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

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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, KT, can be written as

      (3.17)upper K Subscript normal upper T Baseline equals StartFraction left-bracket upper S Subscript normal upper W Baseline upper S Subscript normal upper C Baseline upper S Subscript normal upper H Baseline right-bracket Over left-bracket upper S Subscript normal upper W Baseline right-bracket left-bracket upper S Subscript normal upper C Baseline right-bracket left-bracket upper S Subscript normal upper H Baseline right-bracket EndFraction equals StartFraction 1 minus a Subscript normal upper T Baseline Over a Subscript normal upper T Superscript 3 Baseline EndFraction StartFraction 9 Over upper C Subscript normal upper T Superscript 2 Baseline EndFraction equals exp left-parenthesis StartFraction minus upper Delta upper H Subscript normal upper T Baseline plus upper T upper Delta upper S Subscript normal upper T Baseline Over italic upper R upper T EndFraction right-parenthesis

      where SWSCSH represents the Watson–Crick–Hoogsteen triplex; ΔHT and ΔST are the van't Hoff enthalpy and entropy of triplex formation, respectively; αT is the molar fraction of the coiled strands in the structured triplex form; and CT 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

      (3.19)upper K Subscript normal upper H Baseline equals StartFraction left-bracket upper S Subscript normal upper W Baseline upper S Subscript normal upper C Baseline upper S Subscript normal upper H Baseline right-bracket Over left-bracket upper S Subscript normal upper W Baseline upper S Subscript normal upper C Baseline right-bracket left-bracket upper S Subscript normal upper H Baseline right-bracket EndFraction equals StartFraction 1 minus a Subscript normal upper H Baseline Over a Subscript normal upper H Baseline left-parenthesis a Subscript normal upper H Baseline minus a Subscript upper W upper C Baseline right-parenthesis EndFraction StartFraction 3 Over upper C Subscript normal upper T Baseline EndFraction equals exp left-parenthesis StartFraction minus upper Delta upper H Subscript normal upper H Baseline plus upper T upper Delta upper S Subscript normal upper H Baseline Over italic upper R upper T EndFraction right-parenthesis

      (3.20)upper K Subscript upper W upper C Baseline equals StartFraction left-bracket upper S Subscript normal upper W Baseline upper S Subscript normal upper C Baseline right-bracket Over left-bracket upper S Subscript normal upper W Baseline right-bracket left-bracket upper S Subscript normal upper C Baseline right-bracket EndFraction equals StartFraction a Subscript normal upper H Baseline minus a Subscript upper W upper C Baseline Over a Subscript upper W upper C Superscript 2 Baseline EndFraction StartFraction 3 Over upper C Subscript normal upper T Baseline EndFraction equals exp left-parenthesis StartFraction minus upper Delta upper H Subscript upper W upper C Baseline plus upper T upper Delta upper S Subscript upper W upper C Baseline Over italic upper R upper T EndFraction right-parenthesis

      where SWSC represents the Watson–Crick duplex; ΔHH, ΔSH, ΔHWC, and ΔSWC are the van't Hoff enthalpies and entropies for the Hoogsteen transition, respectively; αH is the molar fraction of the Hoogsteen strand in the structured triplex state for the Hoogsteen transition; and αWC 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 αWC and αH 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, KD, can be given by

      (3.23)upper K Subscript normal upper D Baseline equals StartFraction left-bracket upper S Subscript normal upper W Baseline upper S Subscript normal upper C Baseline right-bracket left-bracket upper S Subscript normal upper H Baseline right-bracket Over left-bracket upper S Subscript normal upper W Baseline right-bracket left-bracket upper S Subscript normal upper C Baseline right-bracket left-bracket upper S Subscript normal upper H Baseline right-bracket EndFraction equals StartFraction 1 minus a Subscript normal upper <p style= Скачать книгу