7162 Nucleic Acids Research, 2011, Vol. 39, No. 16 Figure 1. CD analysis indicates the presence of G4-DNA in two oligonucleotides (Poly A Zic1 DNA 47-mer and c-Myc DNA 51-mer) and the absence of G4-DNA in a third oligonucleotide (Scrambled Zic1 DNA 47-mer). (A) Depiction of guanine quartet structure with each guanine participating in four hydrogen bonds and a potassium cation coordinately bound (purple). (B–D) Schematic depiction of (B) a tetramolecular, parallel G4-DNA structure, (C) a unimolecular antiparallel G4-DNA structure, and (D) a unimolecular parallel G4-DNA structure. (E) CD spectrum of Poly A Zic1 DNA 47-mer in 50 mM KCl (blue trace 25 C, red trace 37 C, green trace 95 C). (F) Melting curve of Poly A Zic1 DNA 47-mer; molar ellipticity at 263 nm versus temperature in 50 mM KCl (blue trace) or 50 mM LiCl (red trace). (G) CD spectrum of c-Myc DNA 51-mer in 50 mM KCl (blue trace 25 C, red trace 37 C, green trace 95 C). (H) Melting curve of c-Myc DNA 51-mer; molar ellipticity at 263 nm versus temperature in 50 mM KCl (blue trace) or 50 mM LiCl (red trace). (I) CD spectrum of Scrambled Zic1 DNA 47-mer in 50 mM KCl (blue trace 25 C, red trace 37 C, green trace 95 C). (J) Melting curve of scrambled Zic1 DNA 47-mer; molar ellipticity at 263 nm versus temperature in 50 mM KCl (blue trace) or 50 mM LiCl (red trace). The stacked G-quartet structure was ﬁrst solved in guanylic acid by Gellert et al. (1), and this binding motif was ﬁrst recognized to form in DNA by Sen and Gilbert (8) working in vitro with DNA oligonucleotide sequences from the immunoglobin switch region. Four separate guanine-rich oligodeoxyribonucleotides formed a parallel, intermolecular, tetramolecular G4-DNA (Figure 1B). Sen and Gilbert (8) proposed such structures could form in the synaptonemal complex of meiotic cells. Although tetramolecular G4-DNA structures are highly thermally stable, they have large kinetic barriers of formation, requiring high concentrations of single-stranded DNA and long periods of time for formation (9). While spe- cialized cellular regions could form tetramolecular G4- DNA, the most common G4-DNA structure predicted to form in cells is the fully intramolecular, unimolecular