Hydrophobic stacking

Hydrophobic stacking provides stability. Intercalating agents stack between bases. 

The precise chemical interactions between an adhesin and its receptor are also important. For example, direct- and water-mediated hydrogen bonds are the most important interactions within the carbohydrate-recognition domain in carbohydrate-binding adhesins on the host cell surface (Weis and Drickamer, 1996). Nonpolar van der Waals interactions and hydrophobic "stacking of the receptor oligosaccharide rings with aromatic amino acid side chains of the bacterial adhesin protein also contribute to oligosaccharide-protein interactions. X-ray structural... 

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. 

Intramolecular interactions between two coordinated amino acids can influence the position of-cis trans equilibrium. These interactions can take the form of hydrophobic stacking interactions, as observed between the side chains of tyrosines in [Cu(L-TyrO)2J and [Pd(L-TyrO)2], or Coulombic attraction between oppositely charged side chains, as in [Cu(HisO)L] (L = Arg, Lys or ornithine).51 The optical configuration of the amino acids is of particular importance for these interactions. For amino acids of the same configuration trans geometry (15) is required, but for amino acids of opposite configuration cis geometry (14) is necessary around the metal centre. 

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]. 

Certain planar aromatic chemicals (drugs) bind to DNA by intercalation. In this process, the intercalation compound inserts between two stacked bps of DNA and positions itself within the center of the DNA double helix. The intercalated molecule is stabilized by hydrophobic stacking interactions with adjacent bps. The binding by intercalation results... 

Frequently, as it has been described before, negative ACp values are usually attributed to the burial of apolar groups from water. However, in many systems it is also thought to be associated with hydrophobic stacking interactions, presumably resulting from the dehydration of highly ordered water molecules surrounding hydrophobic surfaces. In order to describe in more detail this observation we will show two examples. 

Seward, E. M., Hopkins, R. B., Sauerer, W., Tam, S.-W., and Diedeiich, F. (1990) Redox-Dependent Binding Ability of a Flavin Cyclophane in Aqueous Solution Hydrophobic Stacking versus Cavity-Inclusion Complexation , J. Am. Chem. Soc. 112, 1783-1790. 

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