Sequence and temperature effect on hydrogen bond disruption in DNA determined by a statistical analysis

1996 ◽  
Vol 25 (1) ◽  
pp. 9-18 ◽  
Author(s):  
Y. Z. Chen ◽  
E. W. Prohofsky
Keyword(s):  
Hydrogen Bond ◽  
Statistical Analysis ◽  
Temperature Effect ◽  
Bond Disruption

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 Bonding to Thiocyanate Anions: Statistical and Quantum-Chemical Analyses

1998 ◽  
Vol 54 (3) ◽  
pp. 316-319 ◽  
Author(s):  
J. P. M. Lommerse ◽  
J. C. Cole
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Statistical Analysis ◽  
Lone Pair ◽  
Unexpected Result ◽  
Acta Cryst ◽  
Energy Calculations ◽  
Acceptor Atom ◽  
Detailed Statistical Analysis ◽  
Nitrogen Lone Pair

A statistical analysis of entries from the CSD (Cambridge Structural Database) showed that the average hydrogen-bond geometry to the nitrogen acceptor atom of the thiocyanate anion was not collinear with respect to the molecular axis of the anion and so not collinear with the nitrogen lone pair [Tchertanov & Pascard (1996). Acta Cryst. B52, 685–690]. This somewhat unexpected result has been investigated further using theoretical energy calculations applying Intermolecular Perturbation Theory in combination with a more detailed statistical analysis of an appropriate CSD dataset. The energy calculations pointed to the formation of the strongest hydrogen bonds in the nitrogen lone-pair direction. The statistical analysis showed that this directionality occurs in cases where the N atom accepts one hydrogen bond only. The non-linear average hydrogen-bond geometry observed in the earlier study can be attributed to multiple hydrogen bonding to the N atom. In such cases, there is a shift away from the optimum orientation.

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

Oxime–Carboxyl Hydrogen Bonds: the Preferred Interaction Determining Crystal Packing of `Carboxyoximes'

1998 ◽  
Vol 54 (6) ◽  
pp. 866-871 ◽  
Author(s):  
J. K. Maurin
Keyword(s):  
Hydrogen Bond ◽  
Statistical Analysis ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Carboxylic Acids ◽  
Quantum Chemical Calculations ◽  
Pyruvic Acid ◽  
Quantum Chemical ◽  
Crystal Packing ◽  
Hydrogen Bond Interactions

The statistical analysis of hydrogen-bond interactions formed by oximes and carboxylic acids has been performed. Ab initio quantum-chemical calculations have been used to rationalize the observed preference for the oxime–carboxyl interaction compared with homologous binding (carboxyl–carboxyl and oxime–oxime). The crystal packing observed in the structure of pyruvic acid oxime (hydroxyiminopyruvic acid) has been explained as the consequence of a combination of the energetically optimal structure of the isolated molecule and the optimal interaction of monomers forming a dimer.

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