Analysis of involvement of GNG motif on G-quadruplex structure formation, when second stretch of guanines was mutated at HOX11 breakpoint region I.
(A) The oligomeric DNA sequence spanning region I, a G-rich strand (MN38) and complementary C rich strand (MN37) were designed from the HOX11 breakpoint region. Mutants of MN38 were also designed and named as MS104, MS115, MS116, MS117. The mutations were introduced such that the second G stretch is altered to thymine (indicated in red) and keeping that as backbone either the first GNG motif (blue) or the second GNG motif (blue) or both are mutated (indicated in red). (B) The radiolabeled G- and C-rich strands along with the mutants were incubated in the presence (+) or absence (-) of KCl (100 mM) and resolved in the absence (left panel) or presence (right panel) of KCl (100 mM), in the gel and running buffer. The substrate, intramolecular (Intra), and intermolecular (Inter) quadruplex structures are indicated. The red boxed ‘Intra’ indicate intramolecular G-quadruplex species involving GNG motifs.