The DNA duplex stability: estimation of the energy of hydrogen
bonds and reactivity using TATA box as model
E. Ramos1,*, J. Gutiérrez-Flores1, C. Mendoza1 and E. Hernández-Lemus2
Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México
A.P. 70-360, 04510, Cd. De México, México
*[email protected]
The spatial structure of the DNA molecule determines the physiological and biochemical
mechanisms in which this carries out its biological functions. Of particular importance to the
spatial structure and stability of the double helix are the hydrogen bonds [1, 2] that join both
strands in the chain. Furthermore, the chemical properties of the DNA chain significantly
determine the selectivity of certain proteins. In this project the energy associated with the
hydrogen bonds in chains of different number of units (from 1 to 14 base pairs) is studied, taking
into account two different models: ideal not relaxed model (that obey conditions of symmetry)
and ideal relaxed model (relaxed structures from the previous model). On the other hand, a first
approach to the selectivity of TBP to the TATA [3] box is done by studying chemical properties of
this genomic region. The study was realized under the framework of DFT [4, 5] using the code
DMol3 [6] (M06-L/DN) implemented in the Materials Studio software suite [7].
From the analysis could be inferred that the average energy of hydrogen bond of the ideal not
relaxed model varies periodically depending on the number of base pairs in the chain. This is
related with the border effects associated with the symmetry of the system, allowing the
differentiation between chains with even or odd number of base pairs. An analytical model for
this development, that allows obtaining the average energy of hydrogen bond for chains of any
size, is proposed. While for the ideal relaxed model, the size of the chain has influence in the
average energy of hydrogen bond existing between thymine and adenine, because the presence
of
neighbors
tends
to
stabilize
this
interaction.
Finally, from the Frontier Molecular Orbitals and Fukui functions [8] can explain, from the chain
of eight base pairs, the way how the binding protein interacts with the TATA box region.
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[7] Materials Studio 2014, Biovia. © 2014 Systèmes, Biovia Software Inc.
[8] R. G. Parr y W. Yang. Density Functional Approach to the Frontier-Electron Theory
of Chemical Reactivity. Journal of the American Chemical Society, 106:4049, 1984.