Structural Properties of DNA

Ding K, Alemduroglu EE, Boersch M, Berger R, Herrmarm A. Engineering the structural properties of DNA block copolymer micelles by molecular recognition. Angew Chem Int Ed 2007 46 1172-1175. 

The Genetic Significance of Nucleic Acids Transformation Is DNA-Mediated Structural Properties of DNA... 

Given the simplicity, it is rather surprising that various dynamic and structural properties of DNA and RNA can successfully be described by this model. One essential feature is that the exponential decay of the bond-bond correlation function defines a characteristic length scale, the persistence length f, as we have already mentioned it,... 

Primary and Secondary Structure. The DNA double helix was first identified by Watson and Crick in 1953 (4). Not only was the Watson-Crick model consistent with the known physical and chemical properties of DNA, but it also suggested how genetic information could be organized and rephcated, thus providing a foundation for modem molecular biology. 

An alternative form of the right-handed double helix is A-DNA. A-DNA molecules differ in a number of ways from B-DNA. The pitch, or distance required to complete one helical turn, is different. In B-DNA, it is 3.4 nm, whereas in A-DNA it is 2.46 nm. One turn in A-DNA requires 11 bp to complete. Depending on local sequence, 10 to 10.6 bp define one helical turn in B-form DNA. In A-DNA, the base pairs are no longer nearly perpendicular to the helix axis but instead are tilted 19° with respect to this axis. Successive base pairs occur every 0.23 nm along the axis, as opposed to 0.332 nm in B-DNA. The B-form of DNA is thus longer and thinner than the short, squat A-form, which has its base pairs displaced around, rather than centered on, the helix axis. Figure 12.13 shows the relevant structural characteristics of the A- and B-forms of DNA. (Z-DNA, another form of DNA to be discussed shortly, is also depicted in Figure 12.13.) A comparison of the structural properties of A-, B-, and Z-DNA is summarized in Table 12.1. 

Our approach to studies of CT in DNA relies on two key features. First is the use of well-characterized DNA assemblies, which include redox probes that are strongly coupled to the DNA w-stack. The importance of well-characterized DNA assemblies, including the redox participants and DNA bases, cannot be overstated. Differences in structural and energetic properties of DNA assemblies, particularly when unaccounted for, may be responsible for drastically different conclusions regarding DNA CT. Furthermore, in order to characterize the DNA w-stack as a medium for CT, it is necessary to employ redox probes that are directly coupled to the w-stack. 

The average DNA helix diameter used in modeling applications such as the ones described here includes the diameter of the atomic-scale B-DNA structure and— approximately—the thickness of the hydration shell and ion layer closest to the double helix [18]. Both for the calculation of the electrostatic potential and the hydrodynamic properties of DNA (i.e., the friction coefficient of the helix for viscous drag) a helix diameter of 2.4 nm describes the chain best [19-22]. The choice of this parameter was supported by the results of chain knotting [23] or catenation [24], as well as light scattering [25] and neutron scattering [26] experiments. 

The analysis of single DNA molecules or small self-assemblies is equally important for medical research, e.g., for the understanding of the DNA sequence-dependent and structure-dependent diseases (recently reviewed [48]), as well as for nanoengineering-oriented research, e.g., understanding of the mechanical properties of DNA [49] that are useful for the construction of future nanodevices. In the following section we will refer to the AFM studies concerning DNA molecules and small self-assembhes as single molecule studies . 

A set of cyclophosphazene-DNA matrices was investigated in order to obtain more information about the possible structural modifications of DNA due to the different possible modes of binding of the drugs and to thus gain insight into the origin of their antitumor properties. 

The Design and Structure-Functional Properties of DNA-Based Immunomodulatory Sequences... 

Xu J, Fogleman EA, Craig SL. Structure and properties of DNA-hased reversible polymers. Macromolecules 2004 37 1863-1870. 

Nanostructures and nanochemistry are growth fields that have connections with the molecular scale and properties of DNA it is not surprising, therefore, that pteridines have been brought into research. Various structural types have been considered, for example, 246. 

Two of the most unique and appealing properties of DNA for molecular electronics are its double-strand recognition and a special structuring that suggests its use for self-assembly. 

---