Journal of Physical Chemistry B, Vol.108, No.26, 9277-9286, 2004
Hydrogen bonding in 5-bromouracil-adenine-5-bromouracil-adenine (T(+)AT(+)A) tetrads
To understand the role of 5-bromouracil-adenine-5-bromouracil-adenine (T(+)AT(+)A) tetrads in the formation of tetraplexes, the relative stability of different conformers of the tetrad and their bonding characteristics have been studied by quantum chemistry methods. The influence of bromine in the formation of the T(+)AT(+)A tetrads has been revealed by comparative studies of thymine-adenine-thymine-adenine (TATA) and uracil-adenine-uracil-adenine (UAUA) tetrads. The stabilization energy of T(+)AT(+)A has been evaluated to be around 40 kcal/mol, comparable to those of TATA and UAUA. The role which the Br atom plays in the stabilization of the tetrads is 2-fold: by improving the proton-donating ability on its N3 position, it reinforces the H-bonding between A and T+, while through electrostatic repulsion with N7 or NI of A, it destabilizes the binding between the AT(+) pairs. The increase of the intra-base-pair binding energy compensates the decrease of the inter-base-pair interaction. This bifurcated H-bond consisting of Br(T+), 04(T+), and H6'(A) which binds two AT. pairs to form the stable T(+)AT(+)A tetrads has been revealed through the atoms-in-molecules (AIM) theory, the complementary method of electron-localization function (ELF), and the electron density difference analysis. The results of this study suggest that TATA might exist in the dimeric intermolecular tetraplexes formed from the 12-nucleotide repeat sequences from human telomeres.