Nucleic noncovalent complexes

There is little or no reaction with adenine, thymine or guanine bases. Polymer mercuration is, in contrast to mononucleotides, influenced by the ionic strength of the reaction mixture the reaction rate is higher at a lower ionic strength. Residues in ss or ds polymers react at essentially the same rate. Two simultaneous reactions occur a noncovalent complexing reaction and a slower covalent introduction of mercury at the 5 position. It is important to remove the complex-bound mercury ions from the nucleic acids because they interfere with the annealing. Both cyanide and iodide are effective in... 

A particular advantage of ESTMS for biomolecule analysis is realized by generating the analyte ions from solution conditions that retain the secondary, tertiary and even quaternary structure of the biomoT ecules. Noncovalent binding of biomolecules has been observed in the ESI mass spectrum and, when operated under the appropriate conditions, the mass spectral data are a direct probe of the solution-phase biomolecule assembly. Protein assemblies, protein-nucleic acid complexes, duplex DNA and other non-covalently bound biomolecule assemblies have been studied using mass spectrometry. 

The strength of noncovalent interactions of nucleic acid complexes is routinely determined by their temperature-dependent melting behavior in solution where the fraction of intact complex (oc) is determined as a function of the temperature of the solution. UV absorption, fluorescence, or circular dichroism is usually employed as the means of detection of biomolecular interactions in this type of experiments. A transition enthalpy can be obtained from the slope of the melting curve as described by Marky and Breslauer and given in Eq. (15.7), where n is the molecularity of the association reaction (e.g., n = 2 for dimerization) and Tm is the melting temperature, normally defined for a = 50%. 

In order to avoid misleading spots on the 2-DE profile and to remove salts, lipids, polysaccharides, or nucleic acids interfering with separation, samples should be solubilized. Solubilization procedure involves disruption of all noncovalently bond protein complexes into a solution of polypeptides. It is the most critical step of 2-DE. 

Once in its native conformation, a protein may associate noncovalently with other proteins, or with nucleic acids or lipids, to form supramolecular complexes such as chromosomes, ribosomes, and membranes. The individual molecules of these complexes have specific, high-affinity binding sites for each other, and within the cell they spontaneously form functional complexes. 

The size and complexity of extended biomacromolecules makes the understanding of the various energy contributions which contribute to their stabilization difficult, since only calculations using simple empirical potential calculations are tractable. Fortunately, the most importance biomacromolecules, DNA and proteins, consist of characteristic building blocks-the nucleic acid bases and amino acids-interacting through noncovalent interactions. The system can therefore be fragmented into smaller components, each of which can be described by means of ab initio quantum chemical methods. 

In related work, Riley and Hobza have provided an assessment of the MP2 method in conjunction with several medium and extended basis sets in the study of various hydrogen bonded and dispersion bound complexes of biological relevance. They report that the MP2/cc-pVTZ method supports the most well balanced description of noncovalent interactions. However, the MP2 method does not provide reliable results for the cyclic hydrogen bonds found in nucleic acid base pairs in combination with any of the basis sets considered by these authors. 

Tris(phenanthroline) complexes of ruthenium(II), cobalt(III), and rhodium(III) are octahedral, substitutionally inert complexes, and as a result of this coordina-tive saturation the complexes bind to double-helical DNA through a mixture of noncovalent interactions. Tris(phenanthroline) metal complexes bind to the double helix both by intercalation in the major groove and through hydrophobic association in the minor groove. " " Intercalation and minor groove-binding are, in fact, the two most common modes of noncovalent association of small molecules with nucleic acids. In addition, as with other small molecules, a nonspecific electrostatic interaction between the cationic complexes and the DNA polyanion serves to stabilize association. Overall binding of the tris(phenanthroline) complexes to DNA is moderate (log K = 4)." ... 

---