Simulative Analysis of a Family of DNA Tetrahedrons Produced by Changing the Twisting Number of Each Double Helix

2021 ◽  
Vol 20 (05) ◽  
pp. 529-537
Author(s):  
Hui Bai ◽  
Jia Li ◽  
Heng Zhang ◽  
Shuya Liu
Keyword(s):  
Cross Correlation ◽  
Double Helix ◽  
Dynamics Simulation ◽  
Conformational Variability ◽  
Double Helices ◽  
Dna Tetrahedron ◽  
Entire Trajectory ◽  
Dna Double Helix ◽  
Twist Number ◽  
Insight Into

In this paper, three tetrahedral nanocages, composed of six DNA double helix edges with all having the twist number 1, 2 or 3, have been characterized using classical molecular dynamics simulation to measure the specific structural and conformational features produced by only changing the twisting number of each double helix. The simulation result indicates that three tetrahedral cages are relatively stable and are maintained along the entire trajectory. Each double helix is more inclined to behave as a whole in the 2TD and 3TD cages than in the 1TD cage according to the cross-correlation maps for three nanocages, and also their local motions are more easily induced by the conformational variability of the thymidine linkers due to the increased flexibility of each helix. Hence, the double helices become the important factors on the structural stability of total cages with the DNA twisting number, and also give the signification contributions to the sizes of these cages conferring the larger spaces of the 2TD and 3TD cages than the 1TD cage. Our result provides an insight into which roles the double helix edges play in assembling DNA polyhedron, and also contribute to improving the loading capacity of DNA tetrahedron in drug delivery.

Effect of temperature on DNA double helix: An insight from molecular dynamics simulation

2012 ◽  
Vol 37 (3) ◽  
pp. 445-455 ◽  
Author(s):  
Sangeeta Kundu ◽  
Sanchita Mukherjee ◽  
Dhananjay Bhattacharyya
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Double Helix ◽  
Dynamics Simulation ◽  
Effect Of Temperature ◽  
Dna Double Helix

scholarly journals Conformational variability of DNA double helix

2020 ◽  
pp. 51-57
Author(s):  
Yu. V. Chesnokov
Keyword(s):  
Gene Expression ◽  
Metal Ions ◽  
Double Helix ◽  
General Structure ◽  
Regulation Of Gene Expression ◽  
Nucleotide Composition ◽  
Conformational Variability ◽  
Living Organisms ◽  
Dna Double Helix

Deoxyribonucleic acid (DNA) is one of the main carriers of hereditary information. The structural physicochemical information of DNA ultimately determines the structure and functioning of all living organisms. In DNA, various mutational events accumulate and recombination events occur, which lead to the variability of organisms and are subject to both natural and artificial selection. The interaction "genotype-environment" inherent in all living organisms is also characteristic of DNA, which is located in the intracellular and intranuclear physicochemical environment of water molecules, sugars, metal ions, pH, nucleotides and other components. The establishment and study of the physicochemical properties of native DNA contributes to not only understanding the mechanisms of the structure of the main hereditary biomolecule, but also to clarify their functioning, as well as interaction with other molecules at the molecular level. The discovery of various forms of double helices: A, Aʹ, B, α-Bʹ, β-Bʹ, C, Cʹ, Cʹʹ, D, E and Z suggests the idea of molecular genetic diversity existing at the DNA level and the establishment of their structural and functional features can lead to an understanding of the implementation of genetic information at the general biological level. The structure of natural DNA as a whole, apparently, does not depend on the sequence and nucleotide composition. For natural molecules - satellite DNA with repeats or DNA without repeats, the presence of only A-, B- and C-forms has been confirmed. The structure of DNA depends not only on temperature, but also on the nature of the cations present. The presence of a certain amount of metal ions in the medium can lead to the transition of the B-form of DNA to the Zform. The B ↔ Z transition modifies the general structure of DNA and, therefore, may be important for the regulation of gene expression. The study of the biological role of Z-DNA, possibly in the near future, will help to understand the mechanism of gene expression, primarily of an epigenetic nature, which has not yet been fully elucidated.

