Base-stacking interaction

Fig. 1 The w-stack of double helical DNA. In this idealized model of B-DNA the stack of heterocyclic aromatic base pairs is distinctly visible within the sugar-phosphate backbone (schematized by ribbons) a view perpendicular to the helical axis b view down the helical axis. It is the stacking of aromatic DNA bases, approximately 3.4 A apart, that imparts the DNA with its unique ability to mediate charge transport. Base stacking interactions, and DNA charge transport, are exquisitely sensitive to the sequence-depen-dent structure and flexibility of DNA...

Cooperation between the many hydrogen bonds and base-stacking interactions makes DNA very stable to chemical treatments. 

The purine and pyrimidine bases are hydrophobic and relatively insoluble in water at the near-neutral pH of the cell. At acidic or alkaline pH the bases become charged and their solubility in water increases. Hydrophobic stacking interactions in which two or more bases are positioned with the planes of their rings parallel (like a stack of coins) are one of two important modes of interaction between bases in nucleic acids. The stacking also involves a combination of van der Waals and dipole-dipole interactions between the bases. Base stacking helps to minimize contact of the bases with water, and base-stacking interactions are very important in stabilizing the three-dimensional structure of nucleic acids, as described later. 

Base-stacking interactions are an important stabilizing force in nucleic acid structures. Describe how base stacking contributes to the tertiary structure of the tRNA molecule. 

Because d(GAATTC) is self-complementary, the intrastrand base-stacking interactions between nearest neighbors are the same on each strand in the duplex. Starting from the 5 end of each strand, the intrastrand base stacks are G-A, A-A, A-T, T-T and T-C. Because of the directionality of the bonding along the phosphodiester backbone and the twist associated with the helical structure, the overlap, within a strand, of two adjacent bases of the same identity, can be different. For example, G-A and A-G represent two different base-stacking interactions within a strand. Upon association with two... 

Table 16.5 Enthalpy and melting temperature results from calorimetric studies of oligonucleotides used to generate data for nearest-neighbor base-stacking interactions. The poly designates a strand of base-pairs of undetermined length.

Since the IR spectrum of an RNA molecule has numerous features, IR spectroscopy is not limited to the determination of the fraction folded only. Depending upon the wavenumber of the transition, IR spectroscopy can distinguish A-U base pairs from G-C base pairs as well as the more complex base pairing schemes found in triple helices (Banyay et al., 2003 Brauns and Dyer, 2005). Similarly, base stacking interactions can be distinguished from base pairing interactions. It has even been shown that transfer RNAs of different species can be distinguished from their IR spectra (Thomas, 1969). 

C.A. Hunter, X.-J. Lu, DNA Base-stacking interactions A comparison of theoretical calculations with oligonucleotide X-ray crystal structures. J. Mol. Biol. 265, 603-619 (1997)... 

J. Sponer, H.A. Gabb, J. Leszczynski, P. Hobza, Base-Base and deoxyribose-base stacking interactions in B-DNA and Z-DNA A quantum-chemical study. Biophys. J. 73,76-87 (1997)... 

Answer Without the base, the ribose ring can be opened to generate the noncyclic aldehyde form. This, and the loss of base-stacking interactions, could contribute significant flexibility to... 

High-frequency, p.m.r. spectroscopy has proved to be an extremely important tool in studies of the structures, conformations, and inter-and intra-molecular base-stacking interactions of nucleosides and nucleotides. The temperature dependence of the chemical shift of the base proton at position 6 (H-6) has been studied at 220 MHz for uridine (36), cytidine (38), and a number of their mono- (37, 39) and... 

The effect of base stacking interaction on the conformation of poly-VAd was also studied by osmometry, intrinsic visosity and light-scattering measurements24). 

The existence of base stacking interaction for poly-VUr was also suggested from UV spectra25). At pH 12, the value of hypochromicity for poly-VUr was 29 to 51 % as compared to 1-ethyluradl. For poly-U solution, the value is only a few percent at room temperature while at lower temperature, about 30% of hypochromicity is observed which is attributed to the formation of a stacked helical polynucleotide structure. It seems therefore likely that the high value of hypochromicity observed for poly-VUr solution may be due to base stacking interactions. 

In solutions of ordered polynncleotides, the heterocyclic bases are stacked, that is, packed vertically one upon the next. The greatest stability is for purine-purine base-stacking interactions. The next are pnrine-pyrimidine interactions, which in turn impart greater stability than pyrimidine-pyrimidine stacking interactions. ... 

A recent study employing ESR spectroscopy and density functional theory calculations has shown that the adenine cation radical (A +) in aqueous glassy solutions of dAdo and of the DNA oligomer (dA) is stabilized by base stacking interactions. The pK of the adenine cation radical in isolated dAdo in aqueous solutions is ca. 1 and, therefore, A " readily deprotonates from its exocylic amine group, nevertheless, these researchers find that the pK of the adenine cation radical in stacked systems to be ca. 8 at 150 K. It appears that the hole delocalizes over several bases, which stabilize it by charge resonance interactions. Calculations show that in the... 

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