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
Author(s):  
S.S. Dzhimak ◽  
M.I. Drobotenko ◽  
A.A. Basov ◽  
A.A. Svidlov ◽  
M.G. Baryshev

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.


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

1998 ◽  
Vol 54 (3) ◽  
pp. 316-319 ◽  
Author(s):  
J. P. M. Lommerse ◽  
J. C. Cole

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.


2007 ◽  
Vol 111 (17) ◽  
pp. 3196-3208 ◽  
Author(s):  
Zhaohui Wang ◽  
Yoonsoo Pang ◽  
Dana D. Dlott

1998 ◽  
Vol 54 (6) ◽  
pp. 866-871 ◽  
Author(s):  
J. K. Maurin

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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