Adenine base pair stability

As pointed out in the previous section, chemical modification of a nucleobase can lead to the situation that a cationic (protonated) nucleobase is involved in base pairing. Two cases are to be differentiated First, the modified base is cationic. This situation is realized in the base pair between 7,9-dimethylguani-nium (58a) or 7-methylguanosinium (58b) and the corresponding neutral betain (cf. Fig. 2). Second, the modified base forces the complementary base to become protonated in order to form hydrogen bond for increased base pair stability. This situation is realized in the pair formed between 06-alkylguanine and protonated cytosine (59b) or adenine (69), and also in the pair between 3-methylguanine and protonated cytosine (60) (cf. above). Of course, the above differentiation is in a way superficial in that simple proton transfer will interconvert the two cases. 

Sponer, J., Sabat, M., Burda, J. V., Leszczynski, J., Hobza, P. (1999). Interaction of the adenine-thymine Watson-Crick and adenine-adenine reverse-Hoogsteen DNA base pairs with hydrated group Ila (Mg2+, Ca2+, Sr2+, Ba2+) and lib (Zn2+, Cd2+, Hg2+) metal cations Absence of the base pair stabilization by metal-induced polarization effects. The Journal of Physical Chemistry B, 103, 2528. 

Section 28 8 The most common form of DNA is B DNA which exists as a right handed double helix The carbohydrate-phosphate backbone lies on the outside the punne and pyrimidine bases on the inside The double helix IS stabilized by complementary hydrogen bonding (base pairing) between adenine (A) and thymine (T) and guanine (G) and cytosine (C)... 

Several base pairs of adenine-thymine, including the WC pair, have also been studied [238], It is found that a charge transfer state exists about 1.5 eV higher than the local nn states. Proton transfer between the bases stabilizes a charge transfer state which then crosses with the ground state facilitating radiationless relaxation. This mechanism is not energetically favorable for non WC pairs. 

Sarai, A., and M. Saito. 1984. Theoretical Studies on the Interaction of Proteins with Base Paris. I. Ab Initio Calculation for the Effect of H-Bonding Interaction of Proteins on the Stability of Adenine-Uracil Pair. Int. J. Quantum Chem. 25, 527-533. 

Contrary to H-bonded nucleic acid base pairs discussed in the previous section, the nature of intermolecular interactions in complexes of stacked bases was analyzed more extensively. The values of minimal, maximal, and average total stabilization energies, corrected for BSSE, for a set comprising over 80 stacked bases, are plotted in Fig. 20.1. In the case of guanine-adenine and adenine-cytosine complexes, the results are presented for two sequence contexts, i.e., A/G-G/A and A/C-C/A. The symbol AA denotes the 2-oxo-adenine - complexes of oxidized bases, and this... 

Kawai K, Saito I (1998). Stabilization of Hoogsteen base pairing by introduction of NH2 group at the C8 position of adenine. Tetrahedron Lett 29 5221—5224. 

Fig. 20.6. Possible stabilization of the A C base pair as seen in the crystal structure of d(CGCGAATTAGCG) by protonation of adenine (left) is more probable than the amino-imino tautomerism (right). Atom designation as in Fig. 20.4 R = sugar residue...

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