Chemistry and Biology of Non-canonical Nucleic Acids. Naoki Sugimoto

Чтение книги онлайн.

СКАЧАТЬ Thermodynamic Analysis for the Intramolecular Triplex and Tetraplex

Upon triplex unfolding the absorbance at 260 nm is known to increase as a result of decreased base stacking, and the absorbance at 295 nm decreases, indicating the presence of cytosine: protonated cytosine base pairs (Hoogsteen base pairs). Similarly, the G-quadruplex unfolding can be monitored by the absorbance at 295 nm (see Chapter 4). The thermodynamic parameters for the intramolecular triplex and tetraplex can be calculated using Eqs. (3.3, 3.7, 3.8) described above if the unfolding process is two-state [14].

      3.5.2 Thermodynamic Analysis for the Intermolecular Triplex

      The unfolding of the triplex-stranded DNAs is strongly dependent on the pH values of the solution medium and falls into three different groups [15]:

       Under acidic conditions (less than pH 6.5)

      The global triplex unfolding proceeds in a monophasic triplex-to-coil collapse

      (3.16)

      and the equilibrium constant, K_T, can be written as

      (3.17)

      where S_WS_CS_H represents the Watson–Crick–Hoogsteen triplex; ΔH_T and ΔS_T are the van't Hoff enthalpy and entropy of triplex formation, respectively; α_T is the molar fraction of the coiled strands in the structured triplex form; and C_T is the total species concentration. At the maximum temperature of the derivative absorbance versus temperature curves (dA/dT vs. T), RT should be equal to ∼0.63 [16]; therefore, the van't Hoff equation can be written as

      (3.18)

       Under near physiological conditions (pH 7.0–7.5)

      The global triplex unfolding proceeds in a biphasic triplex-to-duplex-to-single transition and can be deconvoluted into two coupled subtransitions, a Hoogsteen transition and a Watson–Crick transition,

and the corresponding equilibrium constants, K_H and K_WC, can be given by, respectively

      (3.19)

      (3.20)

      where S_WS_C represents the Watson–Crick duplex; ΔH_H, ΔS_H, ΔH_WC, and ΔS_WC are the van't Hoff enthalpies and entropies for the Hoogsteen transition, respectively; α_H is the molar fraction of the Hoogsteen strand in the structured triplex state for the Hoogsteen transition; and α_WC is the molar fraction of the Watson–Crick duplex in the corresponding coiled state for the Watson–Crick transition. Although the two transitions may overlap each other in a certain range, this cross-effect can be nearly neglected at the melting temperatures, and the values of α_WC and α_H at which the derivative absorbance vs. temperature curves reach their maxima should be ∼0.42 and ∼0.50, respectively [17]. Thus, the van't Hoff equations can be simplified by

      (3.21)

      (3.22)СКАЧАТЬ