Freeze Fracture-Electron Microscopy of Spermidine-Single DNA Double Helices

1981 ◽  
Vol 39 ◽  
pp. 440-441 ◽  
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx ◽  
Thomas C. Reynolds
Keyword(s):  
Double Helix ◽  
Freeze Fracture ◽  
Dna Complexes ◽  
Etching Technique ◽  
Deep Well ◽  
Ice Surface ◽  
Double Helices ◽  
Freeze Fracture Electron Microscopy ◽  
Dna Double Helix

Torus shaped spermidine-DNA structures formed in vitro are thought to have a DNA organization similar to that in bacteriophage. In addition to toroidal structures in our preparations we have found large aggregates often interconnected with fibres comprised of one or more DNA double helices. The detailed organization of these interconnecting fibres will help illuminate little-understood theoretical aspects of the packing and bending properties of the DNA double helix. Previously, spermidine-DNA complexes have been dryed onto a substrate film and metal coated at an 11.3° angle. In contrast, the freeze-fracture, deep-etching technique was used because it could reveal hydrated spermidine-DNA complexes in their solution configuration. This preliminary report describes single double helical DNA-spermidine fibres suspended over unshadowed regions of the ice surface.Calf Thymus DNA (5 g/ml) was condensed with 1 mM spermidine at 0°C, for 1 hr in 1 mM NaCl, 10 mM Tris, pH 7.0. The solution was rapidly frozen on a Balzer's deep well pedestal in propane at -190°C. Samples were freeze-fractured and deepetched for 13 min at -97°C with a Balzer's 300 Freezing Microtome.

Protamine-DNA interaction

1978 ◽  
Vol 36 (2) ◽  
pp. 200-201
Author(s):  
D.P. Bazett-Jones ◽  
F.P. Ottensmeyer
Keyword(s):  
Small Volume ◽  
Double Helix ◽  
Dna Interaction ◽  
Dark Field ◽  
Sperm Head ◽  
Nuclear Proteins ◽  
Field Electron Microscopy ◽  
Dark Field Electron ◽  
Dna Double Helix ◽  
Positively Charged

Dark field electron microscopy has been used for the study of the structure of individual macromolecules with a resolution to at least the 5Å level. The use of this technique has been extended to the investigation of structure of interacting molecules, particularly the interaction between DNA and fish protamine, a class of basic nuclear proteins of molecular weight 4,000 daltons.Protamine, which is synthesized during spermatogenesis, binds to chromatin, displaces the somatic histones and wraps up the DNA to fit into the small volume of the sperm head. It has been proposed that protamine, existing as an extended polypeptide, winds around the minor groove of the DNA double helix, with protamine's positively-charged arginines lining up with the negatively-charged phosphates of DNA. However, viewing protamine as an extended protein is inconsistent with the results obtained in our laboratory.

Correlational Methods for Analysis of Dance Movements

2011 ◽  
Vol 29 (supplement) ◽  
pp. 283-304 ◽  
Author(s):  
Timothy R. Brick ◽  
Steven M. Boker
Keyword(s):  
Motion Capture ◽  
Mirror Symmetry ◽  
Cross Correlation ◽  
The Other ◽  
Free Form ◽  
Motion Capture Data ◽  
Complex Interactions ◽  
Dance Movements ◽  
Time Lagged ◽  
Insight Into

Among the qualities that distinguish dance from other types of human behavior and interaction are the creation and breaking of synchrony and symmetry. The combination of symmetry and synchrony can provide complex interactions. For example, two dancers might make very different movements, slowing each time the other sped up: a mirror symmetry of velocity. Examining patterns of synchrony and symmetry can provide insight into both the artistic nature of the dance, and the nature of the perceptions and responses of the dancers. However, such complex symmetries are often difficult to quantify. This paper presents three methods – Generalized Local Linear Approximation, Time-lagged Autocorrelation, and Windowed Cross-correlation – for the exploration of symmetry and synchrony in motion-capture data as is it applied to dance and illustrate these with examples from a study of free-form dance. Combined, these techniques provide powerful tools for the examination of the structure of symmetry and synchrony in dance.

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