Periodic B-Z junction induced by recurring A…A mismatches in CAG repeat expansion.

<p>(A) 18mer DNA duplex with 6 A…A mismatches used in the present MD simulation. (B) Time vs RMSD profile showing the significant conformational change from the starting model. (C-H) Histogram corresponding to: <i>glycosyl</i> conformation of (C) A’s & (D) G’s, twist angles at all the (E) CA (F) AG & (G) GC steps and epsilon at (H) CA step over 291-300ns. (I) Cartoon diagram showing the conformational changes from B- to Z-DNA during the simulation. Note that terminal 2 base pairs on either ends are not included due to end fraying effect.