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. Author manuscript; available in PMC: 2010 Jul 10.
Published in final edited form as: J Mol Biol. 2009 May 13;390(2):319–338. doi: 10.1016/j.jmb.2009.05.005

Fig. 1.

Fig. 1

TAR variants used in this study. (a) Secondary structure for TARwt, with changes (boxed) used to make the single mutants A34U and U37A, and the double mutant A34U:U37A. Also shown are truncations at the base of the stem present in the three shortened hairpin TARs: shTAR51, shTAR47, and shTAR43, which remove 3, 5, and 7 base pairs, respectively. A34U can dimerize with U37A (denoted ‘[A34U + U37A]’), while alone each forms a stable monomer; A34U:U37A forms a self-complementary dimer. (b) Secondary structure for self-complementary TAR (scTAR). This variant deletes the three bulges present in TAR, while retaining the two GU wobbles at positions 6 and 9; in addition, it is mutated on the 3’-side of its loop to add perfect self-complementarity. Also shown are changes used to make perfectly self-complementary TAR (pscTAR), in which the two GU wobbles are converted to Watson-Crick GC base pairs.