Duplex concentration-dependent

Let us consider a general melting process. If one defines a as the concentration of monomer strands in the duplex and cjot as the total monomer strand concentration, then one can derive relationships between the van t Hoff enthalpy and the temperature derivative of a at Tm to show that there is a concentration dependence of Tm for the melting of some duplexes and not others. 

When Tm is concentration dependent, an additional method" can be used to determine the thermodynamic quantities associated with melting. For example, consider the dissociation of a duplex that is formed from a self-complementary bimolecular process. The reverse reactions to those given in reactions (16.23) or (16.24) are specific examples of such processes. As Table 16.2 shows, the equilibrium constant for such a dissociation process is given by... 

The optical results at low salt concentration have been interpreted in terms of the presence of the two conformations given by reactions (16.24) and (16.25). The latter structure is only partially double-stranded and incorporates the hairpin loop region in which four bases are not paired. The lower transition temperature, which is concentration-dependent, with the larger melting enthalpy is ascribed to the disruption of the full duplex structure, which is a bimolecular process. The higher temperature transition (with a lower transition enthalpy) is attributed to the disruption of the hairpin structure, which is a... 

The d(CGCGAATTCGCG)2 Duplex. When studied at comparable salt (NaCl) and duplex concentrations, the duplex of d(CGCGAATTCGCG) was found to have about the same Tm by DSC measurements (344 K) and by the temperature-dependent changes in the NMR chemical shifts of nonexchangeable GC and AT protons (345 K). At 0.01 M NaCl, the calorimetric enthalpy was 376 kJmol-1 of duplex, while the van t Hoff enthalpy evaluated from equation (16.28) was found to be 393 kJ-mol-1 of duplex. At a 10-fold higher salt concentration, the calorimetric enthalpy was 427 kJ-mol-1 of duplex, while the van t Hoff enthalpy was 310 kJ-mol-1 of duplex. From the ratio of the van t Hoff enthalpy to the calorimetric enthalpy at the higher salt concentration, it was estimated that 9 out of 12 base-pairs melt together in the cooperative unit, while all melt simultaneously at the low salt concentrations. 

Figure 12.5 DNA hybridization reactions performed on ZnO NR arrays. (A) Strong fluorescence emission is observed from a sample containing fully complementary ssDNA strands whereas no signal is detected from noncomplementary strands. (B and C) Concentration dependent assays displaying the detection sensitivity of ZnO NR platforms. Data shown in red and blue correspond to assays empolying a covalent and non-covalent linking scheme of DNA strands on ZnO respectively. (D) Fluorescence emission due to duplex DNA formation on open-squared ZnO NR arrays. The easy integration potentkl of ZnO NR arrays into high density platforms is...

Diffusion of DNA molecules in solution is also concentration dependent. The diffusion coefficient for short DNA duplexes (8 to 20 base pairs) increases slightly with concentration over the range 0 to 20 mg/mL [59]. The diffusion coefficient for linear DNA fragments also increases with concentration for example, the diffusion coefficient for a 2,311 base pair restriction fragment increases over the concentration range 0 to 450 fig/mL according to ... 

The thermal stability of the duplex, and therefore the possibilities of observation under optimal conditions for NMR spectroscopy (ambient temperature, low or medium ionic strength, 1 10 mM oligomer concentration) depends upon several factors, e.g. 

Notice the particular features of this kind of ohgonucleotide the hexameric sequence is said to be self-complementary, since two identical molecules can form a duplex via Watson and Crick bases. It may also be noted from Figure 7.5 that two parallel pathways compete for the formation of the template T, namely the template-dependent, autocatalytic pathway, and the template-independent, non-autocatalytic one. This competition is the reason why the initial rate of the autocatalytic synthesis was found to be proportional to the square root of the template concentration -something that von Kiedrowski and colleagues called the square-root law of autocatalysis. As Burmeister (1998) put it ... 

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