scholarly journals Coupled Schrödinger equations as a model of interchain torsional excitation transport in the DNA model

2021 ◽  
Author(s):  
Margarita A. Kovaleva ◽  
Leonid Manevitch
Keyword(s):  
Small Amplitude ◽  
Energy Transport ◽  
Double Helix ◽  
Schrodinger Equations ◽  
Type Model ◽  
Schrödinger Equations ◽  
Weakly Coupled ◽  
Dna Strands ◽  
Dna Double Helix ◽  
Nonstationary Dynamics

Abstract In this report we consider two weakly coupled Schrödinger equations as a model of interchain energy transport in the DNA double-helix. We employ a reduction of the Yakushevich-type model that considers the torsional dynamics of the DNA. In previous works, only small amplitude excitations and stationary dynamics were investigated, whereas we focus on the nonstationary dynamics of the double helix. In this report we consider two weakly coupled Schrödinger equations as a reduced model of interchain energy transport in the DNA double-helix torsional model. We employ a reduction of the Yakushevich-type model that considers the torsional dynamics of the DNA as effective chains of pendula. In previous works, only small amplitude excitations and stationary dynamics were investigated, whereas we focus on the nonstationary dynamics of the double helix. We consider the system to be a model of two weakly interacting DNA strands. Assuming that initially only one of the chains is excited in the form of a breather, we demonstrate the existence of an invariant that allows us to reduce the order of the problem and examine the system of the phase plane. The analysis demonstrates the utility of an analytical tool for predicting the periodic interchain excitation transitions of its localisation on one of the chains. The technique also takes into account the spreading of the excitations over time.

scholarly journals Influence of perylenediimide–pyrene supramolecular interactions on the stability of DNA-based hybrids: Importance of electrostatic complementarity

2014 ◽  
Vol 10 ◽  
pp. 1589-1595 ◽  
Author(s):  
Christian B Winiger ◽  
Simon M Langenegger ◽  
Oleg Khorev ◽  
Robert Häner
Keyword(s):  
Double Helix ◽  
Building Blocks ◽  
Supramolecular Interactions ◽  
Stacking Interactions ◽  
Average Value ◽  
Π Stacking ◽  
Dna Strands ◽  
Polycyclic Aromatic ◽  
The Stability ◽  
Dna Double Helix

Aromatic π–π stacking interactions are ubiquitous in nature, medicinal chemistry and materials sciences. They play a crucial role in the stacking of nucleobases, thus stabilising the DNA double helix. The following paper describes a series of chimeric DNA–polycyclic aromatic hydrocarbon (PAH) hybrids. The PAH building blocks are electron-rich pyrene and electron-poor perylenediimide (PDI), and were incorporated into complementary DNA strands. The hybrids contain different numbers of pyrene–PDI interactions that were found to directly influence duplex stability. As the pyrene–PDI ratio approaches 1:1, the stability of the duplexes increases with an average value of 7.5 °C per pyrene–PDI supramolecular interaction indicating the importance of electrostatic complementarity for aromatic π–π stacking interactions.

Symmetry-adapted digital modeling II. The double-helix B-DNA

2016 ◽  
Vol 72 (3) ◽  
pp. 312-323 ◽  
Author(s):  
A. Janner
Keyword(s):  
Dimensional Space ◽  
Double Helix ◽  
Three Dimensional ◽  
Reduction Factor ◽  
Lattice Points ◽  
Three Dimensions ◽  
Coarse Grained ◽  
Digital Modeling ◽  
Dna Strands ◽  
Dna Double Helix

The positions of phosphorus in B-DNA have the remarkable property of occurring (in axial projection) at well defined points in the three-dimensional space of a projected five-dimensional decagonal lattice, subdividing according to the golden mean ratio τ:1:τ [with τ = (1+\sqrt {5})/2] the edges of an enclosing decagon. The corresponding planar integral indicesn1,n2,n3,n4(which are lattice point coordinates) are extended to include the axial indexn5as well, defined for each P position of the double helix with respect to the single decagonal lattice ΛP(aP,cP) withaP= 2.222 Å andcP= 0.676 Å. A finer decagonal lattice Λ(a,c), witha=aP/6 andc=cP, together with a selection of lattice points for each nucleotide with a given indexed P position (so as to define a discrete set in three dimensions) permits the indexing of the atomic positions of the B-DNA d(AGTCAGTCAG) derived by M. J. P. van Dongen. This is done for both DNA strands and the single lattice Λ. Considered first is the sugar–phosphate subsystem, and then each nucleobase guanine, adenine, cytosine and thymine. One gets in this way a digital modeling of d(AGTCAGTCAG) in a one-to-one correspondence between atomic and indexed positions and a maximal deviation of about 0.6 Å (for the value of the lattice parameters given above). It is shown how to get a digital modeling of the B-DNA double helix for any given code. Finally, a short discussion indicates how this procedure can be extended to derive coarse-grained B-DNA models. An example is given with a reduction factor of about 2 in the number of atomic positions. A few remarks about the wider interest of this investigation and possible future developments conclude the paper.

