scholarly journals Commentary on the Work of Jimak S.S. et al. “Mathematical Modeling of Open States in Double Stranded DNA Molecule Depending on 2H/1H Ratio”

2020 ◽  
Vol 15 (1) ◽  
pp. 1-3
Author(s):  
A.S. Shigaev
Keyword(s):  
Mathematical Modeling ◽  
Mathematical Biology ◽  
Biological Function ◽  
Bond Energies ◽  
Dna Molecule ◽  
Double Stranded Dna ◽  
Open States

The article is analyzed Jimak S.S. et al. “Mathematical modeling of open state accounting as a function of 2H/1H ratio in a double-stranded DNA molecule”, appeared in “Mathematical Biology and Bioinformatics”. The values of H-bond energies used in the simulation as a parameter are estimated. A new mechanism for the effect of DNA deuteration on biological function of DNA described by authors is proposed.

scholarly journals Mathematical Modeling of Open States in Double Stranded DNA Molecule Depending on 2H/1H Ratio

2019 ◽  
Vol 14 (2) ◽  
pp. 612-624 ◽  
Author(s):  
S.S. Dzhimak ◽  
M.I. Drobotenko ◽  
A.A. Basov ◽  
A.A. Svidlov ◽  
M.G. Baryshev
Keyword(s):  
Mathematical Modeling ◽  
Hydrogen Bond ◽  
Deuterium Atom ◽  
Living System ◽  
Dna Molecule ◽  
Dna Base Pair ◽  
A Chain ◽  
Time Required ◽  
Open States ◽  
Bond Disruption

The evaluation results of the possible deuterium atoms effect on the DNA base pair opening are presented in the article. The cause of these processes is the replacement of protium with deuterium atom due to the increase of energy required to break the hydrogen bond. These processes can be studied by method of mathematical modeling, with account of open states between base pairs being the key condition of the adequacy of the mathematical model of the DNA. The experiment data show that the presence of deuterium in a chain of nucleotides can cause - depending on the value of hydrogen bond disruption energy - both increase and decrease in probability of open states occurrence. For example: hydrogen bond disruption energy of 0.358·10-22 n·m, non-zero probability of open states occurrence is observed in case of the absence of deuterium in the molecule, and with hydrogen bond disruption energy of 0.359·10-22 n·m or more such probability equals zero. Also, when one deuterium atom is present in a molecule, non-zero probability is observed even with hydrogen bond disruption energy equal to 0.368·10-22 n·m (i.e. more than 0.358·10-22 n·m). Thus participation of deuterium atoms in the formation of hydrogen bonds of double helixes of a DNA molecule can cause the changes in the time required for transfer of genetic information, which can explain the effect of even minor deviations in deuterium concentration in a medium on metabolic processes in a living system.

scholarly journals High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast

2017 ◽  
Author(s):  
Yi Yin ◽  
Margaret Dominska ◽  
Eunice Yim ◽  
Thomas D. Petes
Keyword(s):  
Type Strain ◽  
Wild Type Strain ◽  
Mitotic Recombination ◽  
Template Switching ◽  
Wild Type ◽  
Dna Breaks ◽  
Repair Synthesis ◽  
Heteroduplex Dna ◽  
Dna Molecule ◽  
Double Stranded Dna

AbstractDouble-stranded DNA breaks (DSBs) can be generated by both endogenous and exogenous agents. In diploid yeast strains, such breaks are usually repaired by homologous recombination (HR), and a number of different HR pathways have been described. An early step for all HR pathways is formation of a heteroduplex, in which a single-strand from the broken DNA molecule pairs with a strand derived from an intact DNA molecule. If the two strands of DNA are not identical, within the heteroduplex DNA (hetDNA), there will be mismatches. In a wild-type strain, these mismatches are removed by the mismatch repair (MMR) system. In strains lacking MMR, the mismatches persist and can be detected by a variety of genetic and physical techniques. Most previous studies involving hetDNA formed during mitotic recombination have been restricted to a single locus with DSBs induced at a defined position by a site-specific endonuclease. In addition, in most of these studies, recombination between repeated genes was examined; in such studies, the sequence homologies were usually less than 5 kb. In the present study, we present a global mapping of hetDNA formed in a UV-treated MMR-defective mlh1 strain. Although about two-thirds of the recombination events were associated with hetDNA with a continuous array of unrepaired mismatches, in about one-third of the events, we found regions of unrepaired mismatches flanking regions without mismatches. We suggest that these discontinuous hetDNAs involve template switching during repair synthesis, repair of a double-stranded DNA gap, and/or Mlh1-independent MMR. Many of our observed events are not explicable by the simplest form of the double-strand break repair (DSBR) model of recombination. We also studied hetDNA associated with spontaneous recombination events selected on chromosomes IV and V in a wild-type strain. The interval on chromosome IV contained a hotspot for spontaneous crossovers generated by an inverted pair of transposable elements (HS4). We showed that HS4-induced recombination events are associated with the formation of very large (>30 kb) double-stranded DNA gaps.

