Guanine quadruplex formation by RNA/DNA hybrid analogs of Oxytricha telomere G₄T₄G₄ fragment

Abstract

Using circular dichroism spectroscopy, gel electrophoresis, and ultraviolet absorption spectroscopy, we have studied quadruplex folding of RNA/DNA analogs of the Oxytricha telomere fragment, G(4)T(4)G(4), which forms the well-known basket-type, antiparallel quadruplex. We have substituted riboguanines (g) for deoxyriboguanines (G) in the positions G1, G9, G4, and G12; these positions form the terminal tetrads of the G(4)T(4)G(4) quadruplex and adopt syn, syn, anti, and anti glycosidic geometries, respectively. We show that substitution of a single sugar was able to change the quadruplex topology. With the exception of G(4)T(4)G(3)g, which adopted an antiparallel structure, all the RNA/DNA hybrid analogs formed parallel, bimolecular quadruplexes in concentrated solution at low salt. In dilute solutions ( approximately 0.1 mM nucleoside), the RNA/DNA hybrids substituted at positions 4 or 12 adopted antiparallel quadruplexes, which were especially stable in Na(+) solutions. The hybrids substituted at positions 1 and 9 preferably formed parallel quadruplexes, which were more stable than the nonmodified G(4)T(4)G(4) quadruplex in K(+) solutions. Substitutions near the 3'end of the molecule affected folding more than substitutions near the 5'end. The ability to control quadruplex folding will allow further studies of biophysical and biological properties of the various folding topologies.

Circular dichroism and guanine quadruplexes

“…The TBA quadruplex is particularly stable in potassium ion solution, while sodium cations do not stabilize it at all (the melting temperature [T m ] in 0.12 M K + was 48°C and less than 20°C in 0.12 M Na + [28]). In contrast to TBA, the d(G 4 T 4 G 4 ) quadruplex is surprisingly more stable in the presence of sodium ions than in the presence of potassium ions (T m values were 57°C and 48°C in 45 mM Na + and K + , respectively [30]). …”

Synchrotron radiation circular dichroism of various G‐quadruplex structures

“…The bands in the UV differ from those of d(G 4 T 4 G 4 ), under conditions that do not give a G-quadruplex (1 mM Na 1 after denaturation); the bands are at 295 nm, 274 nm, 256 nm, 236 nm, and 211 nm. 30 There have been past attempts to associate VUV CD bands with a specific property of DNA. 7,31 It has been postulated that the CD signal is indicative of the handedness of the helical structure of DNA, and that a strong negative band at $190 nm is related to the left-handedness of Z-DNA.…”

Role of loops in the guanine quadruplex formation by DNA/RNA hybrid analogs of G4T4G4

“…The melting transition was shifted by about 10 • C to higher temperatures in K + as compared to Na + solutions, whereas the T m of G 4 T 4 G 4 decreased by about the same value. The lower thermal stability of G 4 T 4 G 4 in K + ions as compared to Na + ions was observed earlier [33].…”

“…The stability and topology of quadruplexes can be influenced by substitutions of specific nucleosides [16,17,[26][27][28][29][30][31] or non-nucleosidic residues [32]. The effects of 8-methyl-2 -deoxyguanosine [27] and 8-bromoguanosine [28][29][30][31] substitutions, which both prefer syngeometry of glycosidic angle, and riboguanines [16,17,33], which conversely strongly prefer anti-glycosidic conformation, have been studied. However, as far as we know, the role of the sugar 2 OH group in quadruplex loops has not yet been evaluated.…”