Protonated polynucleotides structures - 22.CD study of the acid-base titration of poly(dG).poly(dC)

Abstract

The acid-base titration (pH 8 --> pH 2.5 --> pH 8) of eleven mixing curve samples of the poly(dG) plus poly(dC) system has been performed in 0.15 M NaCl. Upon protonation, poly(dG).poly(dC) gives rise to an acid complex, in various amounts according to the origin of the sample. We have established that the hysteresis of the acid-base titration is due to the non-reversible formation of an acid complex, and the liberation of the homopolymers at the end of the acid titration and during the base titration: the homopolymer mixtures remain stable up to pH 7. A 1G:1C stoichiometry appears to be the most probable for the acid complex, a 1G:2C stoichiometry, as found in poly(C(+)).poly(I).poly(C) or poly(C(+)).poly(G).poly(C), cannot be rejected. In the course of this study, evidence has been found that the structural consequences of protonation could be similar for both double stranded poly(dG).poly(dC) and G-C rich DNA's: 1) protonation starts near pH 6, dissociation of the acid complex of poly(dG).poly(dC) and of protonated DNA take place at pH 3; 2) the CD spectrum computed for the acid polymer complex displays a positive peak at 255 nm as found in the acid spectra of DNA's; 3) double stranded poly(dG).poly(dC) embedded in triple-stranded poly(dG).poly(dG).poly(dC) should be in the A-form and appears to be prevented from the proton induced conformational change. The neutral triple stranded poly(dG).poly(dG).poly(dC) appears therefore responsible, although indirectly, for the complexity and variability of the acid titration of poly(dG).poly(dC) samples.

Acid-facilitated Supramolecular Assembly of G-quadruplexes in d(CGG)β4

“…Such speculation appears to be consistent with observations by others, indicating that the presence of cytosines (15) or high monocation concentration (22) facilitates the parallel G-quadruplex formation and the most recent report on the observation of stable tetraplex formation of oligomers with CGG repeats in 0.2 M KCl, especially those with 5-methylated cytosines (23). C ϩ ⅐C base pairing had been shown to result in a greatly enhanced positive CD at wavelengths above 280 nm (24,25) and to form parallel duplexes (26,27). CD spectral studies on poly(dC-dT) even led to the proposal that this polynucleotide forms a structure consisting of a core of C⅐C ϩ base pairs and individually looped-out thymidyl residues in acidic solutions (28 -30).…”

CD Spectral Comparisons of the Acid-Induced Structures of Poly[d(A)]Poly[r(A)], Poly[d(C)], and Poly[r(C)]

“…At pH values below the p~ of7 .3 for the major transition, there is a gradual uptake of protons as the pH is reduced (16), although the CD spectrum is affected in a minor way until a pH of3-4 is reached (51). Below pH 4, changes occur in the CD spectrum (at 0.15 M NaCl) that are not reversible until the pH is again increased to above 7 (51).…”

Magnesium ion-dependent triple-helix structure formed by homopurine-homopyrimidine sequences in supercoiled plasmid DNA.

“…5 does not require the protonation ofcytosine residues. Linear poly(dG)-poly(dG)-poly(dC) seems to form stably in solution at neutral pH asjudged by acid titration analysis (27). This is also true for another linear polypurine/polypurine/polypyrimidine triplex consisting of an A A*U triplet (28).…”