Fig. 7: Potential role of switchback DNA in repeat sequences.
From: The unusual structural properties and potential biological relevance of switchback DNA
a A pair of repeat sequences that can form a conventional duplex or switchback DNA. b Simulated structures of repeat sequences forming conventional duplex or switchback DNA. c Root mean square fluctuations (RMSF) of residues in conventional duplex and switchback DNA. d Calculated thermodynamic parameters of conventional duplex and switchback DNA formed by repeat sequences. e Design of a double crossover (DX) motif scaffold to place two interacting regions in parallel orientation. The 3’ ends of the interacting regions contain a fluorophore and a quencher to monitor the interaction. f Hybridization of interacting region 1 containing a (CAG)4 sequence with interacting region 2 containing a (CTG)4 sequence forms a switchback DNA, reducing fluorescence signal. Two controls were used in this study. The interacting region 2 in the first control contains two repeating units of CTG and six thymines (denoted (CTG)2T6), and the interacting region 2 in the second control contains twelve thymines (denoted T12). g Non-denaturing PAGE analysis of DX scaffold containing different interacting regions. h Fluorescence analysis of the interaction between the two regions on the DX scaffold. (CAG)4:(CTG)4 shows less fluorescence, indicating the formation of a switchback structure. Data represent mean and standard deviations of experiments performed with three replicates. The data shown in (g) are representative of experiments performed twice (n = 2) with similar reproducible results. Source data are provided as a Source Data file.
