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

Chemistry and Biology of Non-canonical Nucleic Acids

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) upper S Subscript normal upper W Baseline upper S Subscript normal upper C Baseline upper S Subscript normal upper H Baseline right harpoon over left harpoon upper S Subscript normal upper W Baseline plus upper S Subscript normal upper C Baseline plus upper S Subscript normal upper H

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) upper T Subscript normal m Superscript negative 1 Baseline equals StartFraction 2 upper R Over upper Delta upper H Subscript normal upper T Baseline EndFraction ln StartFraction upper C Subscript normal upper T Baseline Over 3.65 EndFraction plus StartFraction upper Delta upper S Subscript normal upper T Baseline Over upper Delta upper H Subscript normal upper T Baseline EndFraction

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,

upper S Subscript normal upper W Baseline upper S Subscript normal upper C Baseline upper S Subscript normal upper H Baseline right harpoon over left harpoon upper S Subscript normal upper W Baseline upper S Subscript normal upper C Baseline plus upper S Subscript normal upper H Baseline right harpoon over left harpoon upper S Subscript normal upper W Baseline plus upper S Subscript normal upper C Baseline plus upper S Subscript normal upper H

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) upper T Subscript normal upper H Superscript negative 1 Baseline equals StartFraction upper R Over upper Delta upper H Subscript normal upper H Baseline EndFraction ln StartFraction upper C Subscript normal upper T Baseline Over 10.35 EndFraction plus StartFraction upper Delta upper S Subscript normal upper H Baseline Over upper Delta upper H Subscript normal upper H Baseline EndFraction

(3.22) upper T Subscript upper W upper C Superscript negative 1 Baseline equals StartFraction upper R Over upper Delta upper H Subscript upper W upper C Baseline EndFraction ln StartFraction upper C Subscript normal upper T Baseline Over 6 EndFraction plus StartFraction upper Delta upper S Subscript upper W upper C Baseline Over upper Delta upper H Subscript upper W upper C Baseline EndFraction

Under alkaline conditions (more than pH 8.0)

The triplex strand is not formed, and the complex unfolding merely includes a monophasic duplex-to-coil transition. That is,

upper S Subscript normal upper W Baseline upper S Subscript normal upper C Baseline plus upper S Subscript normal upper H Baseline right harpoon over left harpoon upper S Subscript normal upper W Baseline plus upper S Subscript normal upper C Baseline plus upper S Subscript normal upper H

and the equilibrium constant, K_D, can be given by

(3.23)Скачать книгу