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

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


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3.1 Potential hydrogen bonding sites in bases of the nucleosides. Hydrogen bonding donor sites are labeled with red arrows, and hydrogen bonding accepter sites are labeled with blue arrows.

      3.2.2 Stacking Interactions

      The π–π stacking interactions refer to the interactions between aromatic rings containing π orbitals in bases of nucleic acids. The individual bases make strong stacking interactions with neighboring bases, which are major contributors to duplex stability (Figure 3.2b). The stacking interactions are much more prevalent in duplexes than in single strands. Base-stacking interactions are London dispersion force interactions and depend on the aromaticity of the bases and their dipole moments. The degree of stabilization afforded by base stacking depends on the DNA sequence. Nearest-neighbor base-stacking interactions are important determinants of duplex stability. The values of free energy change at 37 °C (−Δupper G 37 Superscript ring) due to stacking interactions during duplex formation are 0.4–1.6 kcal mol−1 [3].

      Moreover, the stacking interactions increase with increasing salt concentration, as high salt concentrations mask the destabilizing charge repulsion between the two negatively charged phosphodiester backbones. The DNA duplex stability increases with increasing salt concentration.

      3.2.3 Conformational Entropy

      In the case of canonical duplex structures, the base stacking decreases the transition dipole moment of bases, which makes UV absorbance at 260 nm of duplex smaller than that of single-stranded state. Heating of nucleic acids causes the strands to be denatured by disrupting the ordered stacking of the bases and breaking hydrogen bonds. The process can be conveniently monitored by an increase in UV absorbance as the duplex unwinds to single strands owing to hyperchromicity.

      Methods to obtain the thermodynamic parameters of enthalpy (ΔH°), entropy (ΔS°), and free energy changes at 25 °C (Δupper G 25 Superscript ring) for the formation of a nucleic acid structure are described below; DNA duplex formation is taken as an example. Data are typically analyzed with a two-state model, which assumes that each strand is either completely paired or unpaired. The equilibrium for the duplex formation is represented as either a self-complementary or non-self-complementary association as follows [4]:

      where A, B, and C indicate the single strands of DNA and A2 and B·C indicate the double-stranded DNA.

Graphs depict the UV melting curves of the self-complementary duplex at 5 μM strand concentration with (a) Tm value and (b) upper and lower baselines. Upper and lower baselines can be represented as Eds = mdsT + bds and Ess = mssT + bss, respectively, where Eds and Ess indicate the absorbance for the double-stranded and single-stranded DNA, respectively. The mds and bds or mss and bss represent the slope and intercept of the upper baseline or lower baseline for the UV melting curve, respectively.

      where Dss and Df indicate the single-stranded (unfolded) and folded DNA structures, respectively.

      (3.4)upper K Subscript o b s Baseline equals left-parenthesis alpha slash 2 right-parenthesis slash left-parenthesis upper C Subscript normal t Baseline slash s right-parenthesis left-parenthesis 1 minus alpha right-parenthesis squared

      where Ct is the total strand concentration,


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