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Additional Supporting Information may be found in the online version of this article.

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Figure 1S - I.]: CD spectra for Ω-DNA bulge loop structures with increasing number of CTG repeats. ((CTG)2- red, (CTG)4- purple, (CTG)6- blue, (CTG)8- green, the parent 22mer duplex lacking a bulge loop shown in black). In panels 1 & 2 the measured experimental data are shown, whereas panels 3 & 4 show the residual spectra after subtraction of the parent duplex contribution and panels 5 & 6 show the normalized residual spectra after normalization by the number of repeats in the loop domain. The native state spectra at 0°C are grouped together in Column A, whereas the denatured state spectra at 90°C are displayed in Column B.

Figure 1 S- II.]: CD spectra for Ω-DNA bulge loop structures with increasing number of TTT repeats. ((TTT)2- red, (TTT)4- purple, (TTT)6- blue, (TTT)8- green, the parent 22mer duplex lacking a bulge loop shown in black). In panels 1 & 2 the measured experimental data are shown, whereas panels 3 & 4 show the residual spectra after subtraction of the parent duplex contribution and panels 5 & 6 show the normalized residual spectra after normalization by the number of repeats in the loop domain. In panels 5 and 6 the corresponding CD spectra for poly T (black line) are shown for comparison. The native state spectra at 0°C are grouped together in Column A, whereas the denatured state spectra at 90°C are displayed in Column B.

FIGURE S2 – I.]: Excess heat capacity curves for Ω-DNA constructs with increasing number of CTG repeats in the loop domain. ((CTG)2– black, (CTG)4– red, (CTG)6– green, (CTG)8– blue.) Average pre and post transition baselines are indicated by stippled lines in magenta. Note the clear indication of a heat capacity change at Tm for all constructs.

FIGURE S2- II.]: Excess heat capacity curves for Ω-DNA constructs with increasing number of TTT repeats in the loop domain. ((TTT)2– black, (TTT)4– red,(TTT)6– green,(TTT)8– blue.) Average pre and post transition baselines are indicated by stippled lines in magenta. Note the clear indication of a heat capacity change at Tm for all constructs.

FIGURE S3-: Excess heat capacity curves for DNA duplexes with increasing number of CAG·CTG base pairs in the center of the molecule. CAG0·CTG0 (22mer) –magenta; CAG2·CTG2 (28mer) – black; CAG4·CTG4 (34mer)– red; CAG6·CTG6 (40mer)– green; CAG8·CTG8 -repeats(46mer) – blue.

Table 1S: Thermodynamic data for Duplexes with increasing number of CAG·CTG base pairs

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