scholarly journals Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA

Molecules ◽  
2020 ◽  
Vol 25 (16) ◽  
pp. 3753 ◽  
Author(s):  
Alexander Basov ◽  
Mikhail Drobotenko ◽  
Alexandr Svidlov ◽  
Eugeny Gerasimenko ◽  
Vadim Malyshko ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
False Negative ◽  
Deuterium Atom ◽  
Base Pairs ◽  
Gene Encoding ◽  
Negative Results ◽  
False Negative Results ◽  
Nitrogenous Base ◽  
Open States ◽  
Different Parts

In the present study, the effect of 2H/1H isotopic exchange in hydrogen bonds between nitrogenous base pairs on occurrence and open states zones dynamics is investigated. These processes are studied using mathematical modeling, taking into account the number of open states between base pairs. The calculations of the probability of occurrence of open states in different parts of the gene were done depending on the localization of the deuterium atom. The mathematical modeling study demonstrated significant inequality (dependent on single 2H/1H replacement in DNA) among three parts of the gene similar in length of the frequency of occurrence of the open states. In this paper, the new convenient approach of the analysis of the abnormal frequency of open states in different parts of the gene encoding interferon alpha 17 was presented, which took into account both rising and decreasing of them that allowed to make a prediction of the functional instability of the specific DNA regions. One advantage of the new algorithm is diminishing the number of both false positive and false negative results in data filtered by this approach compared to the pure fractile methods, such as deciles or quartiles.

Exploration of Spin-Dependent Thermoelectricity in the Chiral Double-Stranded DNA Molecule Coupled to Ferromagnetic Leads

2019 ◽  
Vol 12 (2) ◽  
Author(s):  
Lei-Lei Nian ◽  
Long Bai ◽  
Wenting Yu ◽  
Jun Tang ◽  
Huichao Li ◽  
...  
Keyword(s):  
Dna Molecule ◽  
Double Stranded Dna

scholarly journals Ensemble of DNA Kinks

2019 ◽  
Vol 224 ◽  
pp. 03005 ◽  
Author(s):  
Ludmila V. Yakushevich ◽  
Larisa A. Krasnobaeva
Keyword(s):  
Hydrogen Bonds ◽  
Dynamic Characteristics ◽  
Dynamic Properties ◽  
Double Helix ◽  
Statistical Properties ◽  
Dna Molecule ◽  
Open States

The DNA open states, which are locally unwound regions of the double helix within which hydrogen bonds between complementary nitrous bases are broken, are often modeled as quasiparticles – DNA kinks. Most of the works on the DNA kinks are devoted to the studies of their dynamic properties, as well as their role in the functioning of the molecule. However, if not one but N open states are formed in the DNA molecule it is reasonable to consider the problem of the statistics of the ensemble of N DNA kinks. The statistical properties of such an ensemble are still poorly understood. In the present work, we study these properties applying new data on the dynamic characteristics of DNA kinks.

scholarly journals Influence of Environmental Parameters on the Stability of the DNA Molecule

Entropy ◽  
2021 ◽  
Vol 23 (11) ◽  
pp. 1446
Author(s):  
Alexander Svidlov ◽  
Mikhail Drobotenko ◽  
Alexander Basov ◽  
Eugeny Gerasimenko ◽  
Anna Elkina ◽  
...  
Keyword(s):  
External Environment ◽  
Environmental Parameters ◽  
High Viscosity ◽  
Rate Of Change ◽  
Dna Molecule ◽  
Twisted State ◽  
Physiological Processes ◽  
Dna Strands ◽  
The Stability ◽  
Open States

Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation—dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases’ vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.

scholarly journals Mechanisms of loading and release of the 9-1-1 checkpoint clamp

2021 ◽  
Author(s):  
Juan C Castaneda ◽  
Marina Schrecker ◽  
Dirk Remus ◽  
Richard K Hite
Keyword(s):  
Conformational Changes ◽  
Atp Hydrolysis ◽  
Clamp Loader ◽  
Opposite Orientation ◽  
Checkpoint Kinase ◽  
Sliding Clamp ◽  
Double Stranded Dna ◽  
Clamp Loading ◽  
Clamp Loaders ◽  
Open States

5' single-stranded/double-stranded DNA serve as loading sites for the checkpoint clamp, 9-1-1, which mediates activation of the apical checkpoint kinase, ATRMec1. However, the basis for 9-1-1's recruitment to 5' junctions is unclear. Here, we present structures of the yeast checkpoint clamp loader, Rad24-RFC, in complex with 9-1-1 and a 5' junction and in a post-ATP-hydrolysis state. Unexpectedly, 9-1-1 adopts both closed and planar open states in the presence of Rad24-RFC and DNA. Moreover, Rad24-RFC associates with the DNA junction in the opposite orientation of processivity clamp loaders with Rad24 exclusively coordinating the double-stranded region. ATP hydrolysis stimulates conformational changes in Rad24-RFC, leading to disengagement of DNA-loaded 9-1-1. Together, these structures explain 9-1-1's recruitment to 5' junctions and reveal new principles of sliding clamp loading.

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