Mathematical Modeling of Open State in DNA Molecule Depending on the Deuterium Concentration in the Surrounding Liquid Media at Different Values of Hydrogen Bond Disruption Energy

2018 ◽  
Vol 483 (5) ◽  
pp. 564-566
Author(s):  
S. Dzhimak ◽  
◽  
M. Baryshev ◽  
O. Lyasota ◽  
L. Fedulova ◽  
...  
Keyword(s):  
Mathematical Modeling ◽  
Hydrogen Bond ◽  
Liquid Media ◽  
Dna Molecule ◽  
Deuterium Concentration ◽  
Bond Disruption ◽  
Surrounding Liquid

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 Mdm-2 binding and TAFII31 recruitment is regulated by hydrogen bond disruption between the p53 residues Thr18 and Asp21

Oncogene ◽  
2002 ◽  
Vol 21 (46) ◽  
pp. 7100-7113 ◽  
Author(s):  
James R Jabbur ◽  
Amy D Tabor ◽  
Xiaodong Cheng ◽  
Hua Wang ◽  
Motonari Uesugi ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Bond Disruption

Hydrogen-Bond Disruption by Vibrational Excitations in Water

2007 ◽  
Vol 111 (17) ◽  
pp. 3196-3208 ◽  
Author(s):  
Zhaohui Wang ◽  
Yoonsoo Pang ◽  
Dana D. Dlott
Keyword(s):  
Hydrogen Bond ◽  
Vibrational Excitations ◽  
Bond Disruption

A mediated hydrogen bond in an α-hydroxycarboxyl group: X-ray structure of (R,R)-N-methyltartramic acid monohydrate and an ab initio study of model systems

1999 ◽  
Vol 55 (4) ◽  
pp. 617-625 ◽  
Author(s):  
Urszula Rychlewska ◽  
Agnieszka Szarecka ◽  
Jacek Rychlewski ◽  
Rafał Motała
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Gas Phase ◽  
Parent Compound ◽  
Model Systems ◽  
Ab Initio Study ◽  
Liquid Media ◽  
X Ray ◽  
The Stability ◽  
High Polarity

The crystal structure of (R,R)-N-methyltartramic acid monohydrate is presented and compared with that of the parent compound, (R,R)-tartaric acid. Despite some conformational differences between the two molecules the packing is very similar, as it is dictated by the carboxyl rather than the amide function. Particular attention is paid to a mediated three-centre hydrogen bond as one of the packing motifs involving the α-hydroxycarboxyl moiety. The stability and geometry of such structures in the gas phase and in solution are examined via theoretical ab initio methods using the RHF/6-311++G** and RHF/6-311++G**/Onsager models, respectively. Liquid media, in particular those of high polarity, are found to stabilize the structures considerably.

scholarly journals Hydrogen Bond Disruption in DNA Base Pairs from 14C Transmutation

2014 ◽  
Vol 118 (35) ◽  
pp. 10430-10435 ◽  
Author(s):  
Michel Sassi ◽  
Damien J. Carter ◽  
Blas P. Uberuaga ◽  
Christopher R. Stanek ◽  
Ricardo L. Mancera ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Base Pairs ◽  
Dna Base ◽  
Dna Base Pairs ◽  
Bond Disruption
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