Watson-Crick base pair stacks

Due to the central role of DNA and proteins in biochemistry and biophysics the computation of the electronic structure of periodic polymers built from nucleotide bases, base pairs, nucleotides and amino acids, respectively, had been of high interest since about twenty years. Early calculations of the band structure of DNA related periodic polymers have been performed with the crystal orbital (CO) method on the basis of different semiempirical levels (1). Recently the results of ab initio Hartree-Fock CO (2, 3) band structure calculations for the four nucleotide base stacks (4-6), the two Watson-Crick base pair stacks (6), the sugar-phosphate chain (4,5) and the three nucleotides cytidine (4,5), adenylic acid and th3nnidine (6) have been reported. These computations represent a significant progress but the following improvements are required for a more accurate description of the electronic structure of real DNA and its transport properties ... 

The DNA double heUx illustrates the contribution of multiple forces to the structure of biomolecules. While each individual DNA strand is held together by covalent bonds, the two strands of the helix are held together exclusively by noncovalent interactions. These noncovalent interactions include hydrogen bonds between nucleotide bases (Watson-Crick base pairing) and van der Waals interactions between the stacked purine and pyrimidine bases. The hehx presents the charged phosphate groups and polar ribose sugars of... 

Modulation of DNA structure and dynamics is also possible using base-pair mismatches. Mismatches exert little influence on the global structure of B-DNA duplexes. Locally, the extent of base stacking perturbation depends sensitively on the nature of the mismatch [139-141]. Therefore, while a CA mismatch introduces a significant distortion in local stacking, the well-stacked GA mismatch is, by many criteria, barely perceptible. The dynamics of mismatched base-pairs may also be significantly distinct from matched Watson-Crick base pairs [9]. We exploit these features of DNA mismatches to probe the sensitivity of DNA-mediated CT to base structure and dynamics. 

Population of i-th site of the chain describing the stack of Watson-Crick base pairs... 

The double helix of DNA [25] and the more complex tertiary structures of RNA [26] are linked together by hydrogen bridges between pairs of nudeobases (approx. 0.5-1.8 kcal mol per Watson-Crick base pair) [27] and by hydrophobic "stacking forces . Fluorinated carbocyclic analogs of these nudeobases have been used to study and elucidate the factors underlying base pairing, replication, and the interaction of the bases with proteins such as DNA polymerases [28]. 

The crystal structure of the duplex [r(guauaca)dC]2, which would be expected to form a self-complementary duplex with an AC mismatch, has been solved and instead shown to form only six Watson-Crick base pairs with two 3 -overhang-ing bases. There are two independent duplexes, each of which is bent, and which stack end to end to form a right-handed super-helix. The overhanging nucleotides are looped out of the structure, with the penultimate adenosine residues forming A-GC base triples. 

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