Nucleic acid complexes, physical properties

A novel application of ionic liquids in biochemistry involved duplex DNA as the anion and polyether-decorated transition metal complexes. When the undiluted liquid DNA-or molten salt-is interrogated electrochemically by a microelectrode, the molten salts exhibit cyclic voltammograms due to the physical diffusion (D-PHYS) of the polyether-transition metal complex. These DNA molten salts constitute a new class of materials whose properties can be controlled by nucleic acid sequence and that can be interrogated in undiluted form on microelectrode arrays (Leone et al., 2001). 

From various physical and biophysical properties of nucleic acid analogs the most important property for the present purpose is their interaction with nucleic acids. The spectrophotometric methods for detection of complex formation were applied to all combinations of polyvinyl polynucleotide analogs and natural polynucleotides (Fig. 3). In aqueous media hypochromic complexes were formed in combinations where the bases in the polynucleotide and analog were complementary. Poly-l-vinylcytosine is soluble in aqueous-propylene glycol base-pair type complexes were detected there also. An analog of polyinosinate, poly-9-vinylhypoxanthine, is soluble only in solutions of a detergent, sodium dodecylsulfate. This detergent intercalates into the polymer and conveys to it an... 

The perplexing difficulties that arise in the crystallization of macromolecules, in comparison with conventional small molecules, stem from the greater complexity, lability, and dynamic properties of proteins and nucleic acids. The description offered above of labile and metastable regions of supersaturation are still applicable to macromolecules, but it must now be borne in mind that as conditions are adjusted to transport the solution away from equilibrium by alteration of its physical and chemical properties, the very nature of the solute molecules is changing as well. As temperature, pH, pressure, or solvation are changed, so may be the conformation, charge state, or size of the solute macromolecules. 

In this chapter, we will describe the coordination properties of nucleic acids, including the consequences on metal interactions of the polyanionic nature of oligonucleotides and the supra-molecular structure of the double-helix. Types of metal sites found in other structures such as G-quartets and complex RNA folds will be described. Small coordination compounds between metals and nucleotides, the monomeric units of polymeric DNA and RNA, have been widely studied and also are included in this review. While the majority of material included in the review is derived from X-ray crystallographic studies, some information from spectroscopy and other physical methods is included where illuminating. 

The majority of difficult separations can be divided into two main classes complex mixtures and challenging pairs (Figure 24.1). Complex mixtures, such as proteins and protein digests, demonstrate random or broad spectrum behavior with respect to their properties, whereas well-behaved analytes such as nucleic acids display predictable behavior determined mainly by the size of the molecule. The analysis of these complex samples requires a separation system with high peak capacity and the ability to cover a broad spectrum of physical properties. 

In this review, we briefly describe the structure and properties of natural nucleic acids before describing the efforts to modify and mimic their physical characteristics and hybridization self-assembly motif. Examples of analogs of nucleobase and backbone are presented as potential synthetic alternatives to the natural biopolymers. These analogs have the capacity to introduce new and innovative functionalities into natural systems or even create completely synthetic supramolecular complexes. 

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