The 2D Structure of the T. brucei Preedited RPS12 mRNA Is Not Affected by Macromolecular Crowding

Table 1

(a) Helix/coil transition temperatures () of the T. brucei RPS12 pre-mRNA derived from the denaturation profiles shown in Figure 1. Macromolecular crowding was mimicked by 6% (w/w) PEG₄₀₀₀. (b) Summary of SHAPE-derived Gibbs free energies () and structural characteristics of the RPS12 transcript in dilute and crowded solvent conditions. In addition, mean and median SHAPE reactivities are provided. (c) Structural features of the RPS12 pre-mRNA in crowded and/or Mg²⁺-free solvent conditions compared to dilute solvent conditions at 2 mM Mg²⁺. : difference Gibbs free energies; sens: sensitivity; ppv: positive predictive value. For a comprehensive comparison, see Table  S1.

(a)

	Dilute +Mg^2+	Crowded +Mg^2+	Dilute	Crowded
	44.1	44.6	34.6	37.1

(b)

	Dilute +Mg^2+	Crowded +Mg^2+	Dilute	Crowded
(kcal/mol)	−127.4	−131.3	−91.1	−91.8
Fraction ss	0.38	0.38	0.43	0.46
Fraction ds	0.62	0.62	0.57	0.54
Mean reactivity	0.45	0.39	0.57	0.61
Median reactivity	0.35	0.32	0.35	0.37
Pseudoknotted	yes	yes	no	no

(c)

	Crowded + Mg^2+ versus dilute + Mg^2+	Dilute versus dilute + Mg^2+	Crowded versus dilute + Mg^2+
(°C)	0.5	−9.5	−7.0
(kcal/mol)	−3.9	36.3	35.6
sens (%)	100	56	52
ppv (%)	100	60	58