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Table 1 Nucleotide substitutions affect the stability of the branched hairpin (BH) and extended hairpin (EH) conformation of TAR.

From: Optimization of the doxycycline-dependent simian immunodeficiency virus through in vitro evolution

  ΔG BH a ΔG EH a ΔΔGBH-EHb culture c
TARwt (SIVmac239) -65.3 -68.2 2.9  
TARm (SIV-rtTA) -67.5 -63.9 -3.6  
+63A-G -67.5 -66.3 -1.2 172, 281, 3115, 481, 6124, 7136, 1328
+63A-G +44C-T -65.9 -63.9 -2.0 1153
+63A-G +21G-A -62.5 -66.6 4.1 4234
+78C-T -65.8 -65.7 -0.1 532, 1037
+78C-T +47T-C -63.7 -64.1 0.4 5198
+21G-A -62.5 -64.2 1.7 948
+21G-A +78C-T +99C-T -58.4 -63.6 5.2 5124
+21G-A +74G-A -58.8 -63.4 4.6 9130
+5G-A +59A-T -63.3 -69.6 6.3 10136
+73T-C -66.5 -65.1 -1.4 11147
+73T-C +49C-T -64.2 -64.9 0.7 8222
+46C-T +72G-A -67.6 -63.6 -4.0 12120
  1. a ΔG values (kcal/mole) as determined with the Mfold RNA analysis software. b ΔΔGBH-EH = ΔGBH-ΔGEH. c Culture in which the mutation is observed (see Figure 2), with the day of earliest detection in superscript.