Base pair stacking

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. 

To test this sensitivity of photoinduced quenching to perturbations in the intervening base pair stack, an assembly was prepared containing an intervening CA base mismatch which disrupts locally the /r-stack between the donor and acceptor. We observed that the yield of CT was reduced in the DNA... 

DNA CT also permits chemistry at a distance. Oxidative DNA damage and thymine dimer repair can proceed in a DNA-mediated reaction initiated from a remote site. These reactions too are sensitive to intervening DNA dynamical structure, and such structures can serve to modulate DNA CT chemistry. The sensitivity of DNA CT to base pair stacking also provides the basis for the design of new DNA diagnostics, tools to detect mutations in DNA and to probe protein-DNA interactions. 

The DNA double helix is stabilized by hydrophobic interactions resulbng from the individual base pairs stacking on top of each other in the nonpolar interior of the double helix (Figs. 4-1 and 4-2). The hydrogen bonds, like the hydrogen bonds of proteins, contribute somewhat to the overall stability of the double helix but contribute greatly to the specificity for forming the correct base pairs. An incorrect base pair would not... 

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-... 

To me the key to DNA electron transfer is this base-pair stacking. Our intercalators were also well stacked and so represented effective probes of... 

No. But that s OK because that kept on pushing us towards better and better experiments. I think that the last experiment that we published in Science this year may have made clear how exquisitely sensitive the electron transfer was to base-pair stacking. In this experiment we no longer appended metal complex intercalators but we simply looked at electron transfer from one modified base to another modified base. In this experiment we used two modified adenines as our fluorescent excited electron acceptor to oxidize guanines. The modified adenines were very similar in structure, very similar in redox characteristics, very similar in energetics. But when they were incorporated into DNA, one was well-stacked in the helix and one was... 

C) Base pairs stacked along the central axis of the molecule... 

Computations were performed also for the nucleotide base stacks and base pair stacks.31-34 In the case of the cytosine (C) stack we have investigated the DOS and hopping conductivity as a function of the basis set and correlation corrections (inverse Dyson equation with MP2 self energy see above). In Figure 3 we show how the DOS changes if one uses instead of an STO-3G a... 

Ans. Base pairs stack one on top of the other in the vertical plane, like the steps in a spiral staircase. Each heterocyclic base in a base pair has hydrophobic attractions with the bases directly above and below it. 

The 7i TC interactions occur in all areas of chemistry and for chemically diverse molecules. The stacking of 7t-delocalized molecules favors cooperative phenomena. such as electron conduction. The n-stacking motifs are key components of the design of molecular materials with ensemble properties. Nucleotide base-pair stacking is fundamental to molecular biology, and aromatic interactions between amino-acid side chains influence protein structure. 

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