DNA duplex formation

Queuing by the post office Building of an ant hill Numbering of book pages DNA duplex formation Oligomeric assembly of hemoglobin... 

Table 4.1 lists several systems that provide examples of MESA [refs. 1 1, 32-58], Most of the systems involve the formation of close-packed arrays, by using objects (from nanometers to millimeters in size) and forces that are spherical or quasi-spherical in symmetry. The scales of these forces range from 1 nm (for hydrogen bonds and van der Waals interactions in DNA/DNA duplex formation) to 10 mm (for capillary bonds and fluid shear). 

With the development of methods for measuring DNA duplex formation came the opportunity to define all species on the basis of genetic similarity. The theoretical and operational aspects of DNA hybridization were elegantly presented by Britten and Kohne,2 and their paper has served as a primer for those now using DNA reassociation techniques. 

Shohda, K., Toyota, T.,Yomo,T., and Saguwara,T. (2003), Direct visualization of DNA duplex formation on the surface of a giant liposome, Chembiochem., 4,778-781. 

Figure 13.1 Cu2+-mediated DNA duplex formation from two artificial oligonucleotide strands bearing one to five hydroxypyridone nucleobases.

In 2005, Heyduk and Heyduk took advantage of the fact that thrombin has two different DNA binding epitopes to facilitate the simultaneous co-association of two different aptamers. Each aptamer was outfitted with a flexible linker region and a DNA sequence that would allow DNA duplex formation and enable simultaneous FRET enhancement. In the absence of the thrombin analyte, the two DNA strands do not associate because the complementary binding region is too short. However, when both sequences are bound to thrombin the increased entropy favors duplex formation and subsequent FRET enhancement (Figure 37). 

Asanuma H, Liang X, Yoshida T, Komiyama M. 2001. Photocontrol of DNA duplex formation by using azobenzene bearing oligonucleotides. ChemBioChem 2(1) 39 44. 

The DNA duplex formation can be detected based on the incorporation or association of a hybridization indicator or changes accrued from the hybridization event. Different indicators can be used in detection of DNA based on the appropriate electrochemical activity selected, it can be either label-free (e.g. guanine, adenine), or label-based (enz5nne-based, ferrous and ferricyanide. Ruthenium bipyridine [Ru (bpy)], methylene blue, Ethidium bromide etc). The hybridization event is detected via the increase or decrease in signal of the redox indicator or changes in conductivity or impedance/capacitance. 

The wealth of experimental thermodynamic data has been used to develop a powerful predictive capacity. As early as 1986, Breslauer [9] illustrated a useful empirical method to predict DNA duplex stability based on nearest-neighbor interactions in the base sequence. AH and AS of all 10 possible nearest-neighbor interactions were extrapolated from a small library of 28 DNA duplexes. The overall AW and AS " of DNA duplex formation could be predicted from the sum of the appropriate empirical values. This rough but robust method has been verified and further refined by more and more available databases of DNA thermodynamics [10,11]. The predictive power of this empirical methodology is a powerful tool for those interested in using DNA in supramolecular (or other) applications for which specific thermodynamics are an important criterion. 

Figure 10.1 Schematic representatiori of DNA hybridization, (a) DNA probe 5 -CCTTACCTCCAACCT-3. (b) DNA duplex formation from two oiigodeoxynucleotide (ODN) strands - DNA probe (5 -CCTTAGGTCCAACCT-3 ) and complementary target DNA (3 -CGAATCCACGTTGCA-5 ). (c) Noncomplementary DNA. Reproduced with permission from [25J. Copyright 2012, American Chemical Society...

Asanuma, H., Liang, X., Yoshida, T., Komiyama, M. (2001). Photo-control of DNA-duplex formation by use of oligonucleotide carrying an azobenzene. ChemBioChem, 2, 39-44. 

The experimentally measured water binding energies of nucleotides provide an important set of data required, for instance, to work out the energetics of DNA duplex formation. The Watson-Crick base pair interaction, in solution, is in constant competition with hydration of the individual bases. Thus, the duplex stability depends on the base-base interaction energy relative to the base-water and water-water interaction. Knowing all of the energetic contributions to a complex system such as solvated... 

However, near physiological NaCl concentration (NaCl 0.1 M), only one transition was observed (T = 14.3°C), and it was attributed to a-RNA/B-DNA duplex formation on the basis of the stoichiometry experiment. 

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