PMC

NAIM analysis of the selected asymmetric sites (G127, A67, A68) in P1 stem and P3a stem of aptamer 1 in VC glycine riboswitch. Interference values (κ) are indicated to the right of each band.

Fig. 3. Quantitative analysis of thiophilic metal ion rescue of R_P and S_P phosphorothioate modifications at A67. (A) A plot of k_obs versus Mn²⁺ concentration is shown for the unmodified ribozyme (PT50; diamonds) and for ribozymes with a site-specific S_P phosphorothioate modification at A67 (A67S_P; circles). (B) Plot of k_obs versus Mn²⁺ concentration for unmodified PT50 (PT50, diamonds) and for ribozymes with a site- specific R_P phosphorothioate modification at A67 (A67R_P; squares). Rate constants for all reactions were determined in a constant background of 10 mM Mg²⁺, 3 M NaCl, 50 mM PIPES pH 5.5 at 50°C. (C) Relative reaction rates (k_rel) for the pro-S_P (A67S_P; circles) or pro-R_P (A67R_P; squares) phosphate oxygen at A67 are plotted as a function of added Mn²⁺ and fit to an equation for binding of a single metal ion (Equation 1, Materials and methods). For A67S_P, K^{Mn, app} = 5.7 ± 0.8 mM; for A67R_P, K^Mn,app >>15 mM. Error bars reflect standard deviation of at least four experiments.

Amplitude and phase of traveling waves obtained from enforcing force and moment boundary conditions at x = 0, L. (a) Amplitudes of the A₂₃ and A₆₇ waves decrease from x = 0 to x = L, whereas the amplitudes of the A₀₁ and A₄₅ waves increase from x = 0 to x = L. The amplitudes of the former two waves are larger than the latter two. (b) Phases ϕ₀₁, ϕ₂₃, ϕ₄₅, and ϕ₆₇ are all constant from x = 0 to x = L. The phase difference between the A₆₇ wave and A₂₃ wave is ∼90°. The parameters used to obtain these plots are ω = 4π rad/s, L = 1.0 mm, K_b = 5.0 × 10⁻¹⁶ Nm², C_n = 0.06 Ns/m², ψ = −45°, EIQ₀ = 4.35 × 10⁻¹² Nm, Q₁L = −1.054 Q₀, and B = 198.4°.

(a) Based on the results of ORG-EcoTILLING in matK-2 fragment of Brassica intraspecies in Figure 3, 19 mutated samples and no mutation sample B26 (as the reference in Figure 3) were selected to mix with B76 (as the reference), respectively. The sample in each lane from left to right in the channel of IRD700 or IRD800 was B26, B51, B60, B64, B65, B66, B68, B69, B73, B74, B76, B79, B81, B90, B91, B92, B93, B94, B95 and B96. CEL I-cleaved heteroduplexes appeared as intense bands (circled in different color geometric figures of IRD 700 channel and corresponding same color ones of IRD 800 channel). (b) ORG-EcoTILLING gel image of validation in polymorphism site 474 of accD gene (Figure S1, Table 7) by using one of the three samples of A64, A65 and A67 as reference with the others. In the channel of IRD700 or IRD800, the lane of 1, 2, and 3; 4, 5 and 6; 7, 8 and 9 were sample A64, A65 and A67, respectively, but the reference of 1, 2, and 3 was A64; the reference of 4, 5 and 6 was A65, and the reference of 7, 8 and 9 was A67. It was obvious that there was different polymorphism in the same position 474 because polymorphism appeared when 65 mixed with A67 (blue arrow showed polymorphism band).