Cation-dependent transition between the quadruplex and Watson-Crick hairpin forms of d(CGCG3GCG)

Abstract

The DNA oligonucleotide d(CGCG3GCG) can form either a Watson-Crick (WC) hairpin or a parallel-stranded quadruplex structure containing six G-quartet base pair assemblies. The exchange between these forms and single strands can be monitored using circular dichroism (CD). NMR results verified the assignment of specific CD bands to quadruplex and hairpin species, respectively. Cations stabilize the quadruplex in the order K+ greater than Ca2+ greater than Na+ greater than Mg2+ greater than Li+ and K+ greater than Rb+ greater than Cs+, indicating that K+ has an optimum ionic radius for complex formation and that ionic charge affects the extent of ion-induced stabilization. The quadruplex is stable in the presence of 40 mM K+ at micromolar DNA concentration and can be kinetically trapped as a metastable form when prepared at millimolar DNA concentration and then diluted into buffer containing 40 mM Na+. The concentration of K+ required to reverse the equilibrium from the hairpin to the quadruplex decreases sharply with increased DNA concentration. The quadruplex has an unusual pKa of ca. 6.8, indicating that C.C+ base pairs are probably forming. This system provides insights into some of the detailed structural characteristics of a ["G4-DNA".ion] complex and an experimental model for the recently proposed "sodium-potassium conformational switch" [Sen, D., & Gilbert, W. (1988) Nature 334, 364-366; Sen, D., & Gilbert, W. (1990) Nature 344, 410-414]. These results may help to explain the lack of cytidine residues in G-rich telomeric DNAs and suggest that methylation of GC-rich duplex DNAs in "GpC islands" may induce quadruplex formation within heterochromatin domains, resulting in reversible chromosomal condensation.

Translational Repression of the Disintegrin and Metalloprotease ADAM10 by a Stable G-quadruplex Secondary Structure in Its 5′-Untranslated Region

“…In the presence of 1 mM LiCl, the CD spectrum was not altered as expected because lithium ions do not support the formation of G-quadruplexes (35, 37, 52). In our experiments, addition of 1 mM NaCl also had no effect on G-quadruplex formation, possibly due to the lower propensity of sodium ions compared with potassium ions to stabilize G-quadruplex structures (32,34,35,37,42,52).…”

Unusual DNA structure of the diabetes susceptibility locus IDDM2 and its effect on transcription by the insulin promoter factor Pur-1/MAZ

“…Different G-quartet isomers form, depending on the DNA strand concentration and cations present (29,30). Intermolecular G-quartets arise from the association of four individual single-stranded G-rich DNA molecules, whereas intramolecular G-quartets are formed from a single strand of G-rich DNA.…”

Evaluating the Effects of the Nonplanarity of Nucleic Acid Bases on NMR, IR, and Vibrational Circular Dichroism Spectra: A Density Functional Theory Computational Study

“…Such an error in the determination of torsion corresponds to a difference in 3 J(C8-H1′) couplings equal to 2.2 Hz. Of note, the error due to neglecting the nonplanarity of nucleobases and geometry deformation at C1′ is 5-10-fold larger than typical experimental error in the determination of 3 J (C8-H1′).…”

“…27 Two years later, Ippel et al showed that the same KEs also hold qualitatively for adenosines. 28 Using the published NMR data and their own results, Ippel et al reparametrized and generalized the KEs for the 3 J couplings across glycosidic bonds in all DNA and RNA nucleosides. 28 29 Their detailed analysis revealed that the KE by Ippel can be used to discriminate syn and anti nucleosides, but it could Figure 1.…”

“…Because the geometry deformations in nucleosides depend specifically on glycosidic-bond orientation, 33 the KEs for the 3 J couplings require nontrivial (nonconstant) phase corrections. In this study, we revised the currently available KEs and used the DFT method to calculate the effects of the structural deformations on the phase of the KEs for the 3 J(C4/2-H1′) and 3 J(C8/6-H1′) scalar couplings as well as the IR and vibrational circular dichroism (VCD) spectra.…”