube formation based on normal mode analysis

A theoretical study on why uncorrugated cross tiles self-assemble into counterintuitive 3D nanotube structures and not planar 2D lattices is presented.

Understanding the Elementary Steps in DNA Tile-Based Self-Assembly.

The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.

Atomic force microscopy of arrays of asymmetrical DNA motifs

DNA can easily be assembled into wide and relatively flat nanostructures that lend themselves to study viaAtomic Force Microscopy (AFM). It is often important to know which side of an assembly the

A modal analysis of carbon nanotube using elastic network model

Although it is widely known that both size and chirality play significant roles in vibration behaviors of single-walled carbon nanotubes (SWCNTs), there haven’t been yet enough studies specifying the

DNA architectonics: towards the next generation of bio-inspired materials.

The use of DNA in nanobiotechnology has advanced to a stage at which almost any two or three dimensional architecture can be designed with high precision, and the inclusion of designer nucleoside analogues adds functionality with addressable groups, which have an influence on the function of the DNA nano-objects.

A mass weighted chemical elastic network model elucidates closed form domain motions in proteins

A mass‐weighted chemical elastic network model (MWCENM) in which the total mass of each residue is assumed to be concentrated on the representative alpha carbon atom and various stiffness values are precisely assigned according to the types of chemical interactions.

Electrical responses of artificial DNA nanostructures on solution-processed In-Ga-Zn-O thin-film transistors with multistacked active layers.

Enhanced sensing ability and stable electrical performance of TFTs were achieved through use of multistacked active layers, and these results compared favorably with those reported for conventional field-effect transistor-based DNA sensors with remarkable sensitivity and stability.

DNA Nanotechnology for Nucleic Acid Analysis: DX Motif‐Based Sensor

A sensor that fluoresces in the presence of specific nucleic acids was designed and characterized, which is a highly selective and affordable tool for the real-time analysis of DNA and RNA.

A Differential Fluorescent Receptor for Nucleic Acid Analysis

The DFR developed in this study represents a cost‐efficient alternative to molecular diagnostic technologies that use fluorescent hybridization probes and requires only one molecular‐beacon‐like fluorescent reporter, which can be used by all three sensors.

DNA-Based Biosensors for the Biochemical Analysis: A Review

A big picture of the DNA biosensor’s advantages is shown, including the functional DNA strands-based biosensors, DNA hybridization- based biosensor, and DNA templated bios Sensors, which have advantages such as wider detection targets, more durable lifetime, and lower production cost.



Modifying the Surface Features of Two-Dimensional DNA Crystals

DNA double-crossover (DX) molecules are rigid DNA motifs that contain two double helices linked at two different points. It is possible to form hydrogen-bonded two-dimensional crystals from DX

Molecular behavior of DNA origami in higher-order self-assembly.

Insight is provided into the formation of higher-order structures from self-assembling DNA origami tiles, revealing their unique behavior in comparison with conventional DNA tiles having smaller dimensions.

Design and characterization of programmable DNA nanotubes.

A new type of nanotube made from DNA double-crossover molecules (DAE-E tiles) is reported and described, explained by a simple model based on the geometry and energetics of B-form DNA.

Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes

The DNA triple crossover (TX) complex described here extends the set of experimentally characterized building blocks and allows for the presence of reporter strands along the molecular diagonal that can be used to relate the inputs and outputs of DNA-based computation.

Toward reliable algorithmic self-assembly of DNA tiles: a fixed-width cellular automaton pattern.

This work uses DNA tiles and DNA origami to grow crystals containing a cellular automaton pattern, providing evidence that programmable molecular self-assembly may be sufficient to create a wide range of complex objects in one-pot reactions.

Nanomaterials based on DNA.

  • N. Seeman
  • Chemistry
    Annual review of biochemistry
  • 2010
This work has shown that it is possible to construct novel DNA-based materials by combining these features in a self-assembly protocol by constructing polyhedrons, whose edges consist of double helical DNA and whose vertices correspond to the branch points.

Sequence-Dependent Flexibility in Promoter Sequences

Several extreme flexible regions related to functionally important elements exist both in prokaryotic promoters and in eukaryotic promoter sequences, DNA flexibility and AT content are highly correlated.

Antiparallel DNA Double Crossover Molecules As Components for Nanoconstruction

Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double crossover molecules, differentiated by the

DNA double-crossover molecules.

It is concluded that the helices between parallel double crossovers must be shielded from each other or distorted from linearity if they are to participate in recombination and be catalyzed by topoisomerases if it occurs within the cell.

Design and self-assembly of two-dimensional DNA crystals

The design and observation of two-dimensional crystalline forms of DNA that self-assemble from synthetic DNA double-crossover molecules that create specific periodic patterns on the nanometre scale are reported.