Cationic interactions base pair stability

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. 

The potential for RNA to act as a catalyst is dictated by its structure as a linear polymer of the four common ribonucleotides. Like DNA, RNA can form double stranded, antiparallel helices via traditional Watson-Crick base pairing. However, the backbone of nucleic acid is highly flexible and RNA can form complex tertiary structures that often involve non-Watson-Crick base pairing to create active site crevices for catalysis. The phosphodiester backbone is charged negatively and interacts electrostatically as well as by direct coordination with solution divalent cations. Ribose, purines, and pyrimidine bases contain both H-bond donors and acceptors that help stabilize higher-order stmcture and provide for substrate positioning, as well as participate in active site interactions. 

The influence of the cations and anions has been discussed separately with the solution properties and reactions in the main focus. It has, however, been known over 100 years that anions play a crucial role for the stabilization and coagulation of colloids. More recently, the contribution of anions on the stabilization of particles, biocolloids, and bubbles has received renewed attention. - In these papers, it has been pointed out that there exists a collaborative interaction between cations and anions upon adsorption of one of the complexes from solution. At high concentrations this effect renders the simple indifferent ions specific and selective to each other. It is also seen as a dependency on the acid-base pair chosen for the regulation of the pH. This effect certainly needs to be added as an extension to (correction of) the DLVO theory. However, as shown in this paper, it is just as probable that the anion and cation collaborate during the adsorption and formation of gels and precipitates at the surface. The presence of such mixed phases has been confirmed experimentally, e.g., during the formation of hydroxoapatite in silica gel layers. ... 

The enhancement of base pairing by metal cation coordination is the difference between the energies which are necessary to separate two H-bonded bases in the presence and absence of the cation. Such effects have been noticed in older theoretical studies [24,25], and polarization enhancement of base pairing has been proposed as a means of stabilizing the Purine.Purine.Pyrimidine triple helices [78]. The enhancement of a base pair arise from two effects a) the classical electrostatic interaction between the cation and remote base (the base which does not interact directly with the cation) and b) the "nonclassical" three-body term originating mainly in polarization effects. 

---