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 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.

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.

Iodo-nitroarenesulfonamides: interplay of hard and soft hydrogen bonds, I...O interactions and aromatic π...π stacking interactions

2001 ◽  
Vol 58 (1) ◽  
pp. 94-108 ◽  
Author(s):  
Craig J. Kelly ◽  
Janet M. S. Skakle ◽  
James L. Wardell ◽  
Solange M. S. V. Wardell ◽  
John N. Low ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Space Group ◽  
Rotation Axes ◽  
Π Stacking ◽  
Structural Database ◽  
A Chain

Molecules of N-(4′-iodophenylsulfonyl)-4-nitroaniline, 4-O2NC6H4NHSO2C6H4I-4′ (1), are linked by three-centre I...O2N interactions into chains and these chains are linked into a three-dimensional framework by C—H...O hydrogen bonds. In the isomeric N-(4′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4NHSO2C6H4NO2-4′ (2), the chains generated by the I...O2N interactions are again linked into a three-dimensional framework by C—H...O hydrogen bonds. Molecules of N,N-bis(3′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4N(SO2C6H4NO2-3′)2 (3), lie across twofold rotation axes in space group C2/c and they are linked into chains by paired I...O=S interactions: these chains are linked into sheets by a C—H...O hydrogen bond, and the sheets are linked into a three-dimensional framework by aromatic π...π stacking interactions. In N-(4′-iodophenylsulfonyl)-3-nitroaniline, 3-O2NC6H4NHSO2C6H4I-4′ (4), there are R^2_2(8) rings formed by hard N—H...O=S hydrogen bonds and R^2_2(24) rings formed by two-centre I...nitro interactions, which together generate a chain of fused rings: the combination of a C—H...O hydrogen bond and aromatic π...π stacking interactions links the chains into sheets. Molecules of N-(4′-iodophenylsulfonyl)-4-methyl-2-nitroaniline, 4-CH3-2-O2NC6H3NHSO2C6H4I-4′ (5), are linked by N—H...O=S and C—H...O(nitro) hydrogen bonds into a chain containing alternating R^2_2(8) and R^2_2(10) rings, but there are no I...O interactions of either type. There are two molecules in the asymmetric unit of N-(4′-iodophenylsulfonyl)-2-nitroaniline, 2-O2NC6H4NHSO2C6H4I-4′ (6), and the combination of an I...O=S interaction and a hard N—H...O(nitro) hydrogen bond links the two types of molecule to form a cyclic, centrosymmetric four-component aggregate. C—H...O hydrogen bonds link these four-molecule aggregates to form a molecular ladder. Comparisons are made with structures retrieved from the Cambridge Structural Database.

scholarly journals Crystal structures of three 3,4,5-trimethoxybenzamide-based derivatives

2016 ◽  
Vol 72 (5) ◽  
pp. 675-682 ◽  
Author(s):  
Ligia R. Gomes ◽  
John Nicolson Low ◽  
Catarina Oliveira ◽  
Fernando Cagide ◽  
Fernanda Borges
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Methoxy Group ◽  
Combined Effect ◽  
Donor Group ◽  
Methoxy Substituent ◽  
A Chain ◽  
Benzamide Derivatives

The crystal structures of three benzamide derivatives,viz. N-(6-hydroxyhexyl)-3,4,5-trimethoxybenzamide, C16H25NO5, (1),N-(6-anilinohexyl)-3,4,5-trimethoxybenzamide, C22H30N2O4, (2), andN-(6,6-diethoxyhexyl)-3,4,5-trimethoxybenzamide, C20H33NO6, (3), are described. These compounds differ only in the substituent at the end of the hexyl chain and the nature of these substituents determines the differences in hydrogen bonding between the molecules. In each molecule, them-methoxy substituents are virtually coplanar with the benzyl ring, while thep-methoxy substituent is almost perpendicular. The carbonyl O atom of the amide rotamer istransrelated with the amidic H atom. In each structure, the benzamide N—H donor group and O acceptor atoms link the molecules intoC(4) chains. In1, a terminal –OH group links the molecules into aC(3) chain and the combined effect of theC(4) andC(3) chains is a ribbon made up of screw relatedR22(17) rings in which the ...O—H... chain lies in the centre of the ribbon and the trimethoxybenzyl groups forms the edges. In2, the combination of the benzamideC(4) chain and the hydrogen bond formed by the terminal N—H group to an O atom of the 4-methoxy group link the molecules into a chain ofR22(17) rings. In3, the molecules are linked only byC(4) chains.

