Quadruplex structural parameters

Table 1 A comparative summary of key structural parameters for duplex and quadruplex folded DNA...

Bi- and tetramolecular structures also give quite comparable enthalpies. However, the validity of the van t Hoff analysis for some of these quadruplexes is questionable, as the melting curve used to determine thermodynamic parameters rarely corresponds to a true equilibrium curve. We will address this point later in the manuscript. An enthalpy of formation of —21 to —26 kcal mol per quartet is found for the G2T2NT2G2 sequence in comparison to —22.5 kcal mol per quartet measured for the G4T4G4 sequence. Concerning parallel quadruplexes, analysis of the calorimetric or thermokinetic data gives a value of —72 kcal moD (ref. 27) and —76.5 kcal moD (ref. 28) for the TG4T sample... 

A rationalisation for their approach is provided in Huppert and Balasubramanian, who consider four principle parameters of importance. These are (a) the strand stoichiometry, (b) the number of stacked tetrads in the quadruplex core, (c) the presence of mutations or deletions, and (d) the length and composition of loops. Some of these parameters may be resolved by consideration of the structures and previously known results, while others are resolved by experimentation. The following descriptions and commentary are also valid for the approach of Todd and Neidle. ... 

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