Stacked DNA base pairs

While the structure of clusters responds to directionally specific electrostatic interactions, their stabilization energy reflects also the intervention of less specific dispersion interactions. This is, e.g., the case for stacked DNA base pairs. Stability of these pairs stems from dispersion energy while their structure is determined by dipole-dipole electrostatic interactions. Dispersion energy plays an important role in stabilizing clusters of biomacromolecules, where it may be the dominant attractive term. 

Hobza, R, Sponer, J., and Polasek, M., H-honded and stacked DNA base pairs cytosine dimer. An ab initio second-order M0ller-Plesset study, J. Am. Chem. Soc. 117, 792-798 (1995). McDowell, S. A. C. and Buckingham, A. D., Isotope effects on the stability of the carbon monoxide-acetylene van der Waals molecule and the hydrogen fluoride dimer, Chem. Phys. Lett. 182, 551-555 (1991). 

D. Sivanesan, K. Babu, S. R. Gadre, V. Subramanian, and T. Ramasami, Does a stacked DNA base pair hydrate better than a hydrogen-bonded one An ab initio study, J. Phys. Chem. A 104, 10887-10894 (2000). 

Does a stacked DNA base pair hydrate better than a hydrogen-bonded one An ab... 

Calculations with Extended Basis Set A PromisingTool for Study of H-Bonded and Stacked DNA Base Pairs. 

Jurecka, R, Nachtigall, R. and Hobza, P. (2001) RI-MP2 calculations with extended basis sets-a promising tool for study of H-bonded and stacked DNA base pairs. Phys. Chem. Chem. Phys., 3, 4578-4582. 

Extended solid state n systems facilitate CT, particularly when doped [4-6]. The analogy between DNA and conductive solid state -stacks therefore establishes that a requisite condition for CT may exist in DNA. DNA contains an array of heterocyclic aromatic base pairs, stacked at a distance of 3.4 A, wrapped within a negatively charged sugar phosphate backbone [7] (Fig. 1). The interactions between the n electrons of the DNA base pairs provide the electronic coupling necessary for CT to occur. 

The analogy drawn between -stacked solids and duplex DNA has provided a useful starting point for experiments to probe and understand DNA-medi-ated CT. As with the -stacked solids, the DNA base pair array can provide an effective medium for long range CT. Mechanistically, however, the differences between DNA and these solid state materials may be even more important to consider. Duplex DNA, as a molecular -stacked structure, undergoes dynamical motion in solution. The time-dependent and sequence-dependent structures that arise serve to modulate and gate CT. Indeed in probing DNA CT as a function of sequence and sequence-dependent structure, we may better understand mechanistically how CT proceeds and how DNA CT may be utilized. 

DNA-mediated charge transport has been a hot topic in chemistry for the last decade. Studies of DNA-mediated guanine radical cation (hole) transport are often focused on the efficiency of the transport between two guanines separated by a large distance, through the /r-stack of DNA base pairs [1-14]. The efficiency of the hole transport could be easily determined if one knew the distance between the hole donor and acceptor, the relative number of holes that reach the acceptor, and the time required for the transport. 

In forming the double-helix polymeric DNA structure, the two sugar-phosphate backbones twist around the central stack of base pairs, generating a major and minor groove. Several conformations, known as DNA polymorphs, are possible. 

Such activity enhancement can be ascribed to planarity of the naphthalene nucleus and its disposition for n-n stacking between the DNA base pairs. There is no literature precedence for involvement of naphthalene in such processes unless it is % electron deficient.211,212 However, our results suggest that both alkylated and acylated naphthalenes are intercalators with bacterial DNA. 

Figure 26. Schematic of the mediation of ET by a jt-stack of aromatic rings, such as the base pairs of duplex DNA. The D and A groups associated with the DNA molecule may be covalently linked to the helix, they may be intercalators, or they may be DNA base pairs.

Bixon and Jortner, Rosch and Voityuk, Olofsson and Larsson, Berlin, Burin, Siebbeles, and Ratner, Orlandi and their coworkers [4, 8, 19-31] have explored the energetics and base-base interactions associated with hole and electron transfer in DNA base-pair stacks. They find nearest-neighbor coupling inter-... 

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