Duplex double-helix stability

Interestingly, to achieve stabilization of the modified duplex, a minimum amount of 15 equiv of Cu " " per duplex was required for the Dipam py-modified double helix, although for the apparentiy less stable Dipicapy duplex, 1 equiv of Cu " " was sufficient. Possible explanations for this observation could be that the binding constant of Cu " " to Dipicapy is higher than that to Dipamapy, and that either (a) the binding constant does not correlate directly with the stabilization of the duplex, or (b) small steric (or electronic) factors related to the presence of the proton on the carboxamide of Dipam have a subtle influence on the duplex stability. 

Abstract The physical aspects of DNA structure and function are overviewed. Major DNA structures are described, which include the canonical Watson-Crick double helix (B form), B , A, Z duplex forms, parallel-stranded DNA, triplexes and quadruplexes. Theoretical models, which are used to treat DNA, are considered with special emphasis on the elastic-rod model. DNA topology, supercoiling and their biological significance are extensively discussed. Recent developments in the understanding of molecular interactions responsible for the stability of the DNA double helix are presented. 

As a result, stacking parameters for all possible contacts have been determined (Protozanova et al. 2004 [56]). Comparing the obtained values of with melting parameters for various contacts, the conclusion was made that the DNA double helix is predominantly stabilized by stacking interactions. For AT pairs the base-pairing contribution is virtually absent while GC pairs stabilize the duplex state but their contribution is pretty small. 

In an aqueous solution, the charge on the backbone makes the strands extremely hydrophilic and soluble however, the aromatic nucleic acid base pairs are much more hydrophobic. Therefore, when a double-stranded duplex forms, the stacked nonpolar base pairs are located at the interior of the structure, reducing contact with water and increasing contact with each other. These net changes in intermolecular forces and balance between hydrophobic and hydrophilic substituents add to the stability of the double helix. 

The stability of a DNA duplex depends on, besides the chemical and physical structure of the DNA itself, many environmental factors such as solvent, temperature, and salt composition and concentration. For example, when a stable DNA duplex is heated to higher temperatures, the double helix structure will be gradually denatured into two coiled single strands. When cooled to room temperature, the two single strands can reassociate to again form the duplex, a process called DNA renaturation (sometimes also called DNA hybridization or annealing). These processes are reversible, as illustrated in the following equilibrium ... 

---