Nucleic bases hydrophobized

The acid-base behavior of nucleotides is dominated by the acidity of the nucleic bases and the phosphate groups (Table 8.5.2). Some remarkable changes in pk values are observed when going from hydrophobic to hydrophilic derivatives (e.g., it is more difficult to protonate the NH2 of adenosine than that of adenine), the acidity of the anomeric pentose proton (typical pk, values 12-13), and the pk 2 value of the phosphate close to 7. At high pH values, the 20H group of ri-bose can also be deprotonated (Shabarova and Bogdanov, 1994). 

It can be seen from the figure that the electrostatic repulsive forces between the macrocations are overwhelmed, probably by hydrophobic attractive forces between their hydrophobic side groups. It should be noted that the complimentary base-base pairing is unimportant in the present case. If this is not the case, the mixtures of APVP and TPVP should show the largest hypochromicity. This, however, is not the case. The importance of the hydrophobic interactions between nucleic acid bases has been proposed by Ts o et al.I9 from thermodynamic parameters of various nucleic acid bases or nucleosides in aqueous media. 

A hypochromicity was observed between THPVP and APVP (or TPVP). Since theophylline is not a nucleic acid base and does not form hydrogen-bonding, these observations indicate that stacking-type hydrophobic forces are important. 

The amino acid sequence of our first aPNA (which we termed backbone 1 or bl) was designed based on this amphipathic hehx sequence (Fig. 5.3 B). Specifically, this aPNA backbone included hydrophobic amino acids (Ala and Aib), internal salt bridges (Glu-(aa)3-Lys-(aa)3-Glu), a macrodipole (Asp-(aa)i5-Lys), and an N-ace-tyl cap to favor a-helix formation. The C-termini of these aPNA modules end in a carboxamide function to preclude any potential intramolecular end effects. Each aPNA module incorporates five nucleobases for Watson-Crick base pairing to a target nucleic acid sequence. 

Ion-exchange resins are cross-linked polymers which are typically polystyrene, cellulose or agarose based. Polystyrene is hydrophobic in nature and useful for inorganic ions and small molecules while cellulose and agarose are hydrophilic and more useful for the larger, biologically important molecules, e.g. proteins and nucleic acids, which either would be adversely affected by a hydrophobic environment or could not gain access to the small pore structure. 

Nucleic acids, proteins, some carbohydrates, and hormones are informational molecules. They carry directions for the control of biological processes. With the exception of hormones, these are macromolecules. In all these interactions, secondary forces such as hydrogen bonding and van der Waals forces, ionic bonds, and hydrophobic or hydrophilic characteristics play critical roles. Molecular recognition is the term used to describe the ability of molecules to recognize and interact bond—specifically with other molecules. This molecular recognition is based on a combination of the interactions just cited and on structure. 

Other methods that are related to affinity chromatography include hydrophobic interaction chromatography and thiophilic adsorption. The former is based on the interactions of proteins, peptides, and nucleic acids with short nonpolar chains on a support. This was first described in 1972 [113,114] following work that examined the role of spacer arms on the nonspecific adsorption of affinity columns [114]. Thiophilic adsorption, also known as covalent or chemisorption chromatography, makes use of immobilized thiol groups for solute retention [115]. Applications of this method include the analysis of sulfhydryl-containing peptides or proteins and mercurated polynucleotides [116]. 

Where nucleic acids are concerned, the enhanced hydrophobicity of abiotic polyfluorinated aromatic bases (e.g., tetrafluorobenzene or tetrafluoroindole deoxyribose derivatives) was exploited as an alternative to natural hydrogen bonding to achieve selective and stable nucleic acid base pairing in duplex DNA [85], The DNA replication was examined using polyfluorinated-nucleotide analogs as substrates. A DNA polymerase active site was able to process the polyfluorinated base pairs more effectively than the analogous hydrocarbon pairs, demonstrating hydrophobic selectivity of polyfluorinated bases for other polyfluorinated bases [86]. 

DNA, functional groups of nucleic acid bases are completely dehydrated and located inside the hydrophobic domain of duplex, forming efficient interhelix hydrogen bonds as shown in Figure 6. 

As with proteins, the nucleic acid polymers can denature, and they have secondary structure. In DNA, two nucleic acid polymer chains are twisted together with their bases facing inward to form a double helix. In doing so, the bases shield their hydrophobic components from the solvent, and they form hydrogen bonds in one of only two specific patterns, called base pairs. Adenine hydrogen bonds only with thymine (or uracil in RNA), and guanine pairs only with cytosine. Essentially every base is part of a base pair in DNA, but only some of the bases in RNA are paired. The double-helix structure... 

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. 

Intercalators associate with dsDNA by insertion between the stacked base pairs of DNA [52], EtBr binds to dsDNA with little to no sequence specificity, with one dye molecule inserting for every 4-5 base pairs [53]. It also binds weakly via a non-intercalative binding mechanism only after the intercalative sites have been saturated [54], Propidium iodide (PRO) is structurally similar to ethidium bromide, and both dyes show a fluorescence enhancement of approximately 20-30 fold upon binding to dsDNA [41]. As well, their excitation maxima shift 30-40 nm upon binding due to the environment change associated with intercalation into the more rigid and hydrophobic interior of the double-stranded nucleic acid structure relative to aqueous solution [41]. 

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