Stereoscopic Visualization of Spermidine-DNA Torus Structure Prepared by the Freeze-Fracture, Deep-Etch Technique

1981 ◽  
Vol 39 ◽  
pp. 438-439
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx ◽  
Thomas C. Reynolds
Keyword(s):  
Double Helix ◽  
Freeze Fracture ◽  
Etching Technique ◽  
Calf Thymus ◽  
Quick Freezing ◽  
Metal Levels ◽  
Dna Strands ◽  
Dna Double Helix ◽  
Stereoscopic Visualization ◽  
Condensed Dna

Freeze-fracture TEM has been used to visualize spermidine-DNA complexes╌a model system for bacteriophage DNA packaging. We have observed the toroidal shape and bacteriophage size (770Å) of spermidine-condensed DNA particles prepared by quick freezing of DNA-spermidine solutions followed by a freeze-fracture, deep-etching technique. Single direction shadowing with low Pt-C metal levels (9Å thick) has allowed us to demonstrate that the freeze-fracture technique is capable of revealing the organization of separate double helical DNA strands on the torus surface. The spermidine-DNA toruses exhibited surface Pt-C decoration consistent with the DNA double helix being circumferentially wrapped to form the torus. In addition, we have demonstrated that a hydrated sample shows the same toroidal shapes that have been previously demonstrated by Chattoraj et. al, in a dehydrated preparation.We performed freeze-fracture TEM studies of spermidine condensed (0.2 mM) Calf Thymus DNA (5 μg/ml) complexes in 1 mM NaCl, 10 mM Tris pH 7.0. Samples were freeze-fractured and etched for 13 min at -97°C.

Structure of DNA and Nucleosome Observed by Ultrahigh-Resolution SEM

1990 ◽  
Vol 48 (3) ◽  
pp. 124-125
Author(s):  
Sumire Inaga ◽  
Hitoshi Osatake ◽  
Akihiro lino ◽  
Keiichi Tanaka
Keyword(s):  
Electron Microscopy ◽  
Double Helix ◽  
Replica Method ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Ultrahigh Resolution ◽  
Naked Dna ◽  
Dna Strands ◽  
Dna Strand ◽  
Dna Double Helix

So far, the ultrastructure of DNA strand and nucleosome had been observed mainly by transmission electron microscopy with some techniques (thin-sectioning, spreading method, replica method and so on). Among them, the freeze-etching replica method gave high magnified images of DNA double helix (Ruben et al., 1989). Further, scanning tunneling microscopy also elucidated the images of major and minor grooves in a helical DNA duplex. Though scanning electron microscopy (SEM) was also applied for observing chromatin structures, it had been difficult to observe clearly such small materials. Because, the resolution of SEM was too poor to investigate such fine structures. The obstruction of resolution, however, was overcome by the development of an ultrahigh resolution SEM (UHS-T1, Tanaka et al., 1985). Using the SEM, we could successfully observed naked DNA strands and nucleosomes of chicken erythrocyte nuclei without any metal-coating.Preparations were made by the microspreading procedure basically according to the method of Seki et al.

Structure of a dimer of the Sulfolobus solfataricus MCM N-terminal domain reveals a potential role in MCM ring opening

2021 ◽  
Vol 77 (6) ◽  
Author(s):  
Martin Meagher ◽  
Madison N. Spence ◽  
Eric J. Enemark
Keyword(s):  
Dna Replication ◽  
Double Helix ◽  
Sulfolobus Solfataricus ◽  
Replication Initiation ◽  
Terminal Domain ◽  
Closed Ring ◽  
Dna Strands ◽  
Ring Structures ◽  
Dna Strand ◽  
Dna Double Helix

Cells strongly regulate DNA replication to ensure genomic stability and prevent several diseases, including cancers. Eukaryotes and archaea strictly control DNA-replication initiation by the regulated loading of hexameric minichromosome maintenance (MCM) rings to encircle both strands of the DNA double helix followed by regulated activation of the loaded rings such that they then encircle one DNA strand while excluding the other. Both steps involve an open/closed ring transformation, allowing DNA strands to enter or exit. Here, the crystal structure of a dimer of the N-terminal domain of Sulfolobus solfataricus MCM with an intersubunit interface that is more extensive than in closed-ring structures, while including common interactions to enable facile interconversion, is presented. It is shown that the identified interface could stabilize open MCM rings by compensating for lost interactions at an open neighbor interface and that the prior open-ring cryo-EM structure of MCM loading has a similar extended interface adjacent to its open interface.

scholarly journals Ionizing Radiation and Human Health: Reviewing Models of Exposure and Mechanisms of Cellular Damage. An Epigenetic Perspective

2018 ◽  
Vol 15 (9) ◽  
pp. 1971 ◽  
Author(s):  
Ernesto Burgio ◽  
Prisco Piscitelli ◽  
Lucia Migliore
Keyword(s):  
Double Helix ◽  
Classical Model ◽  
Experimental Models ◽  
Cellular Damage ◽  
Low Doses ◽  
Dna Strands ◽  
High Doses ◽  
Living Organisms ◽  
Tissue Reactions ◽  
Dna Double Helix

We reviewed available evidence in medical literature concerning experimental models of exposure to ionizing radiations (IR) and their mechanisms of producing damages on living organisms. The traditional model is based on the theory of “stochastic breakage” of one or both strands of the DNA double helix. According to this model, high doses may cause the breaks, potentially lethal to the cell by damaging both DNA strands, while low doses of IR would cause essentially single strands breaks, easily repairable, resulting in no permanent damages. The available evidence makes this classical model increasingly less acceptable, because the exposure to low doses of IR seems to have carcinogenic effects, even after years or decades, both in the exposed individuals and in subsequent generations. In addition, the cells that survived the exposure to low doses, despite being apparently normal, accumulate damages that become evident in their progeny, such as nonclonal chromosomal aberrations, which can be found even in cells not directly irradiated due to the exchange of molecular signals and complex tissue reactions involving neighboring or distant cells. For all these reasons, a paradigm shift is needed, based on evidence and epigenetics.

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