Energy base stacking

Bases stacked rather than hydrogen bonded have also been studied with quantum chemical methods [182, 244-247]. The nature of excited states in these systems has been debated and theoretical calculations are called to decide on the degree of excited state localization or delocalization, as well as the presence and energy of charge transfer states. The experimentally observed hypochromism of DNA compared to its individual bases has been known for decades [248], Accurate quantum chemical calculations are limited in these systems because of their increased size. Many of the reported studies have used TDDFT to calculate excited states of bases stacked with other bases [182, 244, 246, 247], However, one has to be cautious when us-... 

Our objective is to understand how the noncovalent interactions responsible for nucleic acid secondary structure (i.e. base stacking and base pairing) affect the photophysics of these multichromophoric systems. Here we describe initial experimental results that demonstrate dramatic differences in excited-state dynamics of nucleic acid polymers compared to their constituent monomers. Although ultrafast internal conversion is the dominant relaxation pathway for single bases, electronic energy relaxation in single-stranded polynucleotides... 

Fig. 5 Base pairing and base stacking free energy contributions to the helix thermal stability, as obtained from experiments with nicked duplexes, (a) Pairing shows negligible or even unfavorable effect on free energy, while stacking (b) gives favorable contribution with strong dependence on T, revealing both enthalpic and entropic effects. Adapted with permission from [9]...

Fig. 6 Dependence of the DNA hybridization free energy on ionic strength. Base-pairing (a) is small and salt-independent, while base-stacking (b) is the main part of the interaction. Adapted with permission from [9]...

The double helices thus constructed are tested for geometric acceptability using semiempirical potential energy functions that reflect the extent of intrastrand base stacking and interstrand base pairing in a miniature dinucleoside monophosphate duplex of the same conformation. As described elsewhere (22), the base stacking potential Vs is chosen to display a minimum at a close to ideal base separation distance of 3.3 /( Energies within... 

Figure 3. Contour diagram of the base stacking potential energy Kg of sequential adenine bases and the hydrogen bonding potential energy VHB of the complementary A T base pairs as a function of the phosphodiester rotation angles

Figure 4. Detailed molecular representation of the theoretically predicted base stacking and base pairing of A (single lines) and T (solid lines) bases in the low energy w a = 105°, 115° helix of Figure 3. The view is drawn perpendicular to the helix axis represented by (- -).

Fig. 20.1 The average, the maximal and the minimal values of intermolecular interaction energy for stacked nucleic acid base complexes calculated at the MP2/aug-cc-pVDZ level of theory...

G. Hill, G. Forde, N. Hill, W.A. Lester Jr., W.A. Sokalski, J. Leszczynski, Interaction energies in stacked DNA bases How important are electrostatics. Chem. Phys. Lett. 381, 729-732 (2003)... 

Therefore, it is possible to conclude that high conformational flexibility of pyrimidine rings does not significantly influence the energy of stacking interaction between bases in DNA macromolecules. 

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