scholarly journals LevioSAM: Fast lift-over of alternate reference alignments

2021 ◽  
Author(s):  
Taher Mun ◽  
Nae-Chyun Chen ◽  
Ben Langmead
Keyword(s):  
Population Genetics ◽  
Coordinate System ◽  
Data Structures ◽  
Succinct Data Structures ◽  
Reference Coordinate System ◽  
Link Type ◽  
A Chain ◽  
Time Required ◽  
Effective Use

AbstractMotivationAs more population genetics datasets and population-specific references become available, the task of translating (“lifting”) read alignments from one reference coordinate system to another is becoming more common. Existing tools generally require a chain file, whereas VCF files are the more common way to represent variation. Existing tools also do not make effective use of threads, creating a post-alignment bottleneck.ResultsLevioSAM is a tool for lifting SAM/BAM alignments from one reference to another using a VCF file containing population variants. LevioSAM uses succinct data structures and scales efficiently to many threads. When run downstream of a read aligner, levioSAM completes in less than 13% the time required by an aligner when both are run with 16 threads.Availabilityhttps://github.com/alshai/[email protected], [email protected]

scholarly journals (Z)-3-(1-Chloroprop-1-enyl)-2-methyl-1-phenylsulfonyl-1H-indole

2013 ◽  
Vol 69 (12) ◽  
pp. o1781-o1781 ◽  
Author(s):  
M. Umadevi ◽  
V. Saravanan ◽  
R. Yamuna ◽  
A. K. Mohanakrishnan ◽  
G. Chakkaravarthi
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Phenyl Ring ◽  
Three Dimensional ◽  
Ring System ◽  
Indole Ring ◽  
Compound C ◽  
Dimensional Network ◽  
A Chain

In the title compound, C18H16ClNO2S, the indole ring system forms a dihedral angle of 75.07 (8)° with the phenyl ring. The molecular structure is stabilized by a weak intramolecular C—H...O hydrogen bond. In the crystal, molecules are linked by weak C—H...O hydrogen bonds, forming a chain along [10-1]. C—H...π interactions are also observed, leading to a three-dimensional network.

Crystal structure of rivastigmine hydrogen tartrate Form I (Exelon®), C14H23N2O2(C4H5O6)

2016 ◽  
Vol 31 (2) ◽  
pp. 97-103 ◽  
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Carbonyl Oxygen ◽  
Strong Hydrogen Bond ◽  
Hydroxyl Groups ◽  
A Chain ◽  
Tartrate Anion

The crystal structure of rivastigmine hydrogen tartrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Rivastigmine hydrogen tartrate crystallizes in space group P21 (#4) with a = 17.538 34(5), b = 8.326 89(2), c = 7.261 11(2) Å, β = 98.7999(2)°, V = 1047.929(4) Å3, and Z = 2. The un-ionized end of the hydrogen tartrate anions forms a very strong hydrogen bond with the ionized end of another anion to form a chain. The ammonium group of the rivastigmine cation forms a strong discrete hydrogen bond with the carbonyl oxygen atom of the un-ionized end of the tartrate anion. These hydrogen bonds form a corrugated network in the bc-plane. Both hydroxyl groups of the tartrate anion form intramolecular O–H⋯O hydrogen bonds. Several C–H⋯O hydrogen bonds appear to contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-064-1501.

Secondary Interactions in Gold(I) Complexes with Thione Ligands, 3. Three Ionic Dimesylamides [1, 2]

2004 ◽  
Vol 59 (11-12) ◽  
pp. 1429-1437 ◽  
Author(s):  
Friedrichsa Friedrichsa ◽  
Peter G. Jones
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Layer Structure ◽  
Chain Structure ◽  
Hydrogen Bond Donor ◽  
Weak Hydrogen Bonds ◽  
Ribbon Structure ◽  
A Chain ◽  
Aurophilic Interactions ◽  
Short Contacts

Three structures of the form bis(thione)gold(I) di(methanesulfonyl)amide [thione = imidazolidine- 2-thione, 1; 1-methyl-imidazolidine-2-thione, 2; thiazolidine-2-thione, 3] were determined; all crystallize with one formula unit in the asymmetric unit. Each N-H hydrogen bond donor forms one classical two-centre hydrogen bond with an anion acceptor. Compound 1 thereby forms a complex layer structure with a layer thickness of 10.17 Å ; the packing may be analysed in terms of thinner subunit layers consisting of interlinked, hydrogen-bonded chains and rings. Compound 2 forms a chain structure consisting of a series of “hairpin bends”, a common feature in the gold complexes of 1-alkyl-imidazolidine-2-thiones. Compound 3 forms a corrugated ribbon structure in which the central region consists of parallel S-Au-S axes linked by aurophilic interactions; the anions exercise a “clamping” function by forming hydrogen bonds at the periphery of the ribbons. Further short contacts can be classed as weak hydrogen bonds C-H ··· X, with X = N, O, S or Au.

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