Titration of poly(dA‐dT) · poly(dA‐dT) in solution at variable NaCl concentration

Abstract

CD and uv absorption data showed that high molecular weight poly(dA-dT) . poly(dA-dT), at 298 K, undergoes an acid-induced transition from B-double helix to random coil in NaCl solutions of different concentrations, ranging from 0.005 to 0.600M. Similarly, titration of the polynucleotide with a strong base causes duplex-to-single strands transition. The base- and acid-induced transitions were both reversible by back-titration (with an acid or, respectively, with a base): the apparent pKa were the same in both directions. However, the number of protons per titratable site (adenine N1) required to reach half-denaturation was in great excess over the stoichiometric value; to a much larger extent, the same effect was observed also for the deprotonation of the N3H sites of thymine. Moreover, in the basic denaturation experiments, at low salt concentrations ([NaCl]< or =0.300M) less acid than calculated was needed to back-titrate the base excess to half-denaturation. Both effects could be qualitatively justified on the basis of the counterion condensation theory of polyelectrolytes and considering the energy barrier created by the negatively charged phosphodiester groups to the penetration of the OH- ions inside the double helix and the screening effect of the Na+ ions on such charges, in the deprotonation experiments.

Determination of pKa values for deprotonable nucleobases in short model oligonucleotides

“…While the influence of negative charges on the dissociation of base groups has been studied in nucleoside 5′-mono-, di-, and triphosphates, as well as in nucleoside 3′-monophosphates and in dinucleoside monophosphates [15][16][17][18][19], few reports have been published on nucleobase deprotonation in polynucleotides or oligonucleotides. The cases found in the literature include long nucleic acid chains, such as poly(dA-dT) [20] and poly(U) [21], as well as the ribotrinucleotides CUC [21], GAA, and GAC [22], which were used to determine the ionization constants for thymine, uracil, and guanine residues contained in these oligomers. The acid-base properties of nucleobases have also been determined, by NMR titration, in slightly longer ribo-oligonucleotides, namely GAAC, GAAAC, GAAAAC [23], and in the hexadeoxyribonucleotide d-AGGCCT [24].…”

Counterion condensation and shape within Poisson–Boltzmann theory

“…Biological polyelectrolytes such as nucleic acids, proteins, and micelles as well as hyperbranched dendrimeric polymers and synthetic nanoparticles are prominent examples of systems whose stability and conformation can be altered by changes in the electrolyte environment. Counterions can drive intramolecular and intermolecular conformational transitions in nucleic acids,2–21 proteins22 and polypeptides,23–26 micelles,27 peptide nucleic acids,28 DNA‐protein29 and DNA‐dendrimer30, 31 complexes, polymer brushes,32 and assemblages of charged nanoparticles 33. Much of biological function depends on the formation and conformational dynamics of biomolecular complexes.…”

PolyAT chemical denaturation in w/o microemulsion

“…3 together with the same plot obtained in aqueous solution. 29 The protonation of polyAT seemed to be a reversible process, with no hydrolysis of the polynucleotide taking place, since the initial UV and CD spectra of the B-form could be obtained by back-titration with a basic microemulsion, at least when no c(À)-form was present.…”

“…Since we have recently studied in detail both the acidic and the alkaline titration of polyAT in solutions of different ionic strength, 29 we decided to undertake a matched study in the cationic quaternary microemulsion CTAB/n-pentanol/nhexane/water and to compare the two sets of